ARQULE INC
S-1/A, 1997-04-03
PHARMACEUTICAL PREPARATIONS
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<PAGE>   1
 
   
     AS FILED WITH THE SECURITIES AND EXCHANGE COMMISSION ON APRIL 3, 1997
    
   
                                                      REGISTRATION NO. 333-22945
    
================================================================================
 
                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549
 
                               ------------------
 
   
                          AMENDMENT NO. 1 TO FORM S-1
    
 
                             REGISTRATION STATEMENT
                                   UNDER THE
                             SECURITIES ACT OF 1933
 
                               ------------------
 
                                  ARQULE, INC.
             (EXACT NAME OF REGISTRANT AS SPECIFIED IN ITS CHARTER)
 
<TABLE>
<S>                                <C>                                <C>
           DELAWARE                             2834                            04-3221586
 (STATE OR OTHER JURISDICTION       (PRIMARY STANDARD INDUSTRIAL             (I.R.S. EMPLOYER
      OF INCORPORATION OR            CLASSIFICATION CODE NUMBER)          IDENTIFICATION NUMBER)
          ORGANIZATION)
</TABLE>
 
                               200 BOSTON AVENUE
                          MEDFORD, MASSACHUSETTS 02155
                                 (617) 395-4100
  (ADDRESS, INCLUDING ZIP CODE, AND TELEPHONE NUMBER, INCLUDING AREA CODE, OF
                   REGISTRANT'S PRINCIPAL EXECUTIVE OFFICES)
 
                               ------------------
 
                                 ERIC B. GORDON
 
                     PRESIDENT AND CHIEF EXECUTIVE OFFICER
                                  ARQULE, INC.
                               200 BOSTON AVENUE
                          MEDFORD, MASSACHUSETTS 02155
                                 (617) 395-4100
 (NAME, ADDRESS, INCLUDING ZIP CODE, AND TELEPHONE NUMBER, INCLUDING AREA CODE,
                             OF AGENT FOR SERVICE)
 
                               ------------------
 
                                   COPIES TO:
 
<TABLE>
    <S>                                              <C>
                 MICHAEL LYTTON, ESQ.                            GEORGE W. LLOYD, ESQ.
              LYNNETTE C. FALLON, ESQ.                      TESTA, HURWITZ & THIBEAULT, LLP
                 PALMER & DODGE LLP                                HIGH STREET TOWER
                  ONE BEACON STREET                                 125 HIGH STREET
             BOSTON, MASSACHUSETTS 02108                      BOSTON, MASSACHUSETTS 02110
                   (617) 573-0100                                   (617) 248-7000
</TABLE>
 
                               ------------------
 
        APPROXIMATE DATE OF COMMENCEMENT OF PROPOSED SALE TO THE PUBLIC:
As soon as practicable after the effective date of this Registration Statement.
 
                               ------------------
 
   
    If any of the securities being registered on this Form are to be offered on
a delayed or continuous basis pursuant to Rule 415 under the Securities Act of
1933 (the "Securities Act"), check the following box. [ ]
    
 
                               ------------------
 
   
    THE REGISTRANT HEREBY AMENDS THIS REGISTRATION STATEMENT ON SUCH DATE OR
DATES AS MAY BE NECESSARY TO DELAY ITS EFFECTIVE DATE UNTIL THE REGISTRANT SHALL
FILE A FURTHER AMENDMENT WHICH SPECIFICALLY STATES THAT THIS REGISTRATION
STATEMENT SHALL THEREAFTER BECOME EFFECTIVE IN ACCORDANCE WITH SECTION 8(a) OF
THE SECURITIES ACT OF 1933 OR UNTIL THE REGISTRATION STATEMENT SHALL BECOME
EFFECTIVE ON SUCH DATE AS THE COMMISSION, ACTING PURSUANT TO SECTION 8(a), MAY
DETERMINE.
    
================================================================================
<PAGE>   2
 
     INFORMATION CONTAINED HEREIN IS SUBJECT TO COMPLETION OR AMENDMENT. A
     REGISTRATION STATEMENT RELATING TO THESE SECURITIES HAS BEEN FILED WITH THE
     SECURITIES AND EXCHANGE COMMISSION. THESE SECURITIES MAY NOT BE SOLD NOR
     MAY OFFERS TO BUY BE ACCEPTED PRIOR TO THE TIME THE REGISTRATION STATEMENT
     BECOMES EFFECTIVE. THIS PROSPECTUS SHALL NOT CONSTITUTE AN OFFER TO SELL OR
     THE SOLICITATION OF AN OFFER TO BUY NOR SHALL THERE BE ANY SALE OF THESE
     SECURITIES IN ANY STATE IN WHICH SUCH OFFER, SOLICITATION OR SALE WOULD BE
     UNLAWFUL PRIOR TO REGISTRATION OR QUALIFICATION UNDER THE SECURITIES LAWS
     OF ANY SUCH STATE.
 
   
                   SUBJECT TO COMPLETION, DATED MARCH 7, 1997
    
 
PROSPECTUS
- ----------
 
                                2,000,000 SHARES
 
                                  ARQULE, INC.
 
   
                              [ARQULE, INC. LOGO]
    
                                  COMMON STOCK
 
   
     Of the 2,000,000 shares of Common Stock offered hereby, 1,632,500 shares
are being sold by ArQule, Inc. and 367,500 shares are being sold by the Selling
Stockholders. The Company will not receive any of the proceeds from the sale of
shares by the Selling Stockholders. See "Principal and Selling Stockholders."
    
 
   
     The Company's Common Stock is quoted on the Nasdaq National Market under
the symbol ARQL. On March 3, 1997, the last reported sale price of the Common
Stock was $19.25 per share. See "Price Range of Common Stock."
    
                               ------------------
 
            THE SHARES OFFERED HEREBY INVOLVE A HIGH DEGREE OF RISK.
   
                    SEE "RISK FACTORS" BEGINNING ON PAGE 6.
    
                               ------------------
 
   
    THESE SECURITIES HAVE NOT BEEN APPROVED OR DISAPPROVED BY THE SECURITIES
       AND EXCHANGE COMMISSION OR ANY STATE SECURITIES COMMISSION NOR HAS
         THE SECURITIES AND EXCHANGE COMMISSION OR ANY STATE SECURITIES
      COMMISSION PASSED UPON THE ACCURACY OR ADEQUACY OF THIS PROSPECTUS.
           ANY REPRESENTATION TO THE CONTRARY IS A CRIMINAL OFFENSE.
    
 
<TABLE>
<CAPTION>
======================================================================================================
                              PRICE TO       UNDERWRITING        PROCEEDS TO     PROCEEDS TO SELLING
                               PUBLIC         DISCOUNT(1)        COMPANY(2)          STOCKHOLDERS
- ------------------------------------------------------------------------------------------------------
<S>                       <C>             <C>                <C>                <C>
Per Share.................        $                $                  $                   $
- ------------------------------------------------------------------------------------------------------
Total(3)..................        $                $                  $                   $
======================================================================================================
</TABLE>
 
(1) See "Underwriting" for indemnification arrangements with the several
    Underwriters.
 
   
(2) Before deducting expenses payable by the Company estimated at $275,000.
    
 
   
(3) The Company has granted to the Underwriters a 30-day option to purchase up
    to 300,000 additional shares of Common Stock solely to cover
    over-allotments, if any. If all such shares are purchased, the total Price
    to Public, Underwriting Discount and Proceeds to Company will be
    $          , $          and $          , respectively. See "Underwriting."
    

                               ------------------
 
   
     The shares of Common Stock are offered by the several Underwriters subject
to prior sale, receipt and acceptance by them and subject to the right of the
Underwriters to reject any order in whole or in part and certain other
conditions. It is expected that certificates for such shares will be available
for delivery on or about             , 1997, at the office of the agent of
Hambrecht & Quist LLC in New York, New York.
    
 
   
HAMBRECHT & QUIST
    
 
   
             OPPENHEIMER & CO., INC.
    
 
                                           VECTOR SECURITIES INTERNATIONAL, INC.
 
   
            , 1997
    
<PAGE>   3
[Four color graphical representation displaying the integration of ArQule's
Combinatorial Drug Design and Development Platform] 


 
     CERTAIN PERSONS PARTICIPATING IN THIS OFFERING MAY ENGAGE IN TRANSACTIONS
THAT STABILIZE, MAINTAIN, OR OTHERWISE AFFECT THE PRICE OF THE COMMON STOCK OF
THE COMPANY, INCLUDING BY ENTERING STABILIZING BIDS OR EFFECTING SYNDICATE
COVERING TRANSACTIONS. FOR A DESCRIPTION OF THESE ACTIVITIES, SEE
"UNDERWRITING."
 
     IN CONNECTION WITH THIS OFFERING, CERTAIN UNDERWRITERS MAY ENGAGE IN
PASSIVE MARKET MAKING TRANSACTIONS IN THE COMMON STOCK ON THE NASDAQ NATIONAL
MARKET IN ACCORDANCE WITH RULE 103 OF REGULATION M UNDER THE SECURITIES EXCHANGE
ACT OF 1934. SEE "UNDERWRITING."
 
     AMAP(TM), Directed Array(TM) and Mapping Array(TM) are trademarks of the
Company for which there are pending applications for registration in the U.S.
Patent and Trademark Office.
<PAGE>   4
 
                               PROSPECTUS SUMMARY
 
     The following summary is qualified in its entirety by the more detailed
information and financial statements, including notes thereto, appearing
elsewhere in this Prospectus.
 
     ArQule, Inc. (the "Company" or "ArQule") has created a new technology
platform for the discovery and production of novel chemical compounds with
commercial potential. The Company has developed proprietary technologies for the
identification and optimization of drug development candidates and
agrichemicals. Using combinatorial chemistry, a modular building block approach
to the development of compounds, structure-guided compound design, high speed
parallel chemical synthesis and information technology, the Company rapidly
develops large, diverse collections of compounds that have the potential to be
biologically active. To date, the Company has entered into collaborative
arrangements with Abbott Laboratories, Monsanto Company, Pharmacia Biotech AB,
Roche Bioscience and Solvay Duphar B.V., and has formed joint discovery programs
with several biotechnology companies.
 
     The Company's goal is to penetrate the product development pipelines of
major pharmaceutical, biotechnology and agrichemical companies and to maximize
the likelihood that active compounds are discovered and successfully developed.
In order to achieve this goal, the Company pursues a strategy designed to
maximize the number of biological targets against which its compounds are
screened. ArQule believes that its technologies will allow its collaborative
partners in the pharmaceutical, biotechnology and agrichemical industries to
accelerate the product development process by several years, permitting them to
realize significant cost reductions and the earlier recovery of research and
development expenditures for successful drugs and agrichemicals. In addition,
the Company believes its technologies will allow researchers to seek solutions
to product development challenges previously deemed too costly or otherwise
impractical because of the inherent limitations of traditional medicinal
chemistry.
 
     Using its proprietary "automated molecular assembly plant" (AMAP(TM))
system and structure-activity relationship ("SAR") data regarding biological
targets and molecular components, ArQule produces significant quantities of pure
small organic compounds in logically structured spatially addressable arrays.
Unlike most current approaches to compound development, ArQule's compound arrays
are created by using structure-guided and rational design tools to
systematically assemble molecular components with properties the Company's
scientists believe are likely to exhibit biological activity. ArQule's compound
arrays are designed around certain core structures or themes. Each compound in
the array is different from the adjacent compounds as a result of a single
structural modification. Each ArQule array omits compounds that are closely
analogous to other compounds in the array, using representative diversity to
create a logical representation of a virtual library of hundreds of times as
many compounds as are in the array. The Company's collaborative partners are
able to realize significant savings by screening the thousands of compounds in
each ArQule array rather than the millions of compounds they represent.
 
     ArQule manufactures and delivers two types of arrays of synthesized
compounds to its pharmaceutical, biotechnology and agrichemical partners: (i)
Mapping Array(TM) compound sets, which are arrays of novel, diverse small
molecule compounds used in screening for lead generation and (ii) Directed
Array(TM) compound sets, which are arrays of compounds that are closely related,
often referred to as "analogs" of a particular lead compound. Both Mapping Array
and Directed Array sets are shipped in industry-standard 96-well microtiter
plates that are compatible with most screening protocols. Under its Mapping
Array Program, ArQule ships a minimum of 100,000 compounds per year in 15 to 20
separate Mapping Array sets, each consisting of 3,000 to 10,000 individual
compounds based on a different theme or core structure chosen by ArQule. Under a
typical Directed Array Program, ArQule provides three to seven Directed Array
sets, each averaging about 1,000 analogs of a particular lead compound chosen by
a collaborator in consultation with ArQule.
 
     ArQule provides its Mapping Array and Directed Array Programs primarily to
partners in the pharmaceutical, biotechnology and agrichemical industries. To
date, ArQule has entered into collabo-
 
                                        3
<PAGE>   5
 
rative arrangements with Abbott Laboratories, Monsanto Company, Pharmacia
Biotech AB, Roche Bioscience and Solvay Duphar B.V., and has formed joint
discovery programs with several biotechnology companies. In exchange for
non-exclusive access to ArQule's Mapping Array Program, the Company's
pharmaceutical and agrichemical partners pay ArQule a combination of up-front
and annual subscription fees as well as a fixed amount for each Directed Array
Program. In addition, these companies have agreed to make payments upon the
achievement of certain milestones and to pay royalties upon the
commercialization of products based on compounds from either the Mapping Array
or the Directed Array Programs. In exchange for providing the arrays to the
Company's biotechnology partners, the Company receives joint ownership of any
potential drugs identified by the biotechnology partner.
 
     ArQule's integrated technologies also present the Company with
opportunities in a number of biological and non-biological fields outside of
drug discovery and agrichemicals. These opportunities include the development of
industrial catalysts and nano-scale polymeric structures for specialized
mechanical applications.
 
                                        4
<PAGE>   6
 
                                  THE OFFERING
 
   
<TABLE>
<S>                                                  <C>
Common Stock offered by the Company................  1,632,500 shares(1)
Common Stock offered by the Selling Stockholders...  367,500 shares(1)
Common Stock to be outstanding after the
  offering.........................................  11,490,862 shares(1)(2)
Use of proceeds....................................  To fund research and product development
                                                     programs and for general corporate and
                                                     working capital purposes.
Nasdaq National Market symbol......................  ARQL
</TABLE>
    
 
                         SUMMARY FINANCIAL INFORMATION
                     (IN THOUSANDS, EXCEPT PER SHARE DATA)
 
   
<TABLE>
<CAPTION>
                                           PERIOD FROM INCEPTION
                                           (MAY 6, 1993) THROUGH               YEAR ENDED
                                               DECEMBER 31,                   DECEMBER 31,
                                           ---------------------     -------------------------------
                                                   1993               1994        1995        1996
                                           ---------------------     -------     -------     -------
<S>                                        <C>                       <C>         <C>         <C>
STATEMENT OF OPERATIONS DATA:
  Revenue................................         $    --            $    85     $ 3,330     $ 7,255
  Loss from operations...................          (1,456)            (4,067)     (1,966)     (3,410)
  Net loss...............................         $(1,465)           $(4,206)    $(2,252)    $(2,993)
  Unaudited pro forma net loss
     per share(3)........................                                        $ (0.33)    $ (0.39)
  Shares used in computing unaudited
     pro forma net loss per share(3).....                                          6,853       7,705
</TABLE>
    
 
   
<TABLE>
<CAPTION>
                                                                          DECEMBER 31, 1996
                                                                      --------------------------
                                                                      ACTUAL      AS ADJUSTED(4)
                                                                      -------     --------------
<S>                                                                   <C>         <C>
BALANCE SHEET DATA:
  Cash, cash equivalents and marketable securities..................  $37,086        $ 66,351
  Working capital...................................................   31,440          60,705
  Total assets......................................................   43,509          72,774
  Capital lease obligations, less current portion...................    1,728           1,728
  Total stockholders' equity........................................   34,621          63,886
</TABLE>
    
 
- ------------------------------
   
(1) Selling Stockholders holding 315,000 of the shares proposed to be sold in
    this offering may elect not to sell all or any such shares. In such event,
    the Company has agreed to increase the number of shares it is selling in
    this offering by the number of shares not sold by Selling Stockholders. See
    "Principal and Selling Stockholders."
    
 
   
(2) Excludes 1,394,920 shares issuable upon the exercise of options outstanding
    as of December 31, 1996 with a weighted average exercise price of $3.62 per
    share.
    
 
   
(3) Unaudited pro forma net loss per share is determined by dividing Net loss by
    Shares used in computing unaudited pro forma net loss per share. For
    information regarding Shares used in computing unaudited pro forma net loss
    per share, see Note 2 of Notes to Financial Statements.
    
 
   
(4) As adjusted to give effect to the sale of 1,632,500 shares of Common Stock
    offered by the Company hereby, after deducting the underwriting discount and
    offering expenses, at an assumed public offering price of $19.25 per share
    and the application of the estimated net proceeds therefrom as set forth in
    "Use of Proceeds."
    
 
                         ------------------------------
 
   
     Except as otherwise noted, all information in this Prospectus assumes (i)
no exercise of the Underwriters' over-allotment option and (ii) the sale of
1,632,500 shares of Common Stock by the Company and 367,500 shares of Common
Stock by the Selling Stockholders. The shares of Common Stock offered hereby
involve a high degree of risk. Investors should carefully consider the
information set forth under "Risk Factors."
    
 
                                        5
<PAGE>   7
 
                                  RISK FACTORS
 
   
     This Prospectus contains forward-looking statements that involve risks and
uncertainties. Actual results could differ materially from those discussed in
the forward-looking statements as a result of certain factors, including those
set forth below and elsewhere in this Prospectus. The following risk factors
should be considered carefully in addition to the other information in this
Prospectus before purchasing the shares of Common Stock offered hereby.
    
 
   
     Limited Operating History; History of Operating Losses; Uncertainty of
Future Profitability.  The Company has had a limited operating history. For the
years ended December 31, 1994, 1995 and 1996, the Company had net losses of
approximately $4.2 million, $2.3 million and $3.0 million, respectively. As of
December 31, 1996, the Company had an accumulated deficit of approximately $10.9
million. The Company's expansion of its operations and enhancements to its
technology will result in significant expenses over the next several years that
may not be offset by significant revenues. The Company expects that revenue for
the foreseeable future and the Company's ability to achieve profitability will
be dependent upon the ability of the Company to enter into additional
collaborative arrangements with customers. To date, all revenue received by the
Company has been derived from up-front fees, payments for compound deliveries,
and research and development funding paid pursuant to collaborative agreements
with the Company's collaborative partners. The Company has not realized any
revenue from the achievement of milestones or royalties from the discovery,
development or sale of a commercial product by one of the Company's
collaborative partners, and there can be no assurance that any such revenue will
be realized. The Company is unable to predict when, or if, it will become
profitable. See "Selected Financial Data" and "Management's Discussion and
Analysis of Financial Condition and Results of Operations."
    
 
   
     Unproven Business Strategy.  The Company's modular building block approach
to chemistry has not yet resulted in the commercialization of a product. The
Company uses chemical building blocks for the purpose of rapidly identifying,
optimizing and obtaining proprietary rights to as many compounds with commercial
potential as possible. The pricing and nature of the Company's programs are such
that there may only be a limited number of companies that are potential
customers for such programs. The Company's ability to succeed is dependent upon
the acceptance by potential customers of the Company's approach to chemistry and
compound analysis as an effective tool in the discovery and development of
compounds with commercial potential. Due to the highly proprietary nature of the
activities being conducted, the central importance of these activities to their
product discovery and development efforts, and the desire to obtain maximum
patent and other proprietary protection on the results of their internal
programs, pharmaceutical, biotechnology and agrichemical companies have
historically conducted lead compound identification and optimization within
their own research departments. There can be no assurance that the Company's
present or future collaborators will not pursue existing or alternative
technology, either independently or in collaboration with others, in preference
to that of the Company or that the Company will be able to attract future
collaborators on acceptable terms or develop a sustainable, profitable business.
See "Business."
    
 
     Competition and the Risk of Obsolescence of Technology.  Competition among
the many organizations actively attempting to identify and optimize compounds
for development in the pharmaceutical industry and in other areas is intense.
ArQule competes with the research departments of pharmaceutical companies,
biotechnology companies, agrichemical companies, combinatorial chemistry
companies and research and academic institutions. Many of these competitors have
greater financial and human resources, and more experience in research and
development, than the Company. Historically, pharmaceutical and agrichemical
companies have maintained close control over their research activities,
including the synthesis, screening and optimization of chemical compounds. Many
of these companies, which represent the greatest potential market for ArQule's
products and services, have developed or are developing internal combinatorial
chemistry and other methodologies to improve productivity, including major
investments in robotics technology to permit the automated parallel synthesis of
compounds. In addition, ArQule competes with biotechnology and combinatorial
chemistry companies that offer a range of products and services. Academic
institutions, governmental
 
                                        6
<PAGE>   8
 
agencies and other research organizations are also conducting research in areas
in which the Company is working, either on their own or in collaboration with
others. The Company anticipates that it will face increased competition in the
future as new companies enter the market and advanced technologies, including
more sophisticated information technologies, become available. The Company's
technological approaches may be rendered obsolete or uneconomical by advances in
existing technological approaches or the development of different approaches by
one or more of the Company's competitors. See "Business--Competition."
 
   
     Limited Sales and Marketing Experience; Expansion of Sales Activities.  To
date, the Company has sold its products to its collaborative partners primarily
through the efforts of its senior management. The Company's senior management
has limited experience in marketing products similar to those of the Company. In
order to achieve significant long-term growth in revenue and its overall
strategic goals, the Company intends to hire several dedicated sales and
marketing personnel. There can be no assurance that the Company will be able to
achieve anticipated expansion of its business, attract a significant number of
new collaborative partners as customers or build an efficient and effective
sales and marketing organization. In the event the Company is unable to achieve
any one or more of the foregoing goals, the Company's business, financial
condition and results of operations could be materially adversely affected. In
addition to the risks inherent in the Company's efforts to market its own
products, the Company's revenue from royalties and milestone payments from its
collaborative partners is substantially dependent upon the marketing efforts of
such collaborative partners as discussed below under "Risk Factors--Dependence
on Third Parties."
    
 
   
     Dependence on Third Parties.  The Company's strategy for the development
and commercialization of its products and services involves the formation of
collaborative arrangements with third parties, initially pharmaceutical,
biotechnology and agrichemical companies. To date, the Company has entered into
numerous such arrangements. There can be no assurance that the Company's
existing collaborations will not be terminated under certain circumstances by
its collaborators and any such terminations could have a material adverse effect
on the Company. There can be no assurance that the Company will be able to
establish additional collaborative arrangements, that any such arrangements will
be on terms favorable to the Company, or that current or future collaborative
arrangements will ultimately be successful. Further, ArQule's receipt of revenue
from collaborative arrangements is affected by the timing of efforts expended by
third parties. The Company's products and services will result in commercialized
pharmaceutical and agrichemical products generating milestone payments and
royalties only after significant preclinical and clinical development efforts or
the completion of preliminary field trials, the receipt of the requisite
regulatory approvals, and the integration of manufacturing capabilities and
successful marketing efforts. With the exception of certain aspects of
preclinical drug development, the Company does not currently intend to perform
any of these activities. Therefore, the Company will be dependent upon the
expertise of, and dedication of sufficient resources by, third parties to
develop and commercialize products. Should a collaborative partner fail to
develop or commercialize a compound or product to which it has obtained rights
from the Company, the Company may not receive any future milestone payments or
royalties associated with such compound or product. Furthermore, there can be no
assurance that any such development or commercialization would be successful or
that disputes will not arise over the application of payment provisions to such
products. There can be no assurance that current or future collaborative
partners will not pursue alternative technologies or develop alternative
products, either on their own or in collaboration with others, including the
Company's competitors, as a means for developing alternative solutions in the
areas targeted by collaborative arrangements with the Company. See
"Business--ArQule's Product Discovery Programs."
    
 
   
     Dependence on Key Employees.  The Company is highly dependent on the
principal members of its scientific and management staff, in particular, Dr.
Joseph C. Hogan, Jr. and Dr. David L. Coffen. The loss of one or more members of
its staff could have a material adverse effect on the Company's business,
financial condition and results of operations. The Company does not maintain key
person life insurance on the life of any employee. The Company's future success
will also depend, in part, on its ability to identify, hire and retain
additional qualified personnel, including individuals with doctorates
    
 
                                        7
<PAGE>   9
 
in basic sciences. There is intense competition for such personnel in the areas
of the Company's activities, and there can be no assurance that the Company will
be able to continue to attract and retain personnel with the advanced technical
qualifications necessary for the development of the Company's business. Failure
to attract and retain key personnel could have a material adverse effect on the
Company's business, financial condition and results of operations. See
"Business--Employees" and "Management."
 
   
     Future Capital Needs; Uncertainty of Additional Funding.  There can be no
assurance that the net proceeds from this offering, together with the Company's
existing capital resources and revenue from operations, will be adequate to fund
the Company's operations through March 1999. The Company may be required to
raise additional capital over a period of several years in order to conduct its
operations. Such capital may be raised through additional public or private
equity financings, as well as collaborative arrangements, borrowings and other
available sources. The Company's capital requirements depend on numerous
factors, including entering into additional collaborative arrangements,
competing technological and market developments, changes in the Company's
existing collaborative relationships, the cost of filing, prosecuting, defending
and enforcing patent claims and other intellectual property rights, the purchase
of additional capital equipment, the progress of the Company's drug discovery
programs and the progress of the Company's collaborators' milestone and
royalty-producing activities. The Company does not currently plan to
independently develop, manufacture or market any products it discovers. Should
the Company choose to develop any such products, however, the Company will
require substantial funds to conduct research and development, preclinical
studies, clinical trials and field trials and to market any products that may be
developed. There can be no assurance that additional funding, if necessary, will
be available on favorable terms, if at all. If adequate funds are not available,
the Company may be required to curtail operations significantly or to obtain
funds by entering into arrangements with collaborative partners or others that
may require the Company to relinquish rights to certain of its technologies,
product candidates, products or potential markets. To the extent that additional
capital is raised through the sale of equity or securities convertible into
equity, the issuance of such securities could result in dilution to the
Company's existing stockholders. See "Management's Discussion and Analysis of
Financial Condition and Results of Operations."
    
 
   
     Dependence on Scale Up and Management of Growth.  The Company's success
will depend on the expansion of its operations and the management of these
expanded operations. To be cost-effective in its delivery of services and
products, the Company must enhance productivity through further automation of
its processes and improvements to its technology. The Company also must
successfully structure and manage multiple additional collaborative
relationships. There can be no assurance that the Company will be successful in
its engineering efforts to further automate its processes or that the Company
will be successful in managing and meeting the staffing requirements of
additional collaborative relationships. Failure to achieve any of these goals
could have a material adverse effect on the Company's business, financial
condition or results of operations. See "Business--ArQule's Product Discovery
Programs" and "--Employees."
    
 
   
     Control By Management and Existing Stockholders.  Upon completion of this
offering, the Company's significant stockholders, executive officers, directors
and affiliated entities together will beneficially own approximately 49.5% of
the outstanding shares of Common Stock (48.3% if the Underwriters'
over-allotment option is exercised in full). As a result, these stockholders,
acting together, will be able to control most matters requiring approval by the
stockholders of the Company, including the election of directors. Such a
concentration of ownership may have the effect of delaying or preventing a
change in control of the Company, including transactions in which stockholders
might otherwise receive a premium for their shares over then current market
prices. See "Principal and Selling Stockholders."
    
 
     Dependence on Patents and Proprietary Rights.  ArQule has one issued patent
and has filed a number of patent applications. There can be no assurance that
patent applications filed by ArQule will result in patents being issued, that
the claims of such patents will offer significant protection of the Company's
technology, or that any patents issued to or licensed by ArQule will not be
challenged, narrowed, invalidated or circumvented. The Company believes its
success will depend in large part on
 
                                        8
<PAGE>   10
 
its ability, and the ability of its licensees and its licensors, to obtain
patents for its technologies and the compounds and other products, if any,
resulting from the application of such technologies, to defend such patents once
obtained and to maintain trade secrets, both in the United States and in foreign
countries. In the absence of such patents, the Company may be unable to prevent
others from utilizing the Company's technology and may need to rely upon
expertise developed during pre-commercial implementation of the technology,
which may not provide the same level of competitive advantages. The commercial
success of the Company will also depend upon avoiding the infringement of
patents issued to others and maintaining the technology licenses upon which
certain of the Company's current products are, or any future products under
development might be, based.
 
     Some of the Company's competitors have, or are affiliated with companies
having, substantially greater resources than the Company, and such competitors
may be able to sustain the costs of complex patent litigation to a greater
degree and for longer periods of time than the Company. Uncertainties resulting
from the initiation and continuation of any patent or related litigation could
have a material adverse effect on the Company's ability to compete in the
marketplace pending resolution of the disputed matters. To date, one patent has
been issued to the Company. There can be no assurance that other patents will
issue to the Company or its licensors as a result of their pending applications
or that, if issued, such patents will contain claims sufficiently broad to
afford protection against competitors with similar technology. Moreover, there
can be no assurance that the Company or its customers will be able to obtain
significant patent protection for compounds or products based upon the Company's
technology. There can be no assurance that any patents issued to the Company or
its collaborative partners, or for which the Company has license rights, will
not be challenged, narrowed, invalidated or circumvented, or that the rights
granted thereunder will provide competitive advantages to the Company.
Litigation, which could result in substantial cost to the Company, may be
necessary to enforce the Company's patent and license rights, to enforce or
defend an infringement claim, or to determine the scope and validity of others'
proprietary rights. If competitors of the Company prepare and file patent
applications in the United States or abroad that claim technology also claimed
by the Company, the Company may have to participate in interference proceedings
declared by the U.S. Patent and Trademark Office to determine the priority of
invention, or opposition proceedings in a foreign patent office, both of which
could result in substantial cost to the Company, even if the outcome is
favorable. An adverse outcome could subject the Company to significant
liabilities to third parties, and require the Company to cease using the
technology or to license disputed rights from third parties, which licenses may
not be available at reasonable cost.
 
     A number of pharmaceutical, biotechnology and agrichemical companies, as
well as research and academic institutions, have developed technologies, filed
patent applications or received patents on various technologies that may be
related to the Company's business. Some of these technologies, applications or
patents may conflict with the Company's technologies or patent applications.
Such conflicts could also limit the scope of the claim of any patents that the
Company may be able to obtain, or result in the rejection of the Company's
patent applications. The Company currently has certain licenses to patents and
patent applications from third parties, and in the future may require additional
licenses from other parties. There can be no assurance that: (i) such licenses
will be obtainable on commercially reasonable terms, if at all; (ii) the patents
underlying such licenses will be valid and enforceable; (iii) patents having
commercially valuable claims will issue from any licensed patent applications;
or (iv) the proprietary nature of any other technology underlying such licenses
will remain proprietary.
 
     The Company relies substantially on certain technologies that are not
patentable or proprietary and are therefore available to the Company's
competitors. The Company also relies on certain proprietary trade secrets and
know-how that are not patentable. Although the Company has taken steps to
protect its unpatented trade secrets and know-how, in part through the use of
confidentiality agreements with its employees, consultants and certain of its
collaborators, there can be no assurance that (i) the agreements will not be
breached; (ii) the Company would have adequate remedies for any
 
                                        9
<PAGE>   11
 
breach; or (iii) the Company's trade secrets will not otherwise become known or
be independently developed or discovered by competitors. See "Business--Patents
and Proprietary Rights."
 
     Possible Volatility of Stock Price.  The market price of the Company's
Common Stock, which is quoted on the Nasdaq National Market, may be subject to
significant fluctuations in response to announcements of technological
innovations or new commercial products by the Company or its competitors,
developments concerning proprietary rights, including patents and litigation
matters, publicity regarding actual or potential results with respect to
products or compounds under development by the Company or its collaborative
partners, regulatory developments in both the United States and foreign
countries, public concern as to the efficacy of new technologies, general market
conditions, as well as quarterly fluctuations in the Company's revenues and
financial results and other factors. In particular, the realization of any of
the risks described in these "Risk Factors" could have a dramatic and adverse
impact on such market price. See "Underwriting."
 
     Anti-Takeover Effect of Certain Charter and By-Law Provisions and Delaware
Law.  The Company's Amended and Restated Certificate of Incorporation (the
"Restated Certificate") authorizes the Board of Directors to issue, without
stockholder approval, up to 1,000,000 shares of preferred stock ("Preferred
Stock") with voting, conversion and other rights and preferences that could
adversely affect the voting power or other rights of the holders of Common
Stock. The issuance of Preferred Stock or of rights to purchase Preferred Stock
could be used to discourage an unsolicited acquisition proposal. In addition,
the possible issuance of Preferred Stock could discourage a proxy contest, make
more difficult the acquisition of a substantial block of the Company's Common
Stock or limit the price that investors might be willing to pay for shares of
the Company's Common Stock. The Restated Certificate provides for staggered
terms for the members of the Board of Directors. A staggered Board of Directors
and certain provisions of the Company's By-laws (the "By-laws") and of Delaware
law applicable to the Company could delay or make more difficult a merger,
tender offer or proxy contest involving the Company. The Company, for example,
is subject to Section 203 of the General Corporate Law of Delaware which,
subject to certain exceptions, restricts certain transactions and business
combinations between a corporation and a stockholder owning 15% or more of the
corporation's outstanding voting stock (an "interested stockholder") for a
period of three years from the date the stockholder becomes an interested
stockholder. These provisions may have the effect of delaying or preventing a
change of control of the Company without action by the stockholders and,
therefore, could adversely affect the price of the Company's Common Stock. See
"Management," "Description of Capital Stock--Preferred Stock" and
"--Anti-Takeover Measures."
 
     Potential Liability Regarding Hazardous Materials.  The research and
development processes of the Company involve the controlled use of hazardous
materials. The Company is subject to federal, state and local laws and
regulations governing the use, manufacture, storage, handling and disposal of
such materials and certain waste products. The risk of accidental contamination
or injury from these materials cannot be completely eliminated. In the event of
such an accident, the Company could be held liable for any damages that result
and any such liability could exceed the resources of the Company. In addition,
there can be no assurance that the Company will not be required to incur
significant costs to comply with environmental laws and regulations in the
future.
 
     Government Regulation.  Although the manufacture, transportation and
storage of the Company's products are subject to the laws and regulations
regarding hazardous materials discussed in the preceding risk factor, the sale
of the Company's products is not subject to significant government regulations.
However, the Company's future profitability is dependent on the sales of
pharmaceuticals and other products developed from the Company's compounds by its
customers and collaborators. Regulation by governmental entities in the United
States and other countries may be a significant factor in the production and
marketing of products that may be developed by a customer or collaborative
partner of the Company. The nature and the extent to which such regulation may
apply to the Company's customers or its collaborative partners will vary
depending on the nature of any such products.
 
                                       10
<PAGE>   12
 
     Virtually all pharmaceutical products developed by the Company's customers
or its collaborative partners will require regulatory approval by governmental
agencies prior to commercialization. In particular, human pharmaceutical
products are subject to rigorous preclinical and clinical testing and other
approval procedures by the U.S. Food and Drug Administration (the "FDA") and by
foreign regulatory authorities. Various federal and, in some cases, state
statutes and regulations also govern or influence the manufacturing, safety,
labeling, storage, record keeping and marketing of such pharmaceutical products.
The process of obtaining these approvals and the subsequent compliance with
appropriate federal and foreign statutes and regulations are time consuming and
require the expenditure of substantial resources. Generally, in order to gain
FDA approval, a company first must conduct preclinical studies in the laboratory
and in animal models to gain preliminary information on a compound's efficacy
and to identify any safety problems. The results of these studies are submitted
as a part of an Investigational New Drug application ("IND") that the FDA must
review before human clinical trials of an investigational drug can start. In
order to commercialize any products, the Company or its customers or its
collaborative partners will be required to sponsor and file an IND and will be
responsible for initiating and overseeing the clinical studies to demonstrate
the safety and efficacy that are necessary to obtain FDA approval of any such
products. Clinical trials are normally done in three phases and generally take
two to five years, but may take longer, to complete. After completion of
clinical trials of a new product, FDA and foreign regulatory authority marketing
approval must be obtained. If the product is classified as a new drug, a New
Drug Application ("NDA") must be filed and approved before commercial marketing
of the drug. The testing and approval processes require substantial time and
effort and there can be no assurance that any approval will be granted on a
timely basis, if at all. NDAs submitted to the FDA can take several years to
obtain approval. Even if FDA regulatory clearances are obtained, a marketed
product is subject to continual review, and later discovery of previously
unknown problems or failure to comply with the applicable regulatory
requirements may result in restrictions on the marketing of a product or
withdrawal of the product from the market as well as possible civil or criminal
sanctions. For marketing outside the United States, the Company will also be
subject to foreign regulatory requirements governing human clinical trials and
marketing approval for pharmaceutical products. The requirements governing the
conduct of clinical trials, product licensing, pricing and reimbursement vary
widely from country to country.
 
     Fertilizers, pesticides and other agrichemical products sold by the
Company's collaborators will be subject to rigorous testing and approval
processes by the U.S. Environmental Protection Agency ("EPA") and similar
regulatory authorities in certain states and in other countries. The process of
obtaining these approvals can be time consuming and costly. There can be no
assurance that such approvals will be granted on a timely basis. See
"Business--Government Regulation."
 
   
     Shares Eligible for Future Sale and Potential Adverse Effect on Market
Price.  Future sales of Common Stock in the public market following this
offering could adversely affect the market price of the Common Stock. Upon
completion of this offering, the Company will have 11,490,862 shares of Common
Stock outstanding, assuming no exercise of currently outstanding options. Of
these shares, approximately 3,018,647 shares and the 2,000,000 shares sold in
this offering (plus any additional shares sold upon exercise of the
Underwriters' over-allotment option) will be freely tradable without restriction
under the Securities Act of 1933, as amended (the "Securities Act"), unless they
are held by "affiliates" of the Company as that term is used under the
Securities Act and the regulations promulgated thereunder. Of the 6,472,215
remaining shares, approximately 5,564,481 shares of Common Stock (plus
approximately 258,857 shares issuable upon exercise of vested options) are
currently eligible for sale under Rules 144 and 701. The remainder of the
approximately 907,734 shares of Common Stock held by an existing stockholder
will become eligible for sale under Rule 144 on April 29, 1997. Stockholders of
the Company, holding in the aggregate 6,195,295 shares of Common Stock, have
agreed, subject to certain limited exceptions, not to sell or otherwise dispose
of any of the shares held by them as of the date of this Prospectus for a period
of 90 days after the date of this Prospectus (the "lock-up period") without the
prior written consent of Hambrecht & Quist LLC. The holders of 6,219,948 shares
of Common Stock have the right in certain circumstances to require the Company
to
    
 
                                       11
<PAGE>   13
 
register their shares under the Securities Act for resale to the public
beginning at the end of the lock-up period. If such holders, by exercising their
demand registration rights, cause a large number of shares to be registered and
sold in the public market, such sales could have an adverse effect on the market
price of the Company's Common Stock. If the Company were required to include in
a Company-initiated registration shares held by such holders pursuant to the
exercise of their piggyback registration rights, such sales may have an adverse
effect on the Company's ability to raise needed capital. See "Shares Eligible
for Future Sale" and "Underwriting."
 
     Broad Management Discretion in Use of Proceeds.  The Company's management
will have broad discretion to allocate proceeds of this offering to uses that it
believes are appropriate. There can be no assurance that the proceeds of this
offering can or will be invested to yield a positive return. See "Use of
Proceeds."
 
     Immediate and Substantial Dilution.  Purchasers of the shares of Common
Stock offered hereby will experience immediate and substantial dilution
estimated at $13.69 in the net tangible book value of their investment from the
assumed public offering price. Additional dilution will occur upon exercise of
outstanding options. See "Dilution" and "Shares Eligible for Future Sale."
 
     Absence of Dividends.  The Company has never paid dividends on its Common
Stock and does not anticipate paying any cash dividends in the foreseeable
future. The Company currently intends to retain its earnings, if any, for the
development of its business.
 
                                       12
<PAGE>   14
 
                                  THE COMPANY
 
     ArQule was incorporated in Delaware in December 1993 and is the successor
to a partnership formed on May 6, 1993. The Company's principal executive
offices are located at 200 Boston Avenue, Medford, Massachusetts 02155, and its
telephone number is (617) 395-4100.
 
                                USE OF PROCEEDS
 
     The net proceeds to the Company from the sale of the Common Stock offered
by the Company hereby, after deducting the underwriting discount and offering
expenses, are estimated to be $29.3 million ($34.7 million if the Underwriters'
over-allotment option is exercised in full and $40.4 million if the
Underwriters' over-allotment option is exercised in full and only 52,500 shares
are sold by Selling Stockholders), at an assumed public offering price of $19.25
per share.
 
     The Company intends to use the net proceeds of the shares offered by the
Company in the offering, together with the Company's existing cash, cash
equivalents, short-term investments and cash generated from operations, for
research and development, working capital and general corporate purposes. Such
general corporate purposes may include acquisitions of other businesses,
technologies, products or capabilities and the funding of joint development
efforts involving selected compounds identified by the biotechnology
collaborators. The Company is not in any negotiations with respect to any such
acquisitions. The amount and timing of the Company's actual expenditures for the
purposes described above will depend upon a number of factors, including the
Company's ability to enter into additional collaborative or licensing
arrangements, as well as the timing and terms of such arrangements. In addition,
the Company's research and development expenditures will vary as programs are
expanded or abandoned and as a result of variability in funding from its
collaborative partners. The Company's management will have broad discretion to
allocate the net proceeds of this offering to uses that it believes are
appropriate. There can be no assurance that the proceeds of this offering can or
will be invested to yield a positive return.
 
     The Company currently believes the net proceeds of the offering, together
with the Company's existing cash, cash equivalents, short-term investments, cash
generated from operations and research funding from corporate collaborators,
will enable the Company to maintain its current and planned operations at least
through March 1999. However, there can be no assurance that this will be the
case. See "Risk Factors--Future Capital Needs; Uncertainty of Additional
Funding" and "Management's Discussion and Analysis of Financial Condition and
Results of Operations--Liquidity and Capital Resources."
 
     Pending use as set forth above, the net proceeds of the offering will be
invested primarily in interest-bearing, investment-grade securities.
 
                                DIVIDEND POLICY
 
     The Company has never paid cash dividends on its Common Stock and does not
anticipate paying any cash dividends in the foreseeable future. The Company
currently intends to retain future earnings, if any, to fund the development of
its business.
 
                                       13
<PAGE>   15
 
                          PRICE RANGE OF COMMON STOCK
 
     The Company's Common Stock began trading on the Nasdaq National Market on
October 16, 1996 under the symbol "ARQL". Prior to October 16, 1996, there was
no public market for the Common Stock or any other securities of the Company.
 
     The following table sets forth, for the periods indicated, the range of the
high and low closing sale prices for the Company's Common Stock:
 
<TABLE>
<CAPTION>
                                                                          HIGH       LOW
                                                                         ------     ------
    <S>                                                                  <C>        <C>
    1996
      Fourth Quarter (from October 16, 1996)...........................  $15.75     $ 9.00
    1997
      First Quarter (through March 4, 1997)............................   24.25      14.75
</TABLE>
 
     As of March 4, 1997, there were approximately 58 holders of record of the
Company's Common Stock.
 
                                 CAPITALIZATION
 
     The following table sets forth, as of December 31, 1996, (i) the actual
capitalization of the Company and (ii) the capitalization of the Company as
adjusted to reflect the sale of the 1,632,500 shares of Common Stock offered by
the Company hereby, after deducting the underwriting discount and offering
expenses, at an assumed public offering price of $19.25 per share and the
application of the estimated net proceeds therefrom as set forth in "Use of
Proceeds". This table should be read in conjunction with the financial
statements, related notes and other financial information included herein.
 
<TABLE>
<CAPTION>
                                                                            DECEMBER 31, 1996
                                                                         -----------------------
                                                                         ACTUAL      AS ADJUSTED
                                                                         -------     -----------
                                                                             (IN THOUSANDS)
<S>                                                                      <C>         <C>
Capital lease obligations, less current portion........................  $  1,728       $  1,728
                                                                         --------       --------
Stockholders' equity:
  Preferred stock, $0.01 par value; 1,000,000 shares authorized; no
     shares issued or outstanding......................................        --             --
  Common stock, $0.01 par value; 30,000,000 shares authorized;
     9,851,487 shares issued and outstanding actual, 11,483,987 shares
     issued and outstanding as adjusted(1).............................        99            115
  Additional paid-in capital...........................................    46,102         75,351
  Accumulated deficit..................................................   (10,934)       (10,934)
  Deferred compensation................................................      (646)          (646)
                                                                         --------       --------
       Total stockholders' equity......................................    34,621         63,886
                                                                         --------       --------
          Total capitalization.........................................  $ 36,349       $ 65,614
                                                                         ========       ========
</TABLE>
 
- ------------------------------
(1) Excludes 1,394,920 shares issuable upon the exercise of options outstanding
    as of December 31, 1996 with a weighted average exercise price of $3.62 per
    share.
 
                                       14
<PAGE>   16
 
                                    DILUTION
 
     The net tangible book value of the Company as of December 31, 1996 was
$34,621,000 or approximately $3.51 per share. Net tangible book value per share
represents the total tangible assets of the Company, less total liabilities,
divided by 9,851,487 shares of Common Stock outstanding. Assuming the receipt by
the Company of the net proceeds from the sale of the 1,632,500 shares of Common
Stock offered by the Company hereby at an assumed public offering price of
$19.25 per share, the pro forma net tangible book value of the Company as of
December 31, 1996 would have been $63,886,000, or $5.56 per share. This
represents an immediate increase in net tangible book value of $2.05 per share
to existing stockholders of the Company and an immediate dilution of $13.69 per
share to new investors purchasing Common Stock in this offering. The following
table illustrates the per share dilution to be incurred by new investors as of
December 31, 1996:
 
<TABLE>
    <S>                                                                   <C>       <C>
    Assumed public offering price per share.............................            $19.25
      Net tangible book value per share at December 31, 1996............  $3.51
      Increase per share attributable to new investors..................   2.05
                                                                          -----
    Pro forma net tangible book value per share after the offering......              5.56
                                                                                    ------
      Dilution per share to new investors...............................            $13.69
                                                                                    ======
</TABLE>
 
     The following table sets forth, as of December 31, 1996, the differences
between the existing stockholders and the new investors with respect to the
number of shares of Common Stock acquired from the Company, the total
consideration paid and the average price per share (at an assumed public
offering price of $19.25 per share):
 
<TABLE>
<CAPTION>
                                           SHARES                      TOTAL
                                         PURCHASED                 CONSIDERATION
                                   ----------------------     -----------------------     AVERAGE PRICE
                                     NUMBER       PERCENT       AMOUNT        PERCENT       PER SHARE
                                   -----------    -------     -----------     -------     -------------
<S>                                <C>            <C>         <C>             <C>         <C>
Existing stockholders(1).........    9,851,487      85.8%     $48,237,000       60.6%        $  4.90
New investors(1).................    1,632,500      14.2       31,426,000       39.4           19.25
                                    ----------     -----      -----------      -----
          Total..................   11,483,987     100.0%     $79,663,000      100.0%
                                    ==========     =====      ===========      =====
</TABLE>
 
- ------------------------------
(1) Sales of 367,500 shares by the Selling Stockholders in this offering will
    reduce the number of shares held by existing stockholders as of December 31,
    1996 to 9,483,987 or 82.6% of total shares outstanding after this offering,
    and will increase the number of shares held by new investors to 2,000,000 or
    17.4% of the total shares outstanding after this offering.
 
     The above information excludes an aggregate of 1,394,920 shares of Common
Stock issuable upon the exercise of options outstanding as of December 31, 1996
with a weighted average exercise price of $3.62 per share. To the extent that
such options are exercised, there will be further dilution to new investors.
 
                                       15
<PAGE>   17
 
                            SELECTED FINANCIAL DATA
                     (IN THOUSANDS, EXCEPT PER SHARE DATA)
 
     The following data, insofar as it relates to the period from inception (May
6, 1993) through December 31, 1993 and for the years 1994, 1995 and 1996, have
been derived from the Company's audited financial statements, including the
balance sheet as of December 31, 1995 and 1996 and the related statements of
operations and of cash flows for the three years ended December 31, 1996 and
notes thereto appearing elsewhere herein. The data should be read in conjunction
with the Financial Statements and the Notes thereto and "Management's Discussion
and Analysis of Financial Condition and Results of Operations" appearing
elsewhere in this Prospectus. The historical results are not necessarily
indicative of the results of operations to be expected in the future.
 
<TABLE>
<CAPTION>
                                               PERIOD FROM INCEPTION
                                               (MAY 6, 1993) THROUGH             YEAR ENDED
                                                   DECEMBER 31,                 DECEMBER 31,
                                               ---------------------    -----------------------------
                                                       1993              1994       1995       1996
                                               ---------------------    -------    -------    -------
<S>                                            <C>                      <C>        <C>        <C>
STATEMENT OF OPERATIONS DATA:
  Revenue....................................         $    --           $    85    $ 3,330    $ 7,255
                                                      -------           -------    -------    -------
  Costs and expenses:
     Cost of revenue.........................              --                --      1,644      4,739
     Research and development................             769             2,806      2,095      3,076
     Marketing, general and administrative...             687             1,346      1,557      2,850
                                                      -------           -------    -------    -------
          Total costs and expenses...........           1,456             4,152      5,296     10,665
                                                      -------           -------    -------    -------
  Loss from operations.......................          (1,456)           (4,067)    (1,966)    (3,410)
  Interest income (expense), net.............              (9)             (139)      (286)       417
                                                      -------           -------    -------    -------
  Net loss...................................         $(1,465)          $(4,206)   $(2,252)   $(2,993)
                                                      =======           =======    =======    =======
  Unaudited pro forma net loss per
     share(1)................................                                      $ (0.33)   $ (0.39)
                                                                                   =======    =======
  Shares used in computing unaudited pro
     forma net loss per share(1).............                                        6,853      7,705
                                                                                   =======    =======
</TABLE>
 
<TABLE>
<CAPTION>
                                                 DECEMBER 31,                  DECEMBER 31, 1996
                                        ------------------------------     --------------------------
                                         1993       1994        1995       ACTUAL      AS ADJUSTED(2)
                                        ------     -------     -------     -------     --------------
<S>                                     <C>        <C>         <C>         <C>         <C>
BALANCE SHEET DATA:
  Cash, cash equivalents and
     marketable securities............  $  595     $   425     $ 7,791     $37,086        $ 66,351
  Working capital (deficit)...........     275      (2,108)      5,074      31,440          60,705
  Total assets........................   1,538       2,321      10,190      43,509          72,774
  Capital lease obligations, less
     current portion..................     376         962         911       1,728           1,728
  Series B mandatorily redeemable
     convertible preferred stock......      --          --       6,888          --              --
  Total stockholders' equity
     (deficit)........................     771      (1,203)     (1,000)     34,621          63,886
</TABLE>
 
- ------------------------------
 
(1) Unaudited pro forma net loss per share is determined by dividing the Net
    loss by Shares used in computing unaudited pro forma net loss per share. For
    information regarding Shares used in computing unaudited pro forma net loss
    per share, see Note 2 of Notes to Financial Statements.
 
(2) Reflects the effect of the sale of 1,632,500 shares of Common Stock offered
    by the Company hereby, after deducting the underwriting discount and
    offering expenses, at an assumed public offering price of $19.25 per share
    and the application of the estimated net proceeds therefrom as set forth in
    "Use of Proceeds."
 
                                       16
<PAGE>   18
 
               MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL
                      CONDITION AND RESULTS OF OPERATIONS
 
OVERVIEW
 
     ArQule is engaged in the discovery and development of novel chemical
compounds with commercial potential in the pharmaceutical, biotechnology and
agrichemical industries. ArQule manufactures and delivers two types of arrays of
synthesized compounds to its pharmaceutical, biotechnology and agrichemical
partners: (i) Mapping Array compound sets, which are arrays of novel, diverse
small molecule compounds used in screening for lead generation and (ii) Directed
Array compound sets, which are arrays of analogs of a particular lead compound
(identified from a Mapping Array set or otherwise), synthesized for the purpose
of optimizing such lead compounds.
 
     The Company currently generates revenue primarily through compound
development from collaborative agreements, which provide for the development and
delivery of Mapping Array and Directed Array sets. The Company's revenue to date
is primarily attributable to five major corporate collaborations: Pharmacia
Biotech AB, entered into in March 1995; Abbott Laboratories, entered into in
June 1995; Solvay Duphar B.V., entered into in November 1995; Roche Bioscience,
entered into in September 1996; and Monsanto Company, entered into in December
1996. Under these collaborations, the Company has received payments of $15.1
million through December 31, 1996 and has recognized $10.4 million as revenue.
The Company recognizes revenue under its corporate collaborations as related
work is performed and arrays are delivered. Payments received from corporate
partners prior to the completion of the related work are recorded as deferred
revenue. License option fees are recognized as the options are granted because
such fees are nonrefundable and the Company has no further obligations to
fulfill. The Company is also entitled to receive milestone and royalty payments
if products generated under the collaborations are developed. The Company has
not received any milestone or royalty payments to date. The Company has
additionally entered into joint discovery agreements with a number of
biotechnology companies to which it has provided Mapping Array and Directed
Array sets in exchange for joint ownership of resulting drug candidates. These
agreements have not yet yielded any significant revenue for the Company.
 
     The Company has not been profitable since inception and has incurred a
cumulative net loss of $10.9 million through December 31, 1996. Losses have
resulted principally from costs incurred in research and development activities
related to the Company's efforts to develop its technologies and from the
associated administrative costs required to support these efforts. The Company's
ability to achieve profitability is dependent on its ability to market its
Mapping Array and Directed Array Programs to pharmaceutical, biotechnology and
agrichemical companies and the joint development and commercialization of
products in which it has an economic interest.
 
RESULTS OF OPERATIONS
 
  Years Ended December 31, 1996 and 1995
 
     Revenue.  The Company's revenue for the year ended December 31, 1996
increased $4.0 million to $7.3 million from $3.3 million for the same period in
1995. This was attributable to a $5.0 million increase in compound development
revenue related to the performance of work and the delivery of Mapping Array and
Directed Array sets under the Company's collaborative agreements, offset by a
$1.0 million decrease in license option fees during the same period. The Company
began recognizing revenue from the Pharmacia Biotech AB, Abbott Laboratories and
Solvay Duphar B.V. collaborations in March, June and November 1995, respectively
and for Roche Bioscience and Monsanto Company in October and December of 1996,
respectively.
 
     Cost of revenue.  The Company's cost of revenue for the year ended December
31, 1996 increased $3.1 million to $4.7 million from $1.6 million for the same
period in 1995. This increase was primarily attributable to the costs of
additional scientific personnel and the necessary supplies and overhead expenses
related to the performance of the work and the delivery of the Mapping Array and
Directed
 
                                       17
<PAGE>   19
 
Array sets pursuant to its collaborative agreements. The Company anticipates
that the aggregate cost of revenue will increase over the next several years as
its business expands.
 
     Research and development expenses.  The Company's research and development
expenses for the year ended December 31, 1996 increased $1.0 million to $3.1
million from $2.1 million for the same period in 1995. This increase was the
result of the Company's expansion of its chemical libraries and related
proprietary technologies. The Company expects research and development spending
to increase over the next several years as the Company further expands its
chemistry discovery and development programs.
 
     Marketing, general and administrative expenses.  The Company's marketing,
general and administrative expenses for the year ended December 31, 1996
increased $1.3 million to $2.9 million from $1.6 million for the same period in
1995. The increase was primarily associated with increased business development
activities, expenses of being a public company, and higher levels of
administrative support for the Company's growth during 1996. These expenses will
likely increase in the aggregate in future periods to support the projected
growth of the Company.
 
     Net interest income (expense).  The Company's net interest income for the
year ended December 31, 1996 was $0.4 million, which compared to a net interest
expense of $0.3 million for the same period in 1995. Higher interest income in
1996 resulted primarily from the Company holding higher cash balances following
its initial public offering of Common Stock in October 1996.
 
     Net loss.  The Company's net loss for the year ended December 31, 1996
increased $0.7 million to $3.0 million from $2.3 million for 1995. The increase
was primarily attributable to operating and development expenses exceeding the
increase in revenue generated from corporate collaborations during 1996.
 
  Years Ended December 31, 1995 and 1994
 
     Revenue.  The Company's revenue for the year ended December 31, 1995
increased to $3.3 million from $0.1 million for the same period in 1994. This
increase was attributable to compound development revenue related to the
performance of work and the delivery of Mapping Array and Directed Array sets
under the Company's collaborative agreements which were entered into during
1995. The Company also recognized a $1.0 million license option fee related to
the Pharmacia Biotech AB collaborative agreement entered into in 1995.
 
     Cost of revenue.  The Company's cost of revenue for the year ended December
31, 1995 was $1.6 million, reflecting costs associated with the development,
production and delivery of compounds pursuant to the corporate collaborations
entered into in 1995. There was no cost of revenue in 1994 as there were no
collaborative agreements during this year and as the Company's efforts were
directed toward the research and development of its technology.
 
     Research and development expenses.  The Company's research and development
expenses for the year ended December 31, 1995 decreased $0.7 million to $2.1
million from $2.8 million for the same period in 1994. This decrease was the
result of the Company focusing, in 1995, on producing compounds delivered
pursuant to its collaborative agreements.
 
     Marketing, general and administrative expenses.  The Company's marketing,
general and administrative expenses for the year ended December 31, 1995
increased $0.3 million to $1.6 million from $1.3 million for the same period in
1994. This increase was primarily due to costs associated with increased
business development activities and administrative support, which accompanied
the Company's expansion during 1995.
 
     Net interest expense.  The Company's net interest expense for the year
ended December 31, 1995 was $0.3 million, which compared to $0.1 million for the
same period in 1994. This increase was primarily attributable to increased use
of capital equipment lease financing.
 
                                       18
<PAGE>   20
 
   
     Net loss.  The Company's net loss for the year ended December 31, 1995
decreased $1.9 million to $2.3 million from $4.2 million for the same period in
1994. The decrease was primarily attributable to the increase in revenue
generated from corporate collaborations.
    
 
LIQUIDITY AND CAPITAL RESOURCES
 
   
     At December 31, 1996, the Company held cash and cash equivalents and
marketable securities with a value of $37.1 million. The Company's working
capital at December 31, 1996 was $31.4 million. The Company has funded
operations through December 31, 1996 with sales of preferred stock and common
stock totaling $45.3 million, payments from corporate collaborators totaling
$15.1 million, and the utilization of capital equipment lease financing totaling
$4.1 million. The Company has maintained a master lease agreement since February
1994. Under the terms of this agreement, the Company has funded certain capital
expenditures through leases with terms of 42 months in duration. As of December
31, 1996, the Company had utilized $3.6 million of the available $8.5 million
financing facility.
    
 
   
     Net cash provided by financing activities for the year ended December 31,
1996 was $30.8 million, primarily reflecting proceeds from the Company's October
1996 initial public offering. Net cash provided by financing activities for the
year ended December 31, 1995 was $7.2 million, largely due to a $7.0 million
equity investment by Solvay Duphar B.V. Net cash provided by financing
activities for the year ended December 31, 1994 was $3.8 million, resulting
mainly from capital contributions and proceeds from bridge financings.
    
 
   
     Net cash provided by operating activities was $0.8 million and $0.7 million
for each of the years ended December 31, 1996 and December 31, 1995,
respectively. The positive cash flow from operating activities primarily
reflects additional payments received from the five corporate collaborators. Net
cash used in operating activities for the year ended December 31, 1994 was $3.8
million, largely due to the Company's scale-up of research and development
activities prior to generating significant revenue.
    
 
     Net cash provided by investing activities during the year ended December
31, 1996 was $2.0 million, resulting primarily from the sale of marketable
securities offset by the purchases of property and equipment. Net cash used in
investing activities for the year ended December 31, 1995 was $5.3 million as
compared to $0.2 million for the year ended December 31, 1994. This increase
primarily reflects purchases of marketable securities.
 
   
     Management estimates that the Company's existing cash equivalents,
short-term investments, cash generated from operations and research funding from
corporate collaborators, will enable the Company to maintain its current and
planned operations at least through March 1999. The Company's cash requirements
may vary materially from those now planned depending upon the results of its
drug discovery and development strategies, the ability of the Company to enter
into any corporate collaborations in the future and the terms of such
collaborations, the results of research and development, the need for currently
unanticipated capital expenditures, competitive and technological advances,
acquisitions, and other factors. There can be no assurance that the Company will
be able to obtain additional customers for the Company's products and services,
or that such products and services will produce revenues adequate to fund the
Company's operating expenses. If the Company experiences increased losses, the
Company may have to seek additional financing from public or private sale of its
securities, including equity securities. There can be no assurance that
additional funding will be available when needed or on acceptable terms.
    
 
                                       19
<PAGE>   21
 
                                    BUSINESS
 
OVERVIEW
 
   
     ArQule has created a new technology platform for the discovery and
production of novel chemical compounds with commercial potential. The Company
has developed proprietary technologies for the identification and optimization
of drug development candidates and agrichemicals. Using combinatorial chemistry,
a modular building block approach to the development of compounds,
structure-guided compound design, high speed parallel chemical synthesis and
information technology, the Company rapidly develops large, diverse collections
of compounds that have the potential to be biologically active. To date, the
Company has entered into collaborative arrangements with Abbott Laboratories,
Monsanto Company, Pharmacia Biotech AB, Roche Bioscience and Solvay Duphar B.V.,
and has formed joint discovery programs with several biotechnology companies.
    
 
   
     The Company's goal is to penetrate the product development pipelines of
major pharmaceutical, biotechnology and agrichemical companies and to maximize
the likelihood that active compounds are discovered and successfully developed.
In order to achieve this goal, the Company pursues a strategy designed to
maximize the number of biological targets against which its compounds are
screened. ArQule believes that its technologies will allow its collaborative
partners in the pharmaceutical, biotechnology and agrichemical industries to
accelerate the product development process by several years, permitting them to
realize significant cost reductions and the earlier recovery of research and
development expenditures for successful drugs and agrichemicals. In addition,
the Company believes its technologies will allow researchers to seek solutions
to product development challenges previously deemed too costly or otherwise
impractical because of the inherent limitations of traditional medicinal
chemistry.
    
 
     The potential market for ArQule's proprietary modular building block
technology is comprised of all consumers of novel chemical compounds, including
developers of drugs, separations media, agrichemical products, industrial
catalysts, specialty materials and other industrial products. The Company's
initial business focus has been on the pharmaceutical, biotechnology and
agrichemical industries.
 
APPLICATION OF THE COMPANY'S TECHNOLOGIES IN THE DRUG DISCOVERY INDUSTRY
 
   
  INDUSTRY BACKGROUND
    
 
     Traditional Drug Discovery and Its Limitations.  Drugs are chemical
compounds that modulate the activity of biological targets associated with
particular disease states to achieve a desired therapeutic effect. The discovery
and development of drugs has traditionally been a lengthy, expensive and often
unsuccessful process. Typically, it takes 12 to 15 years from the original
concept of modulating the activity of a particular biological target to the
market introduction of a drug that performs such a function. The average cost of
bringing a new drug to market has been estimated to be in excess of $300
million.
 
     The first major step in the drug discovery process is the identification of
one or more compounds that interact with a biological target, such as an enzyme,
receptor or other protein, that is associated with a disease state. To identify
such a compound, collections of compounds are tested or screened for activity
with respect to the biological target. A compound that interacts with a target
is referred to as a hit, and a hit with characteristics making it suitable as a
potential drug is referred to as a lead compound.
 
                                       20
<PAGE>   22
 
<TABLE>

                                           TRADITIONAL DRUG DISCOVERY PROCESS
<CAPTION>
                              
<S>               <C>            <C>          <C>           <C>            <C>             <C>
                                                      Secondary  
                         Development                  Assays and
                          of Assays                  Other Tests                  Preclinical                  
                    Incorporating Target          (6 to 12 months)                Development
                                                                                      
                                                                                      
                                                                                      
                                                                                          
                                                                                      
____________      ___________   __________   ___________  ____________   ____________   ______________
                                                                                           Clinical
   Unmet            Relevant                                  Lead           Drug           Trials/
Therapeutic _____  Biological __   Assays ___     Hit   ___ Compound  ___ Development__    Regulatory
   Need             Target                                                 Candidate         Approval
____________     ___________    __________   ___________   ____________  ____________    ______________
                                                                        
                                _________                               
                                 Natural/                               
                                 Synthetic                              
                                  Product                                
           Cellular               Libraries                             Lead       
          Molecular              __________                          Optimization
           Biology                                                (average 2 years)
                                     
                                     
                                     
                                 Screening
                            (6 months to 2 years)
                              


__________________________________ Average Time to Market: 12 to 15 years__________________________________
                                        Average Cost: $300+ million
                              
</TABLE>

 
 
     Historically, drug developers have obtained collections of chemical
compounds for screening from natural product sources and by synthesis. These
collections are often neither sufficiently diverse to be likely to result in a
hit nor preselected to include compounds with promising structures or desirable
drug characteristics. This random screening approach has yielded a relatively
small percentage of hits and only a relatively small portion of those hits have
resulted in lead compounds.
 
     The second major step in the drug discovery process is the optimization of
a lead compound by the sequential synthesis and testing of variations, or
analogs, of a lead compound to identify promising drug development candidates. A
drug development candidate is a lead compound that in preclinical studies
demonstrates pharmacological efficacy, lack of toxicity, potency, selectivity
and other desirable characteristics such as oral availability, cell penetration
and stability. Using traditional medicinal chemistry, lead optimization has
required an average of two years of synthesizing hundreds of analogs of a lead
compound and has been the most expensive and time consuming part of the drug
development process prior to clinical testing. The synthesis of a single
compound analog takes approximately 7 to 10 days and costs approximately $7,500.
As a result, a chemist is usually able to synthesize only 100 to 200 analogs per
year. On average, as many as 6,000 chemical compounds may be synthesized per
successful drug at a cost of approximately $45 million in chemistry costs.
 
     Drug Development in Transition.  Lower profit margins, shorter product
lives, the proliferation of generic drugs, managed care and cost containment
initiatives, combined with scientific and technological advances, have created
powerful incentives for drug developers to explore new technologies to discover
novel drugs more quickly and cost effectively. The growing biotechnology and
gene discovery (genomics) industries are rapidly identifying numerous new
biological targets and developing highly sensitive assays incorporating these
targets. Advances in robotics have led to automated high throughput screening
systems, allowing biologists to assay large numbers of chemical compounds
against novel targets. These developments have resulted in increased demand for
large and diverse collections of novel compounds.
 
     In addition, in recent years, structure-guided and rational drug design
approaches have allowed scientists, using structure-activity relationship
("SAR") data about biological targets, to design compounds that are likely to
show activity with respect to a biological target. These developments,
 
                                       21
<PAGE>   23
 
together with the developments referred to in the preceding paragraph, have
resulted in a proliferation of hits, generating demand for tools to rapidly
create analogs of hits and optimize lead compounds.
 
     Current Combinatorial Chemistry Technology and Its Limitations.  
Combinatorial chemistry is the rapid creation of hundreds of thousands of
chemical compounds, most of which do not exist in nature, for the purpose of
rapidly identifying hits through random screening. Current combinatorial
chemistry has been successful in producing large numbers of compounds and
correspondingly large numbers of hits. However, current combinatorial chemistry
techniques have been less successful in generating lead compounds and,
ultimately, drug development candidates for some or all of the following
reasons:
 
     - Time-Consuming Isolation of Hits.  In certain combinatorial chemistry
       applications, large numbers of chemical compounds are synthesized and
       screened in mixtures. Hits must therefore be isolated from the mixtures,
       which is a costly, slow, labor-intensive process.
 
     - Lack of Structural and SAR Information.  Once a hit is isolated, many
       current combinatorial techniques fail to facilitate the identification of
       the structure of the hit or to provide SAR data to guide the lead
       optimization process.
 
     - Incompatibility with Drug Developers' Screening Protocols.  Many
       combinatorial compounds are produced in a format that is incompatible
       with standard screening protocols of drug developers. In addition, once a
       hit is found and the compound is isolated, significant additional work
       must often be performed by the combinatorial chemistry company to
       determine the structure of the compound. Drug developers relying on this
       format may therefore be required to transfer hits to the combinatorial
       chemistry company.
 
     - Limitations of Solid Phase Chemistry.  Several combinatorial chemistry
       techniques involve the production of compounds using solid phase
       chemistry in which compounds are attached to small beads. Because many
       compounds with desirable chemistries cannot be synthesized using solid
       phase chemistry, collections of compounds based exclusively on solid
       phase chemistry may have limited diversity.
 
     - Limited Compound Quantities.  Certain current combinatorial chemistry
       techniques produce very small quantities of each compound, which limits
       further testing once a lead compound is found and precludes archiving of
       compounds for future testing against additional targets.
 
     - Scale-Up Limitations.  Many current combinatorial chemistry techniques
       involve laboratory methods that cannot be easily translated into large
       scale manufacturing processes. This creates the possibility that active
       compounds will be identified that are difficult or impractical to produce
       in quantities necessary for clinical trials or commercial production.
 
     - Unproductive Screening.  Because certain combinatorial chemistry
       techniques involve the screening of random compounds without preselection
       for desirable drug characteristics, suitable lead compounds often can be
       identified only after many unproductive screenings. In addition, testing
       of mixtures frequently produces equivocal or false positive screening
       results because the observed activity with a biological target is caused
       by several compounds within the mixture rather than the interaction of an
       individual compound with a target, leading to further unproductive
       screening.
 
     Although recent developments in combinatorial chemistry have shortened the
time between identifying a biological target and obtaining a hit in the target
assay, the proliferation of hits has not led to a commensurate increase in lead
compounds. In addition, current combinatorial chemistry techniques have not
significantly improved the lead optimization process and, therefore, have not
significantly shortened the time it takes to produce a drug development
candidate from a lead compound.
 
                                       22
<PAGE>   24
 
  THE ARQULE REVOLUTION
 
     ArQule believes its modular building block technology overcomes many of the
limitations of current combinatorial chemistry approaches by achieving targeted
diversity to accelerate the identification and optimization of lead compounds.
Targeted diversity is the design of diverse compound arrays that are biased
toward specific biological targets by selecting molecules from a variety of
chemical classes and constructing compound arrays in a manner believed to
increase the probability of discovering one or more active compounds for those
biological targets.
 
     Many organic molecules, including amino acids, peptides, nucleosides,
carbohydrates, steroids and alkaloids, may be viewed as comprised of structural
components, consisting of a scaffold, or core structure, around which a set of
substituent groups and connectors (bonds) is varied. ArQule's scientists have
developed proprietary methods for selecting and combining molecular components,
or building blocks, to produce arrays of compounds that possess properties they
believe will exhibit activity in biological systems.
 
     Using SAR data regarding biologically active compounds and modular
molecular components, ArQule's synthetic and computational chemists work
together to rapidly design compound arrays that include all combinations of a
set of selected building blocks around a common core structure or theme.
ArQule's arrays are created by using structure-guided and rational drug design
tools to systematically select and assemble molecular building blocks with
properties the Company's scientists believe are likely to exhibit biological
activity. Each compound in the array is different from the adjacent compound as
a result of a single structural modification. Each ArQule array omits compounds
that are closely analogous to other compounds in the array, using representative
diversity to create a logical representation of a virtual library of hundreds of
times as many compounds as are in the array. Drug developers are able to realize
significant savings by screening the thousands of compounds in each ArQule array
rather than the millions of compounds they represent. In addition, the SAR data
of compounds within the array provides a navigational tool for lead optimization
by indicating the most promising investigational direction for analoging.
 
     In order to enhance the effectiveness of this modular building block
technology, ArQule integrates the following tools:
 
     - structure-guided design;
 
     - a proprietary "automated molecular assembly plant" (AMAP) system for high
       speed parallel synthesis, purification and structural verification of
       chemical compounds; and
 
     - proprietary computer applications that facilitate the integration of all
       of the Company's proprietary technologies.

[Graphical representation displaying the integration of ArQules Combinational
Drug Design and Development Platform]
 
                                       23
<PAGE>   25
 
     Structure-Guided Design.  ArQule's scientists believe that the likelihood
of generating a drug development candidate can be substantially increased if the
collection of compounds used for screening is created using three-dimensional
structural and SAR data. The Company designs its arrays based on chemical
structures that are believed to be biologically active and also on SAR data
regarding a particular target and a particular lead compound. Using this data,
as well as knowledge of the chemical reactions that are feasible using high
speed parallel synthesis, ArQule's scientists design logically arranged arrays
of diverse compounds that can easily be synthesized. The Company believes that
this approach will accelerate the lead discovery and optimization process by
increasing the probability of identifying a lead compound that will result in a
drug development candidate.
 
     The AMAP High Speed Parallel Synthesis System.  Using its "automated
molecular assembly plant" (AMAP) system, ArQule synthesizes, purifies and
verifies structural information for individual compounds through automated high
speed parallel synthesis. The AMAP system is capable of synthesizing thousands
of compounds per day, each in milligram quantities adequate for multiple
screens, analyzing such compounds for structural integrity and purity,
registering the structural data in a relational database, and delivering the
compounds in a 96-well microtiter plate format for high throughput screening.
 
     Integrated Proprietary Computer Applications ("Informatics").  ArQule has
developed a proprietary information system which incorporates (i) databases of
the molecular structures of building blocks and the compounds in its arrays,
(ii) multi-dimensional matrix geometry which provides guidance for the creation
of the Company's spatially addressable arrays of compounds containing systematic
variations of modular building blocks, (iii) instructions for the robotics
involved in the AMAP parallel synthesis production process, (iv) resulting
databases of structural information regarding the compounds produced in any
particular array which can be supplied in a format compatible with customers'
own data registration systems and (v) databases of SAR data regarding particular
compounds and their molecular components contained in an array generated when
these compounds are screened against biological targets. This integrated
information system enables ArQule to gather and apply data on an ongoing basis
to enhance the efficiency of the production process and to design compounds
based on a growing knowledge of the structure and activity of its molecular
components.
 
  ADVANTAGES OF ARQULE'S COMBINATORIAL DRUG DISCOVERY AND DEVELOPMENT PLATFORM
 
     The Company believes the integration of its technological capabilities
offers a unique combinatorial drug discovery and development platform. This
platform offers the following significant advantages over current combinatorial
chemistry approaches:
 
     - Elimination of Isolation Issues.  Unlike combinatorial chemistry
       processes involving the production of synthesized compounds in mixtures,
       ArQule's AMAP system produces one compound per well, with each well
       containing a known compound with a high level of purity.
 
     - Enhanced Structural and SAR Data.  ArQule produces arrays using
       preselected modular building blocks that its scientists believe are
       likely to produce lead compounds with desirable characteristics, and, in
       the case of Directed Array sets, based upon the SAR data of the target
       and/or lead compound. As a result, the Company believes the success rate
       for drugs developed using its arrays will be improved and the risk of
       downstream clinical failure will be reduced. The wealth of SAR data
       available with respect to compounds in its arrays will also facilitate
       the development of analogs for the further optimization of active
       compounds.
 
     - Compatibility with Drug Developers' Screening Protocols.  ArQule's
       compounds are delivered to its collaborators in 96-well microtiter plates
       containing one known compound per well. This delivery format is
       compatible with most existing screening protocols and permits the owner
       of the assay to screen compounds in its own laboratories, thereby having
       complete control over the screening process.
 
                                       24
<PAGE>   26
 
     - Solution and Solid Phase Chemistry.  ArQule's compounds may be produced
       using either solution or solid phase chemistry, permitting the creation
       of a broad range of novel chemical compounds.
 
     - Significant Compound Quantities.  ArQule's compounds are delivered to its
       collaborators in milligram quantities, permitting the collaborator to
       engage in extensive testing of a lead compound or to screen compounds
       against multiple biological targets without having to obtain additional
       samples from the Company.
 
     - Ease of Scale-Up.  ArQule's compounds are produced using fully
       reproducible and scalable manufacturing processes.
 
     - Reduction in Unproductive Screening.  By creating logical arrays of
       compounds based on known structural and SAR data and eliminating
       compounds that are closely analogous to others in the array, ArQule
       believes that fewer compounds will need to be screened prior to
       identifying compounds with activity. In addition, because ArQule delivers
       single compounds for screening, such compounds do not generate the false
       positives and false negatives associated with screening mixtures of
       compounds.
 
     ArQule believes these significant advantages will allow its collaborative
partners to accelerate the drug discovery process by several years by shortening
the time required to identify a lead compound and to optimize that compound into
a drug development candidate. This acceleration should permit drug developers to
realize significant cost reductions and the earlier recovery of research and
development expenditures for successful drugs.
 
APPLICATION OF THE COMPANY'S TECHNOLOGIES IN THE AGRICHEMICAL INDUSTRY
 
     Industry Background.  Agrichemicals are chemical products used in the
agricultural industry. Examples of agrichemicals are herbicides, pesticides,
fungicides, bactericides and soil treatment agents. Historically, agrichemical
developers have obtained chemical compounds for screening from natural product
sources and by traditional medicinal synthesis, and then screened those
compounds against whole organisms rather than specific molecular targets. Lead
compounds have traditionally been optimized using medicinal chemistry techniques
similar to those used in the drug industry. Agrichemicals are also expensive and
time-consuming to develop. As an example, the American Crop Protection
Association estimates that development, testing, and regulatory approval of a
pesticide product typically requires eight to ten years and may cost up to $50
million.
 
     As in the case of the pharmaceutical industry, the agrichemical industry is
under pressure to identify lead compounds for the development of new products.
As patents expire on existing products and generic equivalents become available,
developers must introduce improved products to stay competitive and maintain
profit margins. To gain market acceptance of a new product at a premium price,
the product must provide some advantage to the customer as compared with
existing products, such as an improvement in environmental profile, user health
and safety, consumer health and safety, user convenience, or effectiveness at
lower concentrations. Alternatively, a producer can maintain profit margins on a
product sold without a premium if that product can be manufactured at a lower
cost. Therefore, products in the agrichemical industry have historically been
subject to a cost-benefit analysis that only recently has affected the
pharmaceutical industry with the advent of managed care.
 
     Combinatorial Chemistry in the Agrichemical Industry.  The agrichemical
industry is now adopting new technologies including high throughput screening
and combinatorial chemistry for many of the same reasons as the pharmaceutical
industry. The limitations of certain combinatorial chemistry techniques, as
described in the context of the pharmaceutical industry, are also applicable to
the agrichemical industry. Indeed, compound quantities and scale-up issues are
perhaps more important to the agrichemical industry than the pharmaceutical
industry.
 
     - Compound Quantities.  The agrichemical industry has historically used
       whole-organism screening methods and has not completed the transition to
       screening for specific molecular targets.
 
                                       25
<PAGE>   27
 
       These whole-organism assays consume quantities of test compounds in
       excess of the quantities produced using certain current combinatorial
       chemistry techniques.
 
     - Scale-Up.  As compared with the pharmaceutical industry, the agrichemical
       industry manufactures and sells larger quantities of product at a lower
       margin. In addition, these products will not succeed in the marketplace
       unless they offer a clear advantage over existing products, with cost-
       effectiveness as a major factor. Because of these constraints, the ease
       and cost of manufacture for a product is a more important consideration
       in the agrichemical industry than in the pharmaceutical industry.
 
     The ArQule Advantage.  The advantages of the ArQule approach to
combinatorial chemistry, as described in the context of the pharmaceutical
industry, are also advantages for the agrichemical industry. Indeed, the ArQule
combinatorial compound discovery and development platform satisfies the
important considerations of adequate compound quantities for initial screening
and ease of scale-up for manufacturing. ArQule's compounds are delivered to its
collaborators in milligram quantities sufficient for whole-organism screening
methods, which are traditionally used in agrichemical development. In addition,
ArQule's compounds are produced using fully reproducible and scalable
manufacturing processes.
 
ARQULE'S PRODUCTS
 
     ArQule's integrated technologies result in the production of significant
quantities of pure small molecule compounds contained in a logically structured
spatially-addressable array. ArQule provides its collaborative partners with two
types of arrays of synthesized compounds: (i) Mapping Array compound sets, which
are arrays of novel, diverse, small molecule compounds used for screening
against biological targets and (ii) Directed Array compound sets, which are
arrays of analogs of a particular lead compound synthesized for the purpose of
optimizing that lead compound.
 
     Mapping Array Program.  ArQule's Mapping Array Program is a multi-year
subscription to annual Mapping Array compound sets which are designed around
certain core structures or themes selected by ArQule. Through this program, the
Company provides 15 to 20 Mapping Array compound sets, on an annual basis, each
containing between 3,000 and 10,000 individual compounds for a minimum aggregate
of 100,000 compounds. The Mapping Array Program is provided to subscribers
without limitation as to the targets against which the compounds may be
screened. ArQule believes this approach will maximize the number of targets
against which its Mapping Array sets are tested, thereby maximizing the
potential for identifying activity for each compound in the array. Initially,
the Company provides its Mapping Array sets on a non-exclusive, subscription fee
basis for screening purposes only. If a compound shows activity in a
subscriber's assay, the subscriber may license that compound from the Company
for development purposes on an exclusive basis, unless such compound has already
been licensed to another collaborative partner. The Company does not provide any
structural information regarding the compounds in the Mapping Array sets until a
particular compound is licensed.
 
     Directed Array Programs.  Under its Directed Array Programs, the Company
provides Directed Array sets in order to optimize lead compounds. In a Directed
Array set, the Company uses its modular building block technology to create
analogs of a lead compound identified by the collaborator, either independently
or as a result of screening a Mapping Array set. Successive Directed Array sets
are generated in order to identify the analog or analogs having the greatest
biological activity and most desirable development characteristics. When
delivering each Directed Array set, the Company provides the collaborator with
structural information for each compound in the array, and each compound is
owned by the collaborator either individually or jointly with ArQule, subject to
the payment of fixed fees, milestones and royalties to the Company. Under a
typical Directed Array Program, ArQule provides three to seven Directed Array
sets, each averaging about 1,000 analogs of a particular lead compound chosen by
a collaborator in consultation with ArQule.
 
                                       26
<PAGE>   28
 
BUSINESS STRATEGY
 
     ArQule's goal is to become the leading drug and chemical product discovery
company by using its high throughput molecular technologies to design,
synthesize and test high performance molecules for health care and specialty
chemical applications. The Company seeks to penetrate the product development
pipelines of pharmaceutical, agrichemical and biotechnology companies and to
maximize the likelihood of the discovery of activity and successful development
of commercial compounds. Key elements of the Company's strategy include:
 
     - Collaborations with Pharmaceutical and Agrichemical Companies.  The
       Company seeks collaborations with those companies that have established
       manufacturing, marketing and sales resources and a strong commitment to
       the development of pharmaceutical or agrichemical products. ArQule offers
       to each of its collaborative partners access to its Mapping Array Program
       for an annual subscription fee and provides, if requested, customized
       Directed Array Programs for a fixed fee. In addition, the Company is
       entitled to payments upon the achievement of certain milestones and
       royalties upon the commercialization of products developed by the
       collaborator from ArQule compounds. The Company plans to pursue
       additional collaborations aggressively to gain access to additional
       targets and development expertise, and to generate additional revenue.
 
     - Joint Discovery Programs with Biotechnology Companies.  Biotechnology
       companies have identified numerous proprietary biological targets and
       assays and therefore represent important potential collaborators for
       joint discovery and development efforts using ArQule's Mapping Array and
       Directed Array sets. ArQule provides Mapping Array and Directed Array
       sets to biotechnology companies in exchange for joint ownership of any
       lead compounds that exhibit activity in the proprietary assays developed
       by the biotechnology company collaborators. ArQule seeks collaborators
       with promising drug development programs in a broad range of therapeutic
       areas.
 
     - Expansion of Proprietary Drug Discovery Capabilities.  The Company
       intends to expand its proprietary drug discovery capabilities by
       developing or acquiring, either independently or in partnership with
       others, proprietary biological targets, proprietary assays and the
       capability to screen its compounds against such assays. The Company will
       also consider investing in the lead optimization and initial preclinical
       and clinical development efforts for selected lead compounds in order to
       realize a greater portion of the value created by its technologies.
 
     - Extension of Chemistry Tools to Other Areas.  The Company intends to
       extend its integrated technologies outside the fields of pharmaceuticals,
       agrichemicals and bioseparations to a variety of other applications,
       including industrial catalysts and polymeric structures for
       non-biological applications.
 
     - Continued Investment in Proprietary Chemistry Technology.  ArQule intends
       to continue its aggressive investment in proprietary chemistry
       technologies through internal development and licensing of third party
       technologies. ArQule will also continue to invest in improving the cost-
       effectiveness of its products through automation and information
       technologies.
 
ARQULE'S PRODUCT DISCOVERY PROGRAMS
 
  Pharmaceutical and Agrichemical Company Collaborations
 
     To date, the Company has entered into the following major collaborations
with pharmaceutical and agrichemical companies:
 
     Abbott Laboratories.  In June 1995, the Company entered into a
collaborative agreement with Abbott Laboratories ("Abbott") pursuant to which
Abbott subscribed to the Company's Mapping Array Program and has the right to
request customized Directed Array sets (the "Abbott Agreement"). To date, the
Company has provided Abbott with several Mapping Array and Directed Array sets.
In
 
                                       27
<PAGE>   29
 
   
August 1996, the Abbott Agreement was amended to provide for the Company to
supply Abbott with additional Mapping Array sets and to eliminate restrictions
on the period during which Abbott may screen the Mapping Array sets. In December
1996, the Abbott Agreement was further amended to extend the term of the Abbott
Agreement until March 1999, to provide for the Company to supply Abbott with
additional Mapping Array sets during such extended period and to provide for the
payment by Abbott of additional research and development funding during such
extended period. Abbott may not terminate the Abbott Agreement prior to March
1999 without cause. Absent early termination, Abbott has agreed to pay the
Company $6.8 million through March 1999. Abbott is also obligated under the
Abbott Agreement to make additional payments upon the achievement of certain
milestones and to pay royalties on the sale of drugs that may result from the
relationship. To date, Abbott has paid the Company an aggregate of $5.0 million
under the Abbott Agreement.
    
 
   
     Monsanto Company.  In December 1996, the Company entered into a
collaborative agreement with Monsanto Company ("Monsanto"), pursuant to which
Monsanto subscribed to the Company's Mapping Array Program and the Company
agreed to synthesize Directed Array sets from compounds provided to the Company
by Monsanto and/or developed by the Company under the Mapping Array Program (the
"Monsanto Agreement"). Assuming Monsanto requests the synthesis of at least one
Directed Array per year over the term of the Monsanto Agreement, the Company
will receive a minimum of $12.0 million over five years. Monsanto is also
obligated to make additional payments upon the achievement of certain milestones
and to pay royalties on sales of products that may result from the relationship.
The Monsanto Agreement expires in December 2001, subject to Monsanto's right to
extend the term of the Monsanto Agreement for two additional one-year periods.
Monsanto has the right to terminate the Mapping Array Program and/or the
Directed Array Program on six months' written notice at any time subject to its
payment of a termination fee equal to the aggregate minimum amount that would
have been paid to the Company by Monsanto under the program to be terminated
over the entire five-year term. To date, Monsanto has paid the Company an
aggregate of $0.8 million under the Monsanto Agreement.
    
 
   
     Pharmacia Biotech AB.  In March 1995, the Company entered into a
collaborative agreement with Pharmacia Biotech AB ("Pharmacia"), a wholly-owned
subsidiary of Pharmacia & Upjohn, Inc., to allow Pharmacia to evaluate the
utility of the Company's technology for the development of products in the
fields of bioseparations, synthesis of biomolecules and cell culture (the
"Pharmacia Agreement"). On the same date, the Company and Pharmacia also signed
an agreement under which Pharmacia has an option to acquire an exclusive,
worldwide license to develop and commercialize specified compounds generated by
the Company in additional fields covered under the Pharmacia Agreement, subject
to the payment by Pharmacia of additional fees and the negotiation and execution
by the parties of a license agreement containing commercially reasonable terms
(the "Option Agreement"). To date, Pharmacia has paid the Company an aggregate
of $2.5 million under the Pharmacia Agreement and the Option Agreement.
    
 
     Roche Bioscience.  In September 1996, the Company entered into a
collaborative agreement with Roche Bioscience ("Roche Bioscience"), a division
of Syntex (U.S.A.) Inc. and indirect subsidiary of Roche Holding Ltd., pursuant
to which the Company will synthesize Directed Array sets from compounds provided
to the Company by Roche Bioscience, developed by the Company internally and/or
developed by the Company as a part of the collaboration (the "Roche Bioscience
Agreement"). Absent early termination, Roche Bioscience will pay the Company
approximately $12.1 million over three years. The parties may jointly agree to
increase the number of Directed Array sets to be provided by the Company under
the Roche Bioscience Agreement, which may result in increased payments to the
Company. Roche Bioscience is also obligated to make additional payments upon the
achievement of certain milestones and to pay royalties on sales of drugs that
may result from the relationship. The Roche Bioscience Agreement expires in
September 1999 and is terminable by Roche Bioscience on or after September 1998
on six months' advance notice. If such termination occurs on September 30, 1998,
the Company will have received payments of approximately $8.4 million from Roche
Bioscience through that date and no further payments, other than milestone
payments and
 
                                       28
<PAGE>   30
 
royalties, will be due to the Company. To date, Roche Bioscience has paid the
Company an aggregate of $3.6 million under the Roche Bioscience Agreement.
 
     Solvay Duphar B.V.  In November 1995, the Company entered into a
collaborative agreement with Solvay Duphar B.V. ("Solvay") pursuant to which
Solvay has subscribed to the Company's Mapping Array Program and has the right
to request customized Directed Array sets (the "Solvay Agreement"). To date, the
Company has provided Solvay with several Mapping Array and Directed Array sets.
Absent early termination, Solvay agreed to pay the Company a minimum of $17.5
million over five years. Solvay is also obligated to make additional payments
upon the achievement of certain milestones and to pay royalties on sales of
drugs that may result from the relationship. The Solvay Agreement expires in
November 2000. Solvay has the right to terminate the Mapping Array Program on
twelve months' written notice at any time subject to its payment of a
termination fee of approximately $1.0 million. Solvay may also terminate the
delivery of Directed Array sets on six months' written notice at any time
subject to its payment of a termination fee equal to a certain percentage of the
aggregate research payments made by Solvay in the year in which notice is given.
If Solvay gave notice to terminate both programs on the date of this Prospectus,
as of the effective termination dates, Solvay would have paid the Company $4.3
million, not including the termination fees. No further payments would be due
from Solvay other than milestone or royalty payments. To date, Solvay has paid
the Company an aggregate of $4.3 million under the Solvay Agreement. In
connection with this collaboration, an affiliate of Solvay, Physica B.V., made a
$7.0 million equity investment in the Company. See "Certain Transactions." Under
the Solvay Agreement, Solvay has the right to license, on an exclusive basis,
lead compounds identified from a Mapping Array set that are active against
specified biological targets and that have not previously been committed to
another of ArQule's collaborative partners or to an internal program of the
Company. Solvay also has the right to use certain of ArQule's technologies
internally.
 
  Joint Discovery Programs with Biotechnology Companies
 
     ArQule has initiated joint programs for lead generation and optimization
with a number of biotechnology companies. Some of ArQule's biotechnology
collaborators and their areas of focus are listed below:
 
<TABLE>
<CAPTION>
COMPANY                               AREA OF FOCUS
- -------                               -------------              
<S>                                   <C>
Aurora Biosciences, Inc.              Mammalian Cell-Based Assays
Cadus Pharmaceuticals Corporation     Signal Transduction
Cubist Pharmaceuticals, Inc.          Infectious Diseases
ICAgen, Inc.                          Ion Channel Receptors
Scriptgen Pharmaceuticals, Inc.       RNA/Protein Interaction
Signal Pharmaceuticals, Inc.          Gene Transcription/Transcription Factors
SUGEN, Inc.                           Signal Transduction
T Cell Sciences, Inc.                 T Cell Activation/Inhibition
</TABLE>
 
     In the United States, small biotechnology companies have been highly
successful in the discovery of biological targets associated with disease
states. Many of these companies, however, lack both (i) large libraries of
chemical compounds to screen against identified targets and (ii) the
sophisticated chemistry expertise required to optimize compounds once a lead
compound has been identified. Under the Company's typical arrangement with a
biotechnology company, ArQule provides Mapping Array sets for screening without
collecting upfront fees, and the biotechnology company executes a preliminary
material transfer agreement. If the collaborator detects an active compound
within a Mapping Array set, and that compound has not been previously committed
to a third party or to an internal ArQule program, the Company and the
collaborator establish a joint discovery program and execute the research
collaboration agreement that is attached to the material transfer agreement. If
the parties are unable to negotiate the scope of a joint discovery program
within a certain period, ArQule has the right to license such compound to any
third party.
 
                                       29
<PAGE>   31
 
     Although ArQule's formal research collaboration agreement varies from
transaction to transaction, it typically establishes a joint drug development
program for the lead compound and a particular target, and gives ArQule shared
control over the program.
 
MARKETING AND SALES
 
     The Company markets its products directly to customers through
participation in trade conferences and seminars and publications in scientific
and trade journals.
 
   
     To date, the Company has sold its products to its collaborative partners
primarily through the efforts of its senior management. The Company's senior
management has limited experience in marketing products similar to those of the
Company. In order to achieve significant long-term growth in revenues and its
overall strategic goals, the Company intends to hire several dedicated sales and
marketing personnel. There can be no assurance that the Company will be able to
achieve anticipated expansion of its business, attract a significant number of
new collaborative partners as customers or build an efficient and effective
sales and marketing organization. In the event the Company is unable to achieve
any one or more of the foregoing goals, the Company's business, financial
condition and results of operations could be materially adversely affected. In
addition to the risks inherent in the Company's efforts to market its own
products, the Company's revenues from royalties and milestone payments from its
collaborative partners are substantially dependent upon the marketing efforts of
such collaborative partners.
    
 
RESEARCH AND DEVELOPMENT
 
   
     ArQule intends to continue its aggressive investment in its proprietary
technologies through internal development and licensing of third party
technologies in order to increase the diversity and improve other
characteristics of the compounds offered. The Company will also continue to
invest in improving the cost-effectiveness of its products and capabilities
through automation and information technologies. The Company is actively
pursuing research projects aimed at identifying and developing new chemistries
to improve and expand on its Mapping Array and Directed Array Programs. The
Company is also undertaking collaborations with other researchers in order to
pursue the possible acquisition of chemistries and other technologies developed
by academic institutions and other third parties.
    
 
PATENTS AND PROPRIETARY RIGHTS
 
     ArQule has one issued patent and has filed a number of patent applications.
There can be no assurance that patent applications filed by ArQule will result
in patents being issued, that the claims of such patents will offer significant
protection of the Company's technology, or that any patents issued to or
licensed by ArQule will not be challenged, narrowed, invalidated or
circumvented. The Company may also be subject to proceedings that result in the
revocation of patent rights previously owned by or licensed to ArQule, as a
result of which the Company may be required to obtain licenses from others to
continue to develop, test or commercialize its products. There can be no
assurance that ArQule will be able to obtain such licenses on acceptable terms,
if at all. In addition, there may be pending or issued patents held by parties
not affiliated with ArQule that relate to the technology utilized by ArQule. As
a result, ArQule may need to acquire licenses, to assert infringement, or
contest the validity, of such patents or other similar patents which may be
issued. ArQule could incur substantial costs in defending itself against patent
infringement claims, interference proceedings, opposition proceedings or other
challenges to its patent rights made by third parties, or in bringing such
proceedings or enforcing any patent rights of its own.
 
   
     The Company also relies upon trade secrets, know-how and continuing
technological advances to develop and maintain its competitive position. In an
effort to maintain the confidentiality and ownership of trade secrets and
proprietary information, the Company requires employees, consultants and certain
collaborators to execute confidentiality and invention assignment agreements
upon
    
 
                                       30
<PAGE>   32
 
commencement of a relationship with the Company. These agreements are intended
to enable the Company to protect its proprietary information by controlling the
disclosure and use of technology to which it has rights and provide for
ownership by the Company of proprietary technology developed at the Company or
with the Company's resources. There can be no assurance, however, that these
agreements will provide meaningful protection for the Company's trade secrets or
other confidential information in the event of unauthorized use or disclosure of
such information or that adequate remedies would exist in the event of such
unauthorized use or disclosure. The loss or exposure of trade secrets possessed
by ArQule could have a material adverse effect on its business.
 
COMPETITION
 
     Many organizations are actively attempting to identify and optimize
compounds for potential pharmaceutical or agrichemical development. The
Company's services and products face competition based on a number of factors,
including size, diversity and ease of use of libraries of compounds, speed and
costs of identifying and optimizing potential lead compounds and patent
position. ArQule competes with the research departments of pharmaceutical
companies, biotechnology companies, agrichemical companies, combinatorial
chemistry companies and research and academic institutions. Many of these
competitors have greater financial and human resources and more experience in
research and development than the Company. Smaller companies may also prove to
be significant competitors, particularly through arrangements with large
corporate collaborators. In addition to competition for customers, these
companies and institutions also compete with the Company in recruiting and
retaining highly qualified scientific and management personnel.
 
     Historically, pharmaceutical and agrichemical companies have maintained
close control over their research activities, including the synthesis, screening
and optimization of chemical compounds. Many of these companies, which represent
a significant potential market for ArQule's products and services, are
developing in-house combinatorial chemistry and other methodologies to improve
productivity, including major investments in robotics technology to permit the
automated parallel synthesis of compounds. In addition, these companies may
already have large collections of compounds previously synthesized or ordered
from chemical supply catalogs or other sources against which they may screen new
targets. Other sources of compounds include extracts from natural products such
as plants and microorganisms and compounds created using rational design.
Academic institutions, governmental agencies and other research organizations
are also conducting research in areas in which the Company is working either on
their own or through collaborative efforts.
 
     The Company anticipates that it will face increased competition in the
future as new companies enter the market and advanced technologies become
available. The Company's processes may be rendered obsolete or uneconomical by
technological advances or entirely different approaches developed by one or more
of the Company's competitors. The existing approaches of the Company's
competitors or new approaches or technology developed by the Company's
competitors may be more effective than those developed by the Company.
 
     There can be no assurance that the Company's competitors will not develop
more effective or more affordable technology or products, or achieve earlier
product development and commercialization than the Company, thus rendering the
Company's technologies and/or products obsolete, uncompetitive or uneconomical.
See "Risk Factors--Competition and the Risk of Obsolescence of Technology."
 
GOVERNMENT REGULATION
 
     Although the manufacture, transportation and storage of the Company's
products are subject to certain laws and regulations discussed in the last
paragraph of this section, the sale of the Company's products is not subject to
significant government regulations. However, the Company's future profitability
is dependent on the sales of pharmaceuticals and other products developed from
the Company's compounds by its customers and collaborators. Regulation by
governmental entities in the
 
                                       31
<PAGE>   33
 
United States and other countries will be a significant factor in the production
and marketing of any pharmaceutical products that may be developed by a customer
of the Company, or in the event the Company decides to develop a drug beyond the
preclinical phase. The nature and the extent to which such regulation may apply
to the Company's customers will vary depending on the nature of any such
pharmaceutical products. Virtually all pharmaceutical products developed by the
Company's customers will require regulatory approval by governmental agencies
prior to commercialization. In particular, human pharmaceutical products are
subject to rigorous preclinical and clinical testing and other approval
procedures by the FDA and by foreign regulatory authorities. Various federal
and, in some cases, state statutes and regulations also govern or influence the
manufacturing, safety, labeling, storage, record keeping and marketing of such
pharmaceutical products. The process of obtaining these approvals and the
subsequent compliance with appropriate federal and foreign statutes and
regulations are time consuming and require the expenditure of substantial
resources.
 
     Generally, in order to gain FDA approval, a company first must conduct
preclinical studies in the laboratory and in animal models to gain preliminary
information on a compound's efficacy and to identify any safety problems. The
results of these studies are submitted as a part of an IND that the FDA must
review before human clinical trials of an investigational drug can start. In
order to commercialize any products, the Company or its customer will be
required to sponsor and file an IND and will be responsible for initiating and
overseeing the clinical studies to demonstrate the safety and efficacy that are
necessary to obtain FDA approval of any such products. Clinical trials are
normally done in three phases and generally take two to five years, but may take
longer, to complete. After completion of clinical trials of a new product, FDA
and foreign regulatory authority marketing approval must be obtained. If the
product is classified as a new drug, the Company or its customer will be
required to file an NDA and receive approval before commercial marketing of the
drug. The testing and approval processes require substantial time and effort and
there can be no assurance that any approval will be granted on a timely basis,
if at all. NDAs submitted to the FDA can take several years to obtain approval.
Even if FDA regulatory clearances are obtained, a marketed product is subject to
continual review, and later discovery of previously unknown problems or failure
to comply with the applicable regulatory requirements may result in restrictions
on the marketing of a product or withdrawal of the product from the market as
well as possible civil or criminal sanctions. For marketing outside the United
States, the Company will also be subject to foreign regulatory requirements
governing human clinical trials and marketing approval for pharmaceutical
products. The requirements governing the conduct of clinical trials, product
licensing, pricing and reimbursement vary widely from country to country.
 
     Fertilizers, pesticides and other agrichemicals are heavily regulated in
the United States. The EPA regulates such products under the Federal
Insecticide, Fungicide and Rodenticide Act ("FIFRA"). Agrichemicals are also
regulated by various state agencies. Some states, such as California, have their
own extensive registration requirements. To develop and commercialize a
pesticide product, detailed and complex procedures must be followed and Federal
approvals obtained under FIFRA. Small scale field testing usually can be
conducted prior to product registration to evaluate product efficacy. To conduct
large scale tests, a company must obtain an Experimental Use Permit which
generally requires satisfactory completion of certain toxicology and
environmental studies. Synthetic chemical pesticides require extensive
toxicology and environmental testing to substantiate product safety prior to
obtaining a product registration. Commercial sale of agrichemicals requires a
product registration for each pest and crop for which the product is used.
 
     The research and development processes of the Company involve the
controlled use of hazardous materials. The Company is subject to federal state
and local laws and regulations governing the use, manufacture, storage, handling
and disposal of such materials and certain waste products. Although the Company
believes that its activities currently comply with the standards prescribed by
such laws and regulations, the risk of accidental contamination or injury from
these materials cannot be eliminated. In the event of such an accident, the
Company could be held liable for any damages that result and any liability could
exceed the resources of the Company. In addition, there can be no assurance that
the
 
                                       32
<PAGE>   34
 
Company will not be required to incur significant costs to comply with
environmental laws and regulations in the future.
 
EMPLOYEES
 
     As of February 28, 1997, ArQule employed 66 people of whom 29 have Ph.D.
degrees. Of these, 45 were engaged in operations, 12 were engaged in research
and development and 9 were engaged in marketing and general administration. None
of ArQule's employees are covered by collective bargaining agreements. ArQule
believes its employee relations are good.
 
FACILITIES
 
     ArQule's research facilities include approximately 51,389 square feet of
laboratory and office space in Medford, Massachusetts pursuant to three lease
agreements. These leases extend through July 30, 2001, at which time the Company
has an option to renew the leases for an additional five year period.
 
     ArQule believes its current facilities are adequate for its current
operations. The Company believes that suitable additional space will be
available to it, when needed, on commercially reasonable terms.
 
LEGAL PROCEEDINGS
 
     In October 1996, two individuals asserted that they are entitled to
compensation from certain of the Company's stockholders and/or the Company equal
to approximately five percent of the equity interests in the Company for
services in connection with the initial financing of the Partnership in 1993. No
litigation has been commenced and settlement discussions are in progress.
However, no assurance can be given that such individuals will not commence
litigation relating to such claims. The Company intends to vigorously defend any
claim brought by such individuals and believes that it has meritorious defenses
to such claims. No assurances can be given regarding the outcome of any such
litigation.
 
     Except as stated above, ArQule is not a party to any other legal
proceedings.
 
                                       33
<PAGE>   35
 
                                   MANAGEMENT
 
EXECUTIVE OFFICERS, KEY EMPLOYEES AND DIRECTORS
 
     The following table sets forth certain information regarding the executive
officers, key employees and directors of the Company as of February 28, 1997:
 
<TABLE>
<CAPTION>
                NAME                   AGE                          POSITION
- -------------------------------------  ---   ------------------------------------------------------
<S>                                    <C>   <C>
Eric B. Gordon.......................  49    President, Chief Executive Officer and Director
Joseph C. Hogan, Jr., Ph.D...........  55    Chairman of the Board, Senior Vice President of
                                             Research and Development, Chief Scientific Officer
David L. Coffen, Ph.D................  58    Vice President of Chemistry
James R. Fitzgerald, Jr..............  52    Vice President, Chief Financial Officer and Treasurer
John M. Sorvillo, Ph.D...............  42    Vice President of Business Development
Steven L. Gallion, Ph.D..............  39    Director, Computational Chemistry
Adrian de Jonge, Ph.D.(1)............  41    Director
Stephen M. Dow(2)....................  41    Director
Allan R. Ferguson(1)(2)..............  54    Director
</TABLE>
 
- ------------------------------
(1) Member of the Audit Committee.
 
(2) Member of the Compensation Committee.
 
     Eric B. Gordon has been the President and Chief Executive Officer of the
Company since January 1996. From 1987 until he joined the Company, Mr. Gordon
served in various capacities in the United States and Europe with Pasteur
Merieux Connaught--U.S., a pharmaceutical company, most recently as Vice
President and Chief Financial Officer. In addition, since 1993 he held the
additional position of Chief Executive Officer of Virogenetics Corporation, a
partially owned joint venture company and since 1994 Vice President and
Treasurer of Pasteur Merieux. Mr. Gordon received his A.M.P. from the Wharton
School of Business of the University of Pennsylvania and his B.S. in Accounting
and Finance from Syracuse University.
 
     Joseph C. Hogan, Jr., Ph.D. is a founder of the Company and has served as
the Chief Scientific Officer and Senior Vice President of Research and
Development since its inception. Dr. Hogan has served as the Chairman of the
Board since January 1996. From 1990 until he founded the Company, Dr. Hogan was
the founder and president of Applied Modular Chemistries, Inc., a chemistry
company. Dr. Hogan received his M.S. and B.S. in Chemistry from Boston College
and his Ph.D. from Boston College and the Max Planck Institut fuer
Kohlenforschung, Muelheim/Ruhr, Germany.
 
     David L. Coffen, Ph.D. has been the Vice President of Chemistry since July
1995. From 1971 until he joined the Company, Dr. Coffen was employed by
Hoffman-LaRoche Inc., a pharmaceutical company, in a variety of positions, most
recently as Vice President of Molecular Sciences. Dr. Coffen received his Ph.D.
in Synthetic Organic Chemistry from the Massachusetts Institute of Technology
and his B.S. in Chemistry from the University of Toronto.
 
     James R. Fitzgerald, Jr. joined the Company in July 1996 as the Vice
President, Chief Financial Officer and Treasurer. From 1988 until he joined the
Company, Mr. Fitzgerald was the Chief Financial Officer of Hoyts Cinemas
Corporation, an owner and operator of cinemas. Mr. Fitzgerald received his
M.B.A. and his B.A. in Economics from Northeastern University.
 
     John M. Sorvillo, Ph.D. joined the Company in December 1995 as Vice
President of Business Development. Prior to joining the Company, Dr. Sorvillo
had provided consulting services to the Company since August 1995. From 1985
until he joined the Company, Dr. Sorvillo was employed by Oncogene Science,
Inc., a biotechnology company, in a variety of positions, most recently as Vice
President and General Manager. Dr. Sorvillo attended the Massachusetts Institute
of Technology
 
                                       34
<PAGE>   36
 
Program for Senior Executives. He received his Ph.D. in Immunology from the New
York University Medical Center and his B.A. in Biology from the City University
of New York, Hunter College.
 
     Steven L. Gallion, Ph.D. joined the Company in 1994 as Research Fellow in
Computational Chemistry. In 1995, he became the Company's Director of
Computational Chemistry. Prior to joining the Company, he was employed by Marion
Merrell Dow, Inc., a pharmaceutical company, as Senior Associate Scientist of
Theoretical Chemistry from 1993 to 1994 and Associate Scientist of Theoretical
Chemistry from 1992 to 1993. From 1989 to 1992, he was Director of Product
Development of Amber Systems, Inc., a molecular modeling software company. He
received his Ph.D. in Physical Chemistry from the University of Georgia and his
B.S. in Chemistry from Southhampton College of Long Island University.
 
     Adrian de Jonge, Ph.D. has been a director of the Company since November
1995. Dr. de Jonge is the Vice President of Research of Solvay's Pharmaceuticals
Division and has held such position since 1994. From 1987 through 1993, Dr. de
Jonge was employed by Solvay in a variety of positions, most recently as Sector
Manager of Drug Discovery.
 
     Stephen M. Dow has been a director of the Company since its inception.
Since 1983, he has been a general partner of Sevin Rosen Funds, a venture
capital investment firm. Mr. Dow serves as a director of Citrix Systems, Inc.,
ViroPharma, Inc. and several privately held companies.
 
     Allan R. Ferguson has been a director of the Company since its inception.
He has been a general partner of Atlas Venture since 1993 and managing partner
of Aspen Ventures since 1991, both venture capital firms. From 1986 through
1991, Mr. Ferguson was the President of 3i Ventures, a venture capital firm.
Prior to his venture capital experience, Mr. Ferguson held senior level
positions in operations at Johnson & Johnson and Damon Biotech. Mr. Ferguson
serves as a director of AutoImmune Inc. and several privately held companies.
 
     The Company's Restated Certificate provides for a classified board of
directors consisting of three classes, with each class being as nearly equal in
number as possible. The term of one class expires and their successors are
elected for a term of three years at each annual meeting of the Company's
stockholders. The Company has designated two class I directors (Messrs. Dow and
Gordon), two class II directors (Mr. Ferguson and Dr. Hogan) and one class III
director (Dr. de Jonge). These class I, class II and class III directors will
serve until the annual meetings of stockholders to be held in 1997, 1998 and
1999, respectively, and until their respective successors are duly elected and
qualified, or until their earlier resignation or removal. The Restated
Certificate provides that directors may be removed only for cause by a majority
of stockholders. See "Description of Capital Stock--Anti-Takeover Measures."
There are no family relationships among any of the directors or executive
officers.
 
BOARD COMMITTEES
 
     The Company has standing Audit and Compensation Committees of the Board of
Directors. The Audit Committee consists of Mr. Ferguson and Dr. de Jonge. The
primary function of the Audit Committee is to assist the Board of Directors in
the discharge of its duties and responsibilities by providing the Board with an
independent review of the financial health of the Company and of the reliability
of the Company's financial controls and financial reporting systems. The Audit
Committee reviews the general scope of the Company's annual audit, the fee
charged by the Company's independent accountants and other matters relating to
internal control systems.
 
     The Compensation Committee of the Board of Directors determines the
compensation to be paid to all executive officers of the Company, including the
Chief Executive Officer. The Compensation Committee's duties include the
administration of the Company's Amended and Restated 1994 Equity Incentive Plan
(the "Equity Plan") and the 1996 Employee Stock Purchase Plan. The Compensation
Committee is currently composed of Messrs. Dow and Ferguson.
 
                                       35
<PAGE>   37
 
SCIENTIFIC ADVISORY BOARD
 
     The Company's Scientific Advisory Board consists of individuals with
demonstrated expertise in various fields who advise the Company concerning
long-term scientific planning, research and development. Members also evaluate
the Company's research program, recommend personnel to the Company and advise
the Company on technology matters. The Scientific Advisory Board has met
collectively and in smaller groups, and its members have also been available
individually to advise the Company on specific scientific and technical issues.
Scientific Advisory Board members are compensated on a time and expenses basis
and have received shares of Common Stock of the Company. In the future,
Scientific Advisory Board members also receive options to purchase shares of
Common Stock of the Company. The Company has entered into consulting agreements
with a number of the Scientific Advisory Board members.
 
     No member of the Scientific Advisory Board is employed by the Company, and
members may have other commitments to or consulting or advisory contracts with
their employers or other entities that may conflict or compete with their
obligations to the Company. Accordingly, such persons are expected to devote
only a small portion of their time to the Company. The members of the Company's
Scientific Advisory Board are:
 
     Amin Arnaout, M.D. is Associate Professor of Medicine at Harvard Medical
School and the Director of the Inflammation and Leukocyte Biology Program at
Massachusetts General Hospital where he is also an Associate Physician. He is an
internationally recognized figure in the field of leukocyte adhesion. He is a
graduate of the American University of Beirut School of Medicine and did his
postgraduate work in internal medicine and nephrology at The Johns Hopkins
University Medical Center, Children's Hospital and the Brigham and Women's
Hospital.
 
     William D. Carlson, M.D., Ph.D. is the Director of Cardiovascular Research
for Harvard Community Health Plan, Associate Physician at Brigham and Women's
Hospital and Assistant Professor of Medicine at Harvard University Medical
School. He is widely known for his work in drug development and structural
biology including the renin-angiotensin and osteogenic growth factor systems. He
received his Ph.D. in Molecular Biophysics and Biochemistry from Yale University
and his M.D. from Yale Medical School.
 
     George L. Kenyon, Ph.D. is the Dean of the School of Pharmacy and Professor
of Chemistry and Pharmaceutical Chemistry at the University of California, San
Francisco. He is widely known for his work in the mechanisms of enzymatic
action, and synthetic and mechanistic chemistry and the development of
structure-based approaches to the rational design of enzymatic inhibitions. He
received his Ph.D. in Organic Chemistry from Harvard University.
 
     Irwin D. Kuntz, Ph.D. is the Acting Director of the Molecular Design
Institute, Chairman of the Graduate Group in Biophysics, and Professor in the
Department of Pharmaceutical Chemistry at the University of California, San
Francisco. He is widely known for his pioneering work in computational
chemistry. He received his Ph.D. in Physical Chemistry from the University of
California, Berkley.
 
     Gregory Petsko, Ph.D. is the Lucille P. Markey Professor of Biochemistry
and Chemistry, and Director of the Rosenteil Basic Medical Sciences Research
Center at Brandeis University. He is widely known for his work in the
development of protein crystallography and its application to exploring
fundamental aspects of protein folding. He received his Ph.D. in Molecular
Biology from Oxford University.
 
     Dagmar Ringe, Ph.D. is the Lucille P. Markey Associate Professor and Chair
of the Graduate Program in Biophysics at Brandeis University. She is
internationally recognized for her contributions to the use of x-ray
crystallography to explore fundamental aspects of drug binding behavior. She
received her Ph.D. in Organic Chemistry from Boston University.
 
                                       36
<PAGE>   38
 
     William R. Roush, Ph.D. is a Distinguished Professor of Chemistry at
Indiana University. He is widely known for his basic studies and applications
for a wide variety of synthetic chemical reactions. He received his Ph.D. in
Chemistry from Harvard University.
 
     K. Barry Sharpless, Ph.D. is the William M. Keck Professor of Chemistry at
The Scripps Research Institute. He is widely known for his pioneering work in
asymmetric chemical synthesis. He received his Ph.D. in Organic Chemistry from
Stanford University.
 
     Harry H. Wasserman, Ph.D. is the Eugene Higgins Professor Emeritus of
Chemistry. He is widely known for his work in the development of new methods in
synthetic organic chemistry. He received his Ph.D. in Organic Chemistry from
Harvard University.
 
1996 DIRECTOR STOCK OPTION PLAN
 
     All of the directors who are not employees of the Company (the "Eligible
Directors") are currently eligible to participate in the Company's 1996 Director
Stock Option Plan (the "Director Plan"). At the time the Director Plan was
adopted and upon the election of a director who was not an Eligible Director at
the time of adoption, such director or directors were or will be, as applicable,
automatically granted an option to purchase 7,500 shares of Common Stock (the
"Initial Options"). The Initial Options become exercisable with respect to 2,500
shares on the date of the Company's next annual meeting of stockholders
following the date of grant and on the date of each annual meeting of
stockholders thereafter. In addition, options under the Director Plan are
automatically granted once a year, at the annual meeting of stockholders of the
Company, to Eligible Directors elected or reelected at the meeting. Each such
Eligible Director receives an option to purchase 3,500 shares of Common Stock
(the "Annual Options") for each year of the term of office to which the director
is elected (normally, 10,500 shares for election to a three-year term of
office). The Annual Options become exercisable with respect to 3,500 shares on
the date on which the Annual Option was granted and on the date of each annual
meeting of stockholders thereafter, so long as the optionee is then an Eligible
Director of the Company. The Initial Options and Annual Options have a term of
ten years, and an exercise price payable in cash or shares of Common Stock. The
Director Plan was adopted by the Board of Directors in August 1996 and,
therefore, Initial Options for 7,500 shares were issued to each of Mr. Dow, Mr.
Ferguson and Dr. de Jonge. The exercise price for the Initial Options granted on
the date of the adoption of the Plan was $11.00, the fair market value on such
date as determined by the Board of Directors. The exercise price for the Initial
Options and the Annual Options will equal the last sale price for the Common
Stock on the business day immediately preceding the date of grant, as reported
on the Nasdaq National Market. As of March 4, 1997, options to purchase a total
of 22,500 shares of Common Stock were outstanding under the Director Plan, and
102,500 shares of Common Stock were reserved for future option grants under the
Director Plan.
 
                                       37
<PAGE>   39
 
EXECUTIVE COMPENSATION
 
     The following table sets forth certain information with respect to the
annual and long-term compensation paid or accrued by the Company for services
rendered to the Company in all capacities for the fiscal years ended December
31, 1995 and 1996 by its Chief Executive Officer, its Chief Financial Officer
and another executive officer of the Company whose total salary exceeded
$100,000 (collectively, the "Named Executive Officers").
 
                           SUMMARY COMPENSATION TABLE
 
<TABLE>
<CAPTION>
                                                                                         LONG-TERM
                                                                                        COMPENSATION
                                                          ANNUAL COMPENSATION              AWARDS
                                                   ----------------------------------   ------------
                                                                         OTHER ANNUAL    SECURITIES
                                                                         COMPENSATION    UNDERLYING       ALL OTHER
        NAME AND PRINCIPAL POSITION         YEAR   SALARY($)  BONUS($)       ($)         OPTIONS(#)    COMPENSATION($)
- ------------------------------------------- -----  --------   --------   ------------   ------------   ---------------
<S>                                         <C>    <C>        <C>        <C>            <C>            <C>
Eric B. Gordon(1)..........................  1996  $219,808      --        $126,195(2)     464,920              --
  President and Chief Executive Officer      1995        --      --              --             --              --

Joseph C. Hogan, Jr., Ph.D. ...............  1996   171,308      --             435(3)          --          30,000(4)
  Chairman of the Board, Senior Vice         1995   150,000      --              --             --              --
  President of Research and Development
  and Chief Scientific Officer

James R. Fitzgerald, Jr.(5)................  1996    51,346      --              --         50,000              --
  Vice President, Chief Financial            1995        --      --              --             --              --
  Officer and Treasurer
</TABLE>
 
- ------------------------------
(1) Mr. Gordon commenced employment with the Company in January 1996. Terms of
    his employment are described under "--Executive Employment Agreements."
 
(2) Consists of reimbursement of relocation expenses incurred by Mr. Gordon
    during the fiscal year ended December 31, 1996 in connection with his
    becoming an employee of the Company.
 
(3) Consists of Medicare taxes owed by Dr. Hogan that were paid by the Company.
 
(4) Consists of amount of indebtedness owed by Dr. Hogan to the Company that was
    forgiven by the Company during the fiscal year ended December 31, 1996.
 
(5) Mr. Fitzgerald commenced employment with the Company in July 1996. Terms of
    his employment are described under "--Executive Employment Agreements."
 
     The following table sets forth certain information regarding options
granted during the fiscal year ended December 31, 1996 by the Company to the
Named Executive Officers:
 
                       OPTION GRANTS IN LAST FISCAL YEAR
 
<TABLE>
<CAPTION>
                                                                                               POTENTIAL REALIZABLE
                                                      INDIVIDUAL GRANTS                          VALUE AT ASSUMED
                                   -------------------------------------------------------        ANNUAL RATES OF
                                   NUMBER OF       PERCENT OF                                       STOCK PRICE
                                   SECURITIES         TOTAL         EXERCISE                       APPRECIATION
                                   UNDERLYING    OPTIONS GRANTED       OR                       FOR OPTION TERM(1)
                                    OPTIONS      TO EMPLOYEES IN   BASE PRICE   EXPIRATION    -----------------------
              NAME                 GRANTED(#)      FISCAL YEAR     ($/SHARE)(2)    DATE        5%($)          10%($)
- ---------------------------------  ----------    ---------------   ----------   ----------    --------       --------
<S>                                <C>           <C>               <C>          <C>           <C>            <C>
Eric B. Gordon...................     77,486(3)         8.3%         $ 0.80       1/23/06     $ 38,984       $ 98,794
                                     387,434(4)        41.5            0.80       1/23/06      194,924        493,976
Joseph C. Hogan, Jr., Ph.D.......         --             --              --            --           --             --
James R. Fitzgerald, Jr..........     50,000(4)         5.4            6.00       7/09/06      188,668        478,123
</TABLE>
 
- ------------------------------
(1) The dollar amounts under these columns are the result of calculations at the
    5% and 10% rates set by the Securities and Exchange Commission and,
    therefore, are not intended to forecast possible future appreciation, if
    any, in the price of the underlying Common Stock. No gain to the optionees
    is possible without an increase in price of the underlying Common Stock,
    which will benefit all stockholders proportionately.
 
                                       38
<PAGE>   40
 
(2) The exercise price of these options is equal to the fair market value of the
    Company's Common Stock on the date of grant, as determined by the Company's
    Board of Directors.
 
   
(3) Options granted under the Company's Amended and Restated 1994 Equity
    Incentive Plan. The shares subject to this option have fully vested.
    
 
   
(4) Options granted under the Company's Amended and Restated 1994 Equity
    Incentive Plan. These options become exercisable as to 25% of the shares on
    each of the first four anniversaries of January 23, 1996 for Mr. Gordon and
    of July 9, 1996 for Mr. Fitzgerald.
    
 
     The following table sets forth certain information concerning exercisable
and unexercisable stock options held by the Named Executive Officers as of
December 31, 1996:
 
              AGGREGATED OPTION EXERCISES IN LAST FISCAL YEAR AND
                        FISCAL YEAR-END OPTION VALUES(1)
 
   
<TABLE>
<CAPTION>
                                    NUMBER OF SECURITIES UNDERLYING            VALUE OF UNEXERCISED
                                          UNEXERCISED OPTIONS                  IN-THE-MONEY OPTIONS
                                          AT FISCAL YEAR-END                   AT FISCAL YEAR-END(2)
                                    -------------------------------       -------------------------------
               NAME                 EXERCISABLE       UNEXERCISABLE       EXERCISABLE       UNEXERCISABLE
- ----------------------------------  -----------       -------------       -----------       -------------
<S>                                 <C>               <C>                 <C>               <C>
Eric B. Gordon....................     77,486            387,434          $ 1,158,416        $ 5,792,138
Joseph C. Hogan, Jr., Ph.D........         --                 --                   --                 --
James R. Fitzgerald, Jr...........         --             50,000                   --            487,500
</TABLE>
    
 
- ------------------------
(1) No options were exercised during the fiscal year ended December 31, 1996 by
    the Named Executive Officers.
 
(2) Based on the difference between closing price of the underlying shares of
    Common Stock on December 31, 1996 as reported by the Nasdaq National Market
    ($15.75) and the option exercise
     price.
 
STOCK PLANS
 
   
     Amended and Restated 1994 Equity Incentive Plan.  The Company's Equity Plan
authorizes the grant of incentive stock options within the meaning of Section
422 of the Internal Revenue Code of 1986, as amended (the "Code"), and
nonqualified stock options for the purchase of an aggregate of 3,200,000 shares
(subject to adjustment for stock splits and similar capital changes) of Common
Stock to employees of the Company and, in the case of non-qualified stock
options, to consultants of the Company or any Affiliate (as defined in the
Equity Plan) capable of contributing to the Company's performance. The Board of
Directors has appointed the Compensation Committee to administer the Equity
Plan. As of December 31, 1996, 1,372,420 shares of Common Stock were subject to
outstanding options granted under the Equity Plan, leaving 1,306,033 shares
available for issuance upon future grants under the Equity Plan.
    
 
     1996 Employee Stock Purchase Plan.  The Company has also adopted an
employee stock purchase plan (the "Purchase Plan") under which employees may
purchase shares of Common Stock at a discount from fair market value. There are
120,000 shares of Common Stock reserved for issuance under the Purchase Plan.
The Purchase Plan is intended to qualify as an employee stock purchase plan
within the meaning of Section 423 of the Code. Rights to purchase Common Stock
under the Purchase Plan are granted at the discretion of the Compensation
Committee, which determines the frequency and duration of individual offerings
under the Plan and the dates when stock may be purchased. Eligible employees
participate voluntarily and may withdraw from any offering at any time before
stock is purchased. Participation terminates automatically upon termination of
employment. The purchase price per share of Common Stock in an offering is 85%
of the lesser of its fair market value at the beginning of the offering period
or on the applicable exercise date and may be paid through payroll deductions,
periodic lump sum payments or a combination of both. The Purchase Plan
terminates on
 
                                       39
<PAGE>   41
 
August 14, 2006. As of December 31, 1996, no shares of Common Stock had been
issued under the Purchase Plan.
 
401(K) PLAN
 
     The Company has a 401(k) savings and retirement plan (the "401(k) Plan")
which covers substantially all employees of the Company. The 401(k) Plan allows
participants to agree to certain salary deferrals which the Company allocates to
the participant's plan account. These amounts may not exceed statutorily
mandated annual limits set forth in the Code. The Company currently does not
match employee contributions to the 401(k) Plan but may do so in the future.
 
EXECUTIVE EMPLOYMENT AGREEMENTS
 
     The Company has entered into employment agreements with Mr. Gordon and Mr.
Fitzgerald. The Company agreed to employ Mr. Gordon as President and Chief
Executive Officer of the Company, effective January 2, 1996, at an annual salary
of $225,000. In connection with this agreement, Mr. Gordon was granted options
to acquire 387,434 shares of Common Stock at $0.80 per share, which vest over
four years, and options to acquire 77,486 shares of Common Stock at $0.80 per
share, which vested upon the achievement of certain milestones. Mr. Gordon has
also been provided with moving and relocation allowances. The agreement provides
for continued employment until termination by either party. If Mr. Gordon is
terminated by the Company without cause, the agreement provides that he will be
entitled to receive his base salary, plus any benefits to which he is entitled
and any options granted to Mr. Gordon which would have otherwise vested, for a
period of up to six months following such termination of employment. In July
1996, the Company also made a loan in the principal amount of $250,000 to Mr.
Gordon. The principal amount of the loan will be repaid in three equal annual
installments beginning in October 1997 and bears interest at the lowest
applicable federal rate of interest as published by the Internal Revenue
Service. See "Certain Transactions."
 
     Under Mr. Fitzgerald's Agreement, the Company has agreed to employ Mr.
Fitzgerald as Vice President and Chief Financial Officer of the Company,
effective July 9, 1996, at an annual salary of $150,000. In connection with the
agreement, Mr. Fitzgerald was granted options, which vest over four years, to
acquire 50,000 shares of Common Stock at $6.00 per share. The agreement provides
for continued employment until termination by either party. If Mr. Fitzgerald is
terminated without cause by the Company during the first year of the agreement,
he will be entitled to receive his base salary, plus any benefits to which he is
entitled and any options granted to Mr. Fitzgerald which would have otherwise
vested, for a period of up to six months.
 
                              CERTAIN TRANSACTIONS
 
     In December 1993, in exchange for the transfer to the Company of
substantially all of the assets and liabilities of ArQule Partners, L.P., a
Delaware limited partnership (the "Partnership"), the Company issued 1,500
shares of its Common Stock to the Partnership, at which time the Partnership
became the sole stockholder of the Company. In November 1994, the Company
declared a stock dividend of 3,332.33 shares of its Common Stock on each
outstanding share of Common Stock held by the Partnership as of October 17,
1994. After certain transfers of Common Stock by the Partnership, in November
1994 all the remaining outstanding shares of Common Stock then held by the
Partnership were surrendered to the Company in exchange for shares of Series A
Convertible Preferred Stock, $0.01 par value per share (the "Series A Preferred
Stock"), which were converted into 4,295,500 shares of Common Stock concurrently
with the closing of the Company's initial public offering.
 
     In November 1993, the Company made a loan in the amount of $63,000 to
Joseph C. Hogan, Jr., Ph.D., Chairman and Chief Scientific Officer of the
Company, which loan is represented by a promissory note due and payable in
November 1996, and was extended to November 1997. The promissory note bears
interest at the lowest applicable federal rate of interest as published by the
Internal Revenue Service. The entire principal and accrued interest is currently
outstanding.
 
                                       40
<PAGE>   42
 
     During the period from August 1994 through February 1995, Sevin Rosen Fund
IV L.P., Atlas Venture Fund, II, L.P. and Atlas Venture Europe Fund B.V. made a
series of bridge loans to the Company in the aggregate amount of $2,400,000 (the
"Bridge Loans") in exchange for promissory notes and warrants to purchase an
aggregate of 155,300, 58,229 and 26,471 shares of Common Stock, respectively,
exercisable at $0.25 per share until the earlier of the effective date of an
initial public offering or various dates through December 31, 1999 (the "Bridge
Warrants"). In November 1995, the principal amount of the promissory notes
representing the Bridge Loans was converted into shares of Series A Preferred
Stock, which were converted into an aggregate of 960,000 shares of Common Stock
concurrently with the closing of the Company's initial public offering. The
Bridge Warrants were exercised on a cashless basis for 234,992 shares of Common
Stock prior to the closing of the Company's initial public offering.
 
     In November 1995, the Company issued 1,800,000 shares of Series B
Convertible Preferred Stock, $.01 par value per share (the "Series B Preferred
Stock"), to Physica B.V. for cash at a purchase price of $3.89 per share. Such
shares of Series B Preferred Stock were converted into 900,000 shares of Common
Stock concurrently with the closing of the Company's initial public offering.
Physica B.V. is an affiliate of Solvay Duphar B.V., with whom the Company has a
major corporate collaboration. See "Business--ArQule's Product Discovery
Programs."
 
     Also in November 1995, the Company made a loan in the amount of $120,000 to
Dr. Hogan. The loan is represented by a promissory note and is secured by shares
of Common Stock issuable to Dr. Hogan upon dissolution of the Partnership. The
loan bears interest at the lowest applicable federal rate of interest as
published by the Internal Revenue Service. The original principal amount of the
loan is forgiven at a rate of 25% per year on each anniversary date of the note
as long as Dr. Hogan is employed by the Company. In November 1996, $30,000 of
the principal amount of the loan was forgiven by the Company. The remaining
principal and accrued interest is currently outstanding.
 
     In April 1996, all accrued interest outstanding on the Bridge Loans through
November 1995 in the aggregate amount of $142,000 was converted into shares of
Series A Preferred Stock, which were converted into an aggregate of 56,714
shares of Common Stock concurrently with the closing of the Company's initial
public offering. In addition, in consideration of the waiver by Physica B.V. of
its anti-dilution rights under the Company's Amended and Restated Certificate of
Incorporation and its right of first refusal with respect to such shares of
Series A Preferred Stock, the Company issued to Physica B.V. additional shares
of Series B Preferred Stock, which were converted into 7,734 shares of Common
Stock concurrently with the closing of the Company's initial public offering.
 
     In July 1996, the Company made a loan in the amount of $250,000 to Eric B.
Gordon, the President, Chief Executive Officer and a director of the Company,
which loan is secured by shares of Common Stock issuable to Mr. Gordon upon the
exercise of stock options. The loan is represented by a promissory note which is
due and payable in three equal annual installments beginning in October 1997 and
which bears interest at the lowest applicable federal rate of interest as
published by the Internal Revenue Service. The entire principal and accrued
interest is currently outstanding.
 
     In February 1997, the Partnership was dissolved and all shares of Common
Stock of the Company held by the Partnership were distributed to its partners.
Sevin Rosen Fund IV L.P., Atlas Venture Fund II, L.P. and Atlas Venture Europe
B.V., which are direct significant stockholders of the Company (collectively,
the "Venture Fund Investors"), Legomer Investors, Inc. ("LII"), Legomer
Technologies, Inc. ("LTI"), The Hogan Family Limited Partnership, of which Dr.
Hogan is a general partner, and certain other persons were partners of the
Partnership and received shares of Common Stock of the Company upon such
Partnership distribution. The Venture Fund Investors hold all of the outstanding
shares of LII. Dr. Hogan holds 50% of the outstanding stock of LTI. See
"Principal and Selling Stockholders."
 
                                       41
<PAGE>   43
 
                       PRINCIPAL AND SELLING STOCKHOLDERS
 
   
     The following table and footnotes set forth certain information regarding
the beneficial ownership of the Company's Common Stock as of March 4, 1997, by
(i) persons known by the Company to be beneficial owners of more than 5% of the
Common Stock, (ii) the Named Executive Officers, (iii) each director of the
Company, (iv) all other Selling Stockholders and (iv) all current executive
officers and directors as a group. Unless otherwise indicated, each of the
Company's stockholders has an address in care of the Company's principal
executive offices.
    
 
   
<TABLE>
<CAPTION>
                                                                                        SHARES
                                          SHARES BENEFICIALLY                        BENEFICIALLY
                                            OWNED PRIOR TO                            OWNED AFTER
                                              OFFERING(1)                             OFFERING(1)
                                          -------------------       SHARES        -------------------
             5% STOCKHOLDERS               NUMBER     PERCENT       OFFERED        NUMBER     PERCENT
- ----------------------------------------- ---------   -------       -------       ---------   -------
<S>                                       <C>         <C>           <C>           <C>         <C>
Atlas Venture(2)......................... 1,366,250    13.86%         --          1,366,250    11.89%
  222 Berkeley Street
  Boston, MA 02116
Physica B.V.(3)..........................   907,734     9.20%         --            907,734     7.90%
  C.J. van Houtenlaan, 36
  1381 CD Weiss
  The Netherlands
Sevin Rosen Fund IV L.P.(4).............. 2,368,832    24.03%         --          2,368,832    20.62%
  13455 Noel Road, Suite 1670
  Dallas, TX 75240
EXECUTIVE OFFICERS AND DIRECTORS
 
Adrian de Jonge, Ph.D.(5)................   907,734     9.20%         --            907,734     7.90%
Stephen M. Dow(6)........................ 2,368,832    24.03%         --          2,368,832    20.62%
Allan R. Ferguson(7)..................... 1,366,250    13.85%         --          1,366,250    11.89%
Eric B. Gordon(8)........................   175,844     1.75%         --            175,844     1.51%
Joseph C. Hogan, Jr., Ph.D.(9)........... 1,237,412    12.54%       180,000(11)   1,057,412     9.19%
James R. Fitzgerald, Jr.(10).............     4,750     *             --              4,750     *
All current executive officers and
  directors as a group (6 persons)(12)... 6,060,822    60.38%       180,000       5,880,822    51.11%
OTHER SELLING STOCKHOLDERS
 
Robert Dishman(13).......................   542,567     5.50%       135,000(14)     407,567     3.55%
Gregory Petsko, Ph.D.....................    50,000     *            25,000          25,000     *
Dagmar Ringe, Ph.D.......................    50,000     *            25,000          25,000     *
William R. Roush, Ph.D...................    50,000     *             2,500          47,500     *
</TABLE>
    
 
- ------------------------------
   
   * Indicates less than 1%.
    
 
   
 (1) Assumes no exercise of the over-allotment option. The number of shares of
     Common Stock deemed outstanding after this offering assumes 1,632,500
     shares of Common Stock are sold by the Company in this offering. Selling
     Stockholders holding 315,000 of the shares proposed to be sold in this
     offering may elect not to sell all or any such shares. In such event, the
     Company has agreed to increase the number of shares it is selling in this
     offering by the number of shares not sold by such Selling Stockholders. See
     footnotes (10) and (13). The persons and entities named in the table have
     sole voting and investment power with respect to the shares beneficially
     owned by them, except as noted below. Share numbers include shares of
     Common Stock issuable pursuant to the outstanding options that may be
     exercised within 60 days after March 4, 1997.
    
 
   
 (2) Consists of (i) 938,766 shares owned by Atlas Venture Fund II, L.P. and
     (ii) 427,484 shares owned by Atlas Venture Europe Fund B. V. (collectively,
     "Atlas Venture"). The voting and investment discretion over the shares
     owned by Atlas Venture Fund II, L.P. is exercised by the general partners
     of Atlas Venture Associates II, L.P., its general partner. The general
     partners of Atlas Venture Associates II, L.P. are Allan R. Ferguson, Barry
     J. Fidelman, Jean-Francois Formela and
    
 
                                       42
<PAGE>   44
 
   
     Christopher J. Spray. Because of this relationship, Allan R. Ferguson, a
     director of the Company, shares voting and investment discretion over such
     shares. Atlas Venture Europe Fund B.V. is a corporation wholly-owned by
     Atlas InvesteringsGroep N.V. ("AIG"). The voting and investment discretion
     over the shares owned by Atlas Venture Europe Fund B.V. is exercised by the
     managing directors of AIG, Michiel A. de Haan and Evert H. Smid. Three
     officers of AIG, Gerard H. Montanus, Hans Bosman and Jaap van Hellemond,
     share voting and investment discretion with these two managing directors
     over the shares held by Atlas Venture Europe Fund B.V. The numbers of
     shares of Common Stock attributed to Atlas Venture assumes a pro rata
     distribution of the shares currently owned by LII to its stockholders
     (which include Atlas Venture). See "Certain Transactions."
    
 
   
 (3) The voting and investment discretion over the shares owned by Physica B.V.
     is exercised by the sole director of Physica B.V., J.W.F. van Ingen.
    
 
   
 (4) Consists of 2,368,832 shares owned by Sevin Rosen Fund IV L.P. ("Sevin
     Rosen"). The voting and investment discretion over the shares owned by
     Sevin Rosen is exercised by the general partner of SRB Associates IV L.P.,
     its general partner. The general partners of SRB Associates L.P. are
     Stephen M. Dow, Jon W. Bayless, Charles H. Phipps, Dennis J. Gorman, and
     John V. Jaggers. Because of this relationship, Stephen M. Dow, a director
     of the Company, shares voting and investment discretion over such shares.
     The number of shares of Common Stock attributed to Sevin Rosen assumes a
     pro rata distribution of the shares currently owned by LII to its
     stockholders (which include Sevin Rosen). See "Certain Transactions."
    
 
   
 (5) Consists of 907,734 shares of Common Stock owned by Physica B.V. Dr. de
     Jonge is Vice President of Research of Solvay's Pharmaceuticals Division,
     an affiliate of Physica B.V. Dr. de Jonge disclaims beneficial ownership of
     the shares held by Physica B.V.
    
 
   
 (6) Consists of 2,368,832 shares owned by or attributed to Sevin Rosen. Mr. Dow
     is a general partner of SRB Associates IV L.P. which is the general partner
     of Sevin Rosen. Mr. Dow disclaims beneficial ownership of the shares owned
     by or attributed to Sevin Rosen, except to the extent of his pecuniary
     interest therein. See footnote (4).
    
 
   
 (7) Consists of 1,366,250 shares owned by Atlas Venture. Mr. Ferguson is a
     general partner of Atlas Venture Associates II, L.P., which is the general
     partner of Atlas Venture Fund II, L.P. Mr. Ferguson disclaims beneficial
     ownership of the shares owned by Atlas Venture, except to the extent of his
     pecuniary interest therein. See footnote (2).
    
 
   
 (8) Consists of (i) 174,344 shares of Common Stock subject to options that are
     presently exercisable and (ii) 1,500 shares of Common Stock held in trust
     for the benefit of his children.
    
 
   
 (9) Consists of (i) 1,107,514 shares held by The Hogan Family Limited
     Partnership, of which Dr. Hogan and his wife are the general partners, (ii)
     117,398 shares that represent Dr. Hogan's pro rata ownership interest in
     the shares currently owned by LTI and (iii) 12,500 shares of Common Stock
     subject to options that are presently exercisable.
    
 
   
(10) Includes 3,750 shares of Common Stock subject to options that are presently
     exercisable.
    
 
   
(11) All of the 180,000 shares are being offered by The Hogan Family Limited
     Partnership. The Hogan Family Limited Partnership may elect not to sell all
     or any of these shares. See footnote (1).
    
 
   
(12) Includes 174,344 shares of Common Stock subject to options that are
     presently exercisable. See footnotes (5), (6), (7), (8), (9) and (10).
    
 
   
(13) Includes (i) 192,210 shares held by Peptide Limited Partnership and (ii)
     117,398 shares that represent Mr. Dishman's pro rata ownership interest in
     the shares currently owned by LTI. Mr. Dishman is the President of Peptide,
     Inc., the general partner of Peptide Limited Partnership.
    
 
   
(14) Consists of (i) 25,000 shares being offered by Peptide Limited Partnership
     and (ii) 110,000 shares being offered by Mr. Dishman. Peptide Limited
     Partnership and Mr. Dishman may elect not to sell all or any of such
     shares. See footnote (1).
    
 
                                       43
<PAGE>   45
 
                          DESCRIPTION OF CAPITAL STOCK
 
     The authorized capital stock of the Company consists of 30,000,000 shares
of Common Stock, $0.01 par value per share, and 1,000,000 shares of Preferred
Stock, $0.01 par value per share. As of the date of this Prospectus, the Company
had 58 shareholders of record. Upon the closing of this offering, the Company
will have 11,490,237 shares of Common Stock outstanding.
 
     The following summary of certain provisions of the Common Stock and
Preferred Stock does not purport to be complete and is subject to, and qualified
in its entirety by, the provisions of the Company's Restated Certificate, which
is included as an exhibit to the Registration Statement, and by the provisions
of applicable law.
 
COMMON STOCK
 
     Holders of Common Stock are entitled to one vote per share on matters to be
voted upon by the stockholders. There are no cumulative voting rights. Holders
of Common Stock are entitled to receive dividends when, as and if declared by
the Board of Directors out of funds legally available therefor. Upon the
liquidation, dissolution or winding up of the Company, holders of Common Stock
share ratably in the assets of the Company available for distribution to its
stockholders, subject to the preferential rights of any then outstanding shares
of Preferred Stock. The Common Stock outstanding upon the effective date of the
Registration Statement, and the shares offered by the Company hereby, upon
issuance and sale, will be fully paid and nonassessable.
 
PREFERRED STOCK
 
     The Company's Board of Directors has the authority to issue up to 1,000,000
shares of Preferred Stock in one or more series and to fix the relative rights,
preferences, privileges, qualifications, limitations and restrictions thereof,
including dividend rights, dividend rates, conversion rights, voting rights,
terms of redemption, redemption prices, liquidation preferences and the number
of shares constituting any series or the designation of such series, without
further vote or action by the stockholders. The Board of Directors could,
without the approval of the stockholders, issue Preferred Stock having voting or
conversion rights that could adversely affect the voting power of the holders of
Common Stock and the issuance of Preferred Stock could be used, under certain
circumstances, to render more difficult or discourage a hostile takeover of the
Company. No shares of Preferred Stock are currently outstanding and the Company
has no present plans to issue any shares of Preferred Stock.
 
ANTI-TAKEOVER MEASURES
 
     In addition to the Board of Directors' ability to issue shares of Preferred
Stock, the Restated Certificate and the By-laws of the Company contain several
other provisions that are commonly considered to discourage unsolicited takeover
bids. The Restated Certificate includes provisions classifying the Board of
Directors into three classes with staggered three-year terms and prohibiting
stockholder action by written consent. Under the Restated Certificate and
By-laws, the Board of Directors may enlarge the size of the Board and fill any
vacancies on the Board. The By-laws provide that nominations for directors may
not be made by stockholders at any annual or special meeting unless the
stockholder intending to make a nomination notifies the Company of its intention
a specified period in advance and furnishes certain information. The By-laws
also provide that special meetings of the Company's stockholders may be called
only by the President or the Board of Directors and require advance notice of
business to be brought by a stockholder before the annual meeting.
 
     In February 1988, a law regulating corporate takeovers (the "Anti-Takeover
Law") took effect in Delaware. In certain circumstances, the Anti-Takeover Law
prevents certain Delaware corporations, including those whose securities are
listed on the Nasdaq National Market, from engaging in a "business combination"
(which includes a merger or sale of more than 10% of the corporation's assets)
with an "interested stockholder" (a stockholder who owns 15% or more of the
corporation's
 
                                       44
<PAGE>   46
 
   
outstanding voting stock) for three years following the date on which such
stockholder became an "interested stockholder" subject to certain exceptions,
unless the transaction is approved by the Board of Directors and the holders of
at least 66 2/3% of the outstanding voting stock of the corporation (excluding
shares held by the interested stockholder). The statutory ban does not apply if,
upon consummation of the transaction in which any person becomes an interested
stockholder, the interested stockholder owns at least 85% of the outstanding
voting stock of the corporation (excluding shares held by persons who are both
directors and officers or by certain employee stock plans). A Delaware
corporation subject to the Anti-Takeover Law may "opt out" of the Anti-Takeover
Law with an express provision either in its certificate of incorporation or
by-laws resulting from a stockholders' amendment approved by at least a majority
of the outstanding voting shares; such an amendment is effective following
expiration of twelve months from adoption. The Company is a Delaware corporation
that is subject to the Anti-Takeover Law and has not "opted out" of its
provisions.
    
 
     The foregoing provisions of Delaware law and the Restated Certificate and
By-laws could have the effect of discouraging others from attempting a hostile
takeover of the Company and, as a consequence, they may also inhibit temporary
fluctuations in the market price of the Common Stock that might result from
actual or rumored hostile takeover attempts. Such provisions may also have the
effect of preventing changes in the management of the Company. It is possible
that such provisions could make it more difficult to accomplish transactions
which stockholders may otherwise deem to be in their best interests.
 
TRANSFER AGENT
 
     The transfer agent and registrar for the Common Stock is American Stock
Transfer & Trust Company.
 
                        SHARES ELIGIBLE FOR FUTURE SALE
 
   
     Upon completion of this offering, the Company will have 11,490,862 shares
of Common Stock outstanding, assuming no exercise of the Underwriters'
over-allotment option or of any other outstanding options. Of these shares,
approximately 3,018,647 shares and the 2,000,000 shares sold in this offering
will be freely tradable, without restriction or further registration under the
Securities Act, except for shares purchased or held by "affiliates" of the
Company as that term is defined in Rule 144 under the Securities Act.
    
 
   
     The remaining 6,472,215 outstanding shares of Common Stock are owned by
existing stockholders and are currently deemed "Restricted Shares" under Rule
144. These may not be resold, except pursuant to an effective registration
statement or an applicable exemption from registration. Of these remaining
shares, approximately 5,564,481 shares of Common Stock are currently eligible
for sale under Rules 144 and 701. The Securities and Exchange Commission has
recently amended Ruled 144 to reduce the required holding periods for Restricted
Shares. As a result of such amendment, which becomes effective in April 29,
1997, an additional 907,734 shares will be eligible for sale under Rules 144 and
701.
    
 
   
     In connection with the Company's initial public offering, which was
completed in October 1996, stockholders of the Company holding an aggregate of
6,824,515 shares entered into an 180-day lock-up agreement that will expire on
April 14, 1997. In connection with this offering, stockholders of the Company,
holding in the aggregate 6,195,295 shares of Common Stock, have agreed to enter
into the 90-day lock-up agreements described below.
    
 
   
     In general, under the recently amended Rule 144, which becomes effective on
April 29, 1997, a person (or persons whose shares are aggregated), including an
affiliate, who has beneficially owned Restricted Shares for at least one year
from the later of the date such Restricted Shares were acquired from the Company
and (if applicable) the date they were acquired from an affiliate, is entitled
to sell, within any three-month period, a number of shares that does not exceed
the greater of 1% of the then outstanding shares of Common Stock or the average
weekly trading volume in the public market
    
 
                                       45
<PAGE>   47
 
during the four calendar weeks preceding such sale. Sales under Rule 144 are
also subject to certain requirements as to the manner and notice of sale and the
availability of public information concerning the Company. All sales of shares
of the Company's Common Stock, including Restricted Shares, held by affiliates
of the Company must be sold under Rule 144, subject to the foregoing volume
limitations and other restrictions.
 
   
     The Company's directors and executive officers and certain of its
stockholders have agreed that they will not, without the prior consent of the
representatives of the Underwriters, offer to sell, sell, contract to sell,
grant any option to sell or otherwise dispose of or require the Company to file
with the Commission a registration statement under the Act to register any
shares of Common Stock or securities convertible or exchangeable for shares of
Common Stock or warrants or other rights to acquire shares of Common Stock
during the 90-day period following the effective date of the Registration
Statement.
    
 
   
     The Company has filed a registration statement under the Securities Act
registering 120,000 shares of Common Stock issuable under the Stock Purchase
Plan. The Company plans to file registration statements under the Securities Act
to register 3,200,000 and 125,000 shares of Common Stock issuable under the
Equity Plan and the Director Plan, respectively, on or about April 14, 1997.
Upon registration, such shares will be eligible for immediate resale upon
exercise, subject, in the case of affiliates, to the volume, manner of sale and
notice requirements of Rule 144.
    
 
   
     No prediction can be made as to the effect, if any, that market sales of
additional shares or the availability of such additional shares for sale will
have an impact on the market price of the Common Stock. Nevertheless, sales of
substantial amounts of Common Stock in the public market may have an adverse
impact on the market price of the Common Stock. See "Risk Factors--Shares
Eligible for Future Sale and Potential Adverse Effect on Market Price."
    
 
REGISTRATION RIGHTS
 
     The holders of the 6,219,948 shares of Common Stock (the "Registrable
Shares") are entitled to certain rights with respect to registration under the
Securities Act of the Registrable Shares. If the Company proposes to register
any of its securities under the Securities Act, either for its own account or
for the account of other security holders, such holders are entitled to notice
of such registration and are entitled to include such Registrable Shares in the
registration. The rights are subject to certain conditions and limitations,
among them, the right of the underwriters of a registered offering to limit the
number of shares included in such registration. Holders of Registrable Shares
benefiting from these rights may also require the Company to file at its expense
a registration statement under the Securities Act with respect to their shares
of Common Stock and, subject to certain conditions and limitations, the Company
is required to use its best efforts to effect such registration. Furthermore,
such holders may, subject to certain conditions and limitations, require the
Company to file additional registration statements on Form S-3 with respect to
such Registrable Shares. In connection with this offering, such holders waived
their right to have shares of Common Stock registered under the Securities Act
as part of this offering.
 
                                       46
<PAGE>   48
 
                                  UNDERWRITING
 
     Subject to the terms and conditions of the Underwriting Agreement, the
Underwriters named below, through their Representatives, Hambrecht & Quist LLC,
Oppenheimer & Co., Inc. and Vector Securities International, Inc., have
severally agreed to purchase from the Company and the Selling Stockholders the
following respective numbers of shares of Common Stock:
 
<TABLE>
<CAPTION>
                                                                           NUMBER OF
                                   UNDERWRITERS                             SHARES
         ----------------------------------------------------------------  ---------
         <S>                                                               <C>
         Hambrecht & Quist LLC...........................................
         Oppenheimer & Co., Inc. ........................................
         Vector Securities International, Inc. ..........................
                                                                           ---------
              Total......................................................  2,000,000
                                                                           =========
</TABLE>
 
     The Underwriting Agreement provides that the obligations of the
Underwriters are subject to certain conditions precedent, including the absence
of any material adverse change in the Company's business and the receipt of
certain certificates, opinions and letters from the Company, its counsel and its
independent auditors and the Selling Stockholders and their counsel. The nature
of the Underwriters' obligation is such that they are committed to purchase all
shares of Common Stock offered hereby if any such shares are purchased.
 
     The Underwriters propose to offer the shares of Common Stock directly to
the public at the public offering price set forth on the cover page of this
Prospectus and to certain dealers at such price less a concession not in excess
of $     per share. The Underwriters may allow, and such dealers may reallow, a
concession not in excess of $     per share to certain other dealers. The
Representatives of the Underwriters have advised the Company and the Selling
Stockholders that the Underwriters do not intend to confirm any shares to any
accounts over which they exercise discretionary authority. After the public
offering of the shares, the offering price and other selling terms may be
changed by the Representatives of the Underwriters.
 
     The Company has granted to the Underwriters an option, exercisable no later
than 30 days after the date of this Prospectus, to purchase up to 300,000
additional shares of Common Stock at the public offering price, less the
underwriting discount, set forth on the cover page of this Prospectus. To the
extent that the Underwriters exercise this option, each of the Underwriters will
have a firm commitment to purchase approximately the same proportion thereof
which the number of shares of Common Stock to be purchased by it shown in the
above table bears to the total number of shares of Common Stock offered hereby.
The Company will be obligated, pursuant to the option, to sell shares to the
Underwriters to the extent the option is exercised. The Underwriters may
exercise such option only to cover over-allotments made in connection with the
sale of shares of Common Stock offered hereby.
 
     The offering of the shares is made for delivery when, as and if accepted by
the Underwriters and subject to prior sale and to withdrawal, cancellation or
modification of the offering without notice. The Underwriters reserve the right
to reject an order for the purchase of shares in whole or in part.
 
     The Company and the Selling Stockholders have agreed to indemnify the
Underwriters against certain liabilities, including liabilities under the
Securities Act, and to contribute to payments the Underwriters may be required
to make in respect thereof.
 
     Certain existing stockholders of the Company, including the Company's
executive officers and directors, who will own in the aggregate 6,195,295 shares
of Common Stock after the offering, have agreed that they will not, without the
prior written consent of Hambrecht & Quist LLC, offer, sell or otherwise dispose
of any shares of Common Stock, options or warrants to acquire shares of Common
Stock or securities exchangeable for or convertible into shares of Common Stock
owned by them
 
                                       47
<PAGE>   49
 
during the 90-day period following the date of this Prospectus. The Company has
agreed that, subject to limited exceptions, it will not, without the prior
written consent of Hambrecht & Quist LLC, offer, sell or otherwise dispose of
any shares of Common Stock, options or warrants to acquire shares of Common
Stock or securities exchangeable for or convertible into shares of Common Stock
during the 90-day period following the date of this Prospectus.
 
     Certain persons participating in this offering may over-allot or effect
transactions which stabilize, maintain or otherwise affect the market price of
the Company's Common Stock at levels above those which might otherwise prevail
in the open market, including by entering stabilizing bids or effecting
syndicate covering transactions. A stabilizing bid means the placing of any bid
or effecting of any purchase, for the purpose of pegging, fixing or maintaining
the price of the Company's Common Stock. A syndicate covering transaction means
the placing of any bid on behalf of the underwriting syndicate or the effecting
of any purchase to reduce a short position created in connection with the
offering. Such transactions may be effected on the Nasdaq National Market, in
the over-the-counter market, or otherwise. Such stabilizing, if commenced, may
be discontinued at any time.
 
                                 LEGAL MATTERS
 
     The validity of the shares of Common Stock offered hereby will be passed
upon for the Company by Palmer & Dodge LLP, Boston, Massachusetts. Michael
Lytton, a partner of Palmer & Dodge LLP, is the Secretary of the Company and
Lynnette C. Fallon, also a partner of Palmer & Dodge LLP, is the Assistant
Secretary of the Company. Certain legal matters in connection with this offering
will be passed upon for the Underwriters by Testa, Hurwitz & Thibeault, LLP,
Boston, Massachusetts.
 
                                    EXPERTS
 
     The financial statements as of December 31, 1995 and 1996 and for each of
the three years in the period ended December 31, 1996 included in this
Prospectus have been so included in reliance on the report of Price Waterhouse
LLP, independent accountants, given on the authority of said firm as experts in
auditing and accounting.
 
                             AVAILABLE INFORMATION
 
     The Company is subject to the informational reporting requirements of the
Exchange Act and in accordance therewith files reports, proxy statements and
other information with the Securities and Exchange Commission (the
"Commission"). Such reports, proxy statements and other information can be
inspected and copied at the public reference facilities maintained by the
Commission at Room 1024, 450 Fifth Street, N.W., Judiciary Plaza, Washington,
D.C. 20549, and at the Commission's following Regional Offices: Chicago Regional
Office, Citicorp Center, 500 West Madison Street, Suite 1400, Chicago, Illinois
60661-2511; and New York Regional Office, 7 World Trade Center, Suite 1300, New
York, New York 10048. Copies of such material can be obtained at prescribed
rates from the Public Reference Section of the Commission at 450 Fifth Street,
N.W., Judiciary Plaza, Washington, D.C. 20549. Such reports and other
information can also be reviewed through the Commission's Web site
(http://www.sec.gov).
 
     Additional information regarding the Company and the shares offered hereby
is contained in the Registration Statement on Form S-1 and the exhibits thereto
filed with the Commission under the Securities Act. This Prospectus does not
contain all of the information contained in such Registration Statement and the
exhibits and schedules thereto. Statements contained in this Prospectus
regarding the contents of any document or contract are qualified in their
entirety by reference to the copy of such contract or document filed as an
exhibit to the Registration Statement. For further information pertaining to the
Company and the shares, reference is made to the Registration Statement and the
exhibits thereto, which may be inspected without charge at, and copies thereof
may be obtained at prescribed rates from, the office of the Commission of 450
Fifth Street, N.W., Judiciary Plaza, Washington, D.C. 20549.
 
                                       48
<PAGE>   50
 
                                  ARQULE, INC.
 
                         INDEX TO FINANCIAL STATEMENTS
 
<TABLE>
<CAPTION>
                                                                                        PAGE
                                                                                        ----
<S>                                                                                     <C>
Report of Independent Accountants.....................................................  F-2
Balance Sheet at December 31, 1995 and 1996...........................................  F-3
Statement of Operations for the three years ended December 31, 1996...................  F-4
Statement of Redeemable Preferred Stock and Stockholders' Equity (Deficit) for the
  three years ended December 31, 1996.................................................  F-5
Statement of Cash Flows for the three years ended December 31, 1996...................  F-6
Notes to Financial Statements.........................................................  F-7
</TABLE>
 
                                       F-1
<PAGE>   51
 
                       REPORT OF INDEPENDENT ACCOUNTANTS
 
To the Board of Directors and
Stockholders of ArQule, Inc.
 
In our opinion, the accompanying balance sheet and the related statements of
operations, of redeemable preferred stock and stockholders' equity (deficit) and
of cash flows present fairly, in all material respects, the financial position
of ArQule, Inc. at December 31, 1996 and 1995, and the results of its operations
and its cash flows for each of the three years in the period ended December 31,
1996, in conformity with generally accepted accounting principles. These
financial statements are the responsibility of the Company's management; our
responsibility is to express an opinion on these financial statements based on
our audits. We conducted our audits of these statements in accordance with
generally accepted auditing standards which require that we plan and perform the
audit to obtain reasonable assurance about whether the financial statements are
free of material misstatement. An audit includes examining, on a test basis,
evidence supporting the amounts and disclosures in the financial statements,
assessing the accounting principles used and significant estimates made by
management, and evaluating the overall financial statement presentation. We
believe that our audits provide a reasonable basis for the opinion expressed
above.
 
/s/ Price Waterhouse LLP

PRICE WATERHOUSE LLP
 
Boston, Massachusetts
February 25, 1997
 
                                       F-2
<PAGE>   52
 
                                  ARQULE, INC.
 
                                 BALANCE SHEET
 
<TABLE>
<CAPTION>
                                                                           DECEMBER 31,
                                                                   ----------------------------
                                                                      1995             1996
                                                                   -----------     ------------
<S>                                                                <C>             <C>
ASSETS
Current assets:
  Cash and cash equivalents......................................  $ 2,989,000     $ 36,586,000
  Marketable securities..........................................    4,802,000          500,000
  Accounts receivable............................................           --          250,000
  Prepaid expenses and other current assets......................      123,000          338,000
  Notes receivable from related parties..........................       93,000          176,000
                                                                   -----------     ------------
          Total current assets...................................    8,007,000       37,850,000
Property and equipment, net......................................    1,994,000        5,293,000
Other assets.....................................................       99,000          139,000
Notes receivable from related parties............................       90,000          227,000
                                                                   -----------     ------------
                                                                   $10,190,000     $ 43,509,000
                                                                   ===========     ============
 
LIABILITIES, REDEEMABLE PREFERRED STOCK
  AND STOCKHOLDERS' EQUITY (DEFICIT)
Current liabilities:
  Current portion of capital lease obligations...................  $   514,000     $  1,138,000
  Accounts payable and accrued expenses..........................      769,000        1,109,000
  Deferred revenue...............................................    1,650,000        4,163,000
                                                                   -----------     ------------
          Total current liabilities..............................    2,933,000        6,410,000
                                                                   -----------     ------------
Capital lease obligations........................................      911,000        1,728,000
                                                                   -----------     ------------
Deferred revenue.................................................      458,000          750,000
                                                                   -----------     ------------
 
Series B mandatorily redeemable convertible preferred stock......    6,888,000          --
                                                                   -----------     ------------
 
Stockholders' equity (deficit):
  Preferred stock, $0.01 par value; 1,000,000 shares authorized;
     no shares issued or outstanding at December 31, 1996              --               --
  Series A convertible preferred stock; 10,511,000 shares issued
     and outstanding at December 31, 1995........................    2,486,000          --
  Common stock, $0.01 par value; 30,000,000 shares authorized;
     522,797 and 9,851,487 shares issued and outstanding at
     December 31, 1995 and 1996, respectively....................        5,000           99,000
  Additional paid-in capital.....................................    4,435,000       46,102,000
  Accumulated deficit............................................   (7,926,000)     (10,934,000)
                                                                   -----------     ------------
                                                                    (1,000,000)      35,267,000
  Deferred compensation..........................................      --              (646,000)
                                                                   -----------     ------------
          Total stockholders' equity (deficit)...................   (1,000,000)      34,621,000
                                                                   -----------     ------------
Commitments and contingency (Note 13)............................      --               --
                                                                   -----------     ------------
                                                                   $10,190,000     $ 43,509,000
                                                                   ===========     ============
</TABLE>
 
   The accompanying notes are an integral part of these financial statements.
 
                                       F-3
<PAGE>   53
 
                                  ARQULE, INC.
 
                            STATEMENT OF OPERATIONS
 
<TABLE>
<CAPTION>
                                                                YEAR ENDED DECEMBER 31,
                                                      -------------------------------------------
                                                         1994            1995            1996
                                                      -----------     -----------     -----------
<S>                                                   <C>             <C>             <C>
Revenue:
  Compound development revenue......................  $    85,000     $ 1,830,000     $ 4,255,000
  Compound development revenue--related party.......           --         500,000       3,000,000
  License option fees...............................           --       1,000,000              --
                                                      -----------     -----------     -----------
                                                           85,000       3,330,000       7,255,000
                                                      -----------     -----------     -----------
Costs and expenses:
  Cost of revenue...................................           --       1,367,000       2,683,000
  Cost of revenue--related party....................           --         277,000       2,056,000
  Research and development..........................    2,806,000       2,095,000       3,076,000
  Marketing, general and administrative.............    1,346,000       1,557,000       2,850,000
                                                      -----------     -----------     -----------
                                                        4,152,000       5,296,000      10,665,000
                                                      -----------     -----------     -----------
     Loss from operations...........................   (4,067,000)     (1,966,000)     (3,410,000)
Interest income.....................................           --         133,000         607,000
Interest expense....................................     (139,000)       (419,000)       (190,000)
                                                      -----------     -----------     -----------
     Net loss.......................................  $(4,206,000)    $(2,252,000)    $(2,993,000)
                                                      ===========     ===========     ===========
Unaudited proforma net loss per share assuming
  conversion of convertible preferred stock (Note
  9):
     Net loss per share.............................                  $     (0.33)    $     (0.39)
                                                                      ===========     ===========
     Shares used in computing net loss per share....                    6,853,000       7,705,000
                                                                      ===========     ===========
</TABLE>
 
   The accompanying notes are an integral part of these financial statements.
 
                                       F-4
<PAGE>   54
 
                                  ARQULE, INC.
 
   STATEMENT OF REDEEMABLE PREFERRED STOCK AND STOCKHOLDERS' EQUITY (DEFICIT)
<TABLE>
<CAPTION>
                                                                                  STOCKHOLDERS' EQUITY (DEFICIT)
                                                                        --------------------------------------------------
                                               SERIES B MANDATORILY
                                              REDEEMABLE CONVERTIBLE      SERIES A CONVERTIBLE
                                                 PREFERRED STOCK             PREFERRED STOCK             COMMON STOCK
                                             ------------------------   -------------------------   ----------------------
                                               SHARES       AMOUNT        SHARES        AMOUNT        SHARES     PAR VALUE
                                             ----------   -----------   -----------   -----------   ----------   ---------
<S>                                          <C>          <C>           <C>           <C>           <C>          <C>
BALANCE AT DECEMBER 31, 1993................                                                             1,500   $  --
Capital contribution from ArQule Partners,
  L.P. (Note 1).............................
3,333.33 for 1 stock split effected in the
  form of a stock dividend..................                                                         4,998,500      50,000
Cancellation of common stock................                                                          (140,528)     (1,000)
Issuance of Series A convertible preferred
  stock in exchange for common stock........                              8,591,000   $    86,000   (4,295,500)    (43,000)
Cancellation of unvested portion of
  restricted stock upon employee
  termination...............................                                                            (9,375)     --
Issuance of common stock purchase warrants
  under bridge financing....................
Net loss....................................
                                                                        -----------   -----------   ----------   ---------
BALANCE AT DECEMBER 31, 1994................                              8,591,000        86,000      554,597       6,000
Employee restricted stock purchases.........                                                            68,200      --
Issuance of common stock purchase warrants
  under bridge financing....................
Cancellation of unvested portion of
  restricted stock upon employee
  termination...............................                                                          (100,000)     (1,000)
Conversion of bridge notes into Series A
  convertible preferred stock...............                              1,920,000     2,400,000
Issuance of Series B mandatorily redeemable
  convertible preferred stock, net of
  issuance costs of $115,000................  1,800,000   $ 6,885,000
Accretion of Series B mandatorily redeemable
  preferred stock to redemption value.......                    3,000
Net loss....................................
                                             ----------   -----------   -----------   -----------   ----------   ---------
BALANCE AT DECEMBER 31, 1995................  1,800,000     6,888,000    10,511,000     2,486,000      522,797       5,000
Conversion of interest on bridge notes to
  Series A convertible preferred stock......                                113,429       142,000
Issuance of Series B mandatorily redeemable
  preferred stock to maintain ownership
  percentage (Note 9).......................     15,468
Cancellation of unvested portion of
  restricted stock upon employee
  termination...............................                                                            (1,875)     --
Employee option exercise....................                                                               625      --
Accretion of Series B mandatorily redeemable
  preferred stock to redemption value.......                   15,000
Conversion of Series B mandatorily
  redeemable preferred stock to common
  stock..................................... (1,815,468)   (6,903,000)                                 907,734       9,000
Conversion of Series A convertible preferred
  stock to common stock.....................                            (10,624,429)   (2,628,000)   5,312,214      54,000
Exercise of warrants pursuant to a cashless
  exercise provision........................                                                           234,992       2,000
Issuance of common stock in connection with
  initial public offering, net of issuance
  costs of $2,979,000.......................                                                         2,875,000      29,000
Compensation related to the grant of common
  stock options.............................
Amortization of deferred compensation.......
Net loss....................................
                                             ----------   -----------   -----------   -----------   ----------   ---------
BALANCE AT DECEMBER 31, 1996................     --       $   --            --        $   --         9,851,487   $  99,000
                                             ==========   ===========   ===========   ===========   ==========   =========
 
<CAPTION>
 
                                              ADDITIONAL                                       TOTAL
                                                PAID-IN     ACCUMULATED      DEFERRED      STOCKHOLDERS'
                                                CAPITAL       DEFICIT      COMPENSATION   EQUITY (DEFICIT)
                                              -----------   ------------   ------------   ----------------
<S>                                          <<C>           <C>            <C>            <C>
BALANCE AT DECEMBER 31, 1993................  $ 2,236,000   $ (1,465,000)                   $    771,000
Capital contribution from ArQule Partners,
  L.P. (Note 1).............................    2,100,000                                      2,100,000
3,333.33 for 1 stock split effected in the
  form of a stock dividend..................      (50,000)                                      --
Cancellation of common stock................        1,000                                       --
Issuance of Series A convertible preferred
  stock in exchange for common stock........      (43,000)                                      --
Cancellation of unvested portion of
  restricted stock upon employee
  termination...............................                                                    --
Issuance of common stock purchase warrants
  under bridge financing....................      132,000                                        132,000
Net loss....................................                  (4,206,000)                     (4,206,000)
                                              -----------   ------------                    ------------
BALANCE AT DECEMBER 31, 1994................    4,376,000     (5,671,000)                     (1,203,000)
Employee restricted stock purchases.........        1,000                                          1,000
Issuance of common stock purchase warrants
  under bridge financing....................       57,000                                         57,000
Cancellation of unvested portion of
  restricted stock upon employee
  termination...............................        1,000                                       --
Conversion of bridge notes into Series A
  convertible preferred stock...............                                                   2,400,000
Issuance of Series B mandatorily redeemable
  convertible preferred stock, net of
  issuance costs of $115,000................
Accretion of Series B mandatorily redeemable
  preferred stock to redemption value.......                      (3,000)                         (3,000)
Net loss....................................                  (2,252,000)                     (2,252,000)
                                              -----------   ------------                    ------------
BALANCE AT DECEMBER 31, 1995................    4,435,000     (7,926,000)                     (1,000,000)
Conversion of interest on bridge notes to
  Series A convertible preferred stock......                                                     142,000
Issuance of Series B mandatorily redeemable
  preferred stock to maintain ownership
  percentage (Note 9).......................
Cancellation of unvested portion of
  restricted stock upon employee
  termination...............................                                                    --
Employee option exercise....................                                                    --
Accretion of Series B mandatorily redeemable
  preferred stock to redemption value.......                     (15,000)                        (15,000)
Conversion of Series B mandatorily
  redeemable preferred stock to common
  stock.....................................    6,894,000                                      6,903,000
Conversion of Series A convertible preferred
  stock to common stock.....................    2,574,000                                       --
Exercise of warrants pursuant to a cashless
  exercise provision........................       (2,000)                                      --
Issuance of common stock in connection with
  initial public offering, net of issuance
  costs of $2,979,000.......................   31,492,000                                     31,521,000
Compensation related to the grant of common
  stock options.............................      709,000                   $ (709,000)         --
Amortization of deferred compensation.......                                    63,000            63,000
Net loss....................................                  (2,993,000)                     (2,993,000)
                                              -----------   ------------    ----------      ------------
BALANCE AT DECEMBER 31, 1996................  $46,102,000   $(10,934,000)   $ (646,000)     $ 34,621,000
                                              ===========   ============    ==========      ============
</TABLE>
 
   The accompanying notes are an integral part of these financial statements.
 
                                       F-5
<PAGE>   55
 
                                  ARQULE, INC.
 
                            STATEMENT OF CASH FLOWS
 
Increase (Decrease) in Cash and Cash Equivalents
 
   
<TABLE>
<CAPTION>
                                                                          YEAR ENDED DECEMBER 31,
                                                                 -----------------------------------------
                                                                    1994           1995           1996
                                                                 -----------    -----------    -----------
<S>                                                              <C>            <C>            <C>
Cash flows from operating activities:
  Net loss.....................................................  $(4,206,000)   $(2,252,000)   $(2,993,000)
  Adjustments to reconcile net loss to net cash (used in)
     provided by operating activities:
       Depreciation and amortization...........................      189,000        506,000      1,171,000
       Amortization of debt discount...........................       25,000        164,000        --
       Amortization of deferred compensation...................      --             --              63,000
       Increase in accounts receivable.........................      --             --            (250,000)
       (Increase) decrease in prepaid expenses and other
          current assets.......................................       41,000        (94,000)      (215,000)
       (Increase) decrease in other assets.....................     (188,000)       203,000        (40,000)
       Increase in notes receivable from related parties.......      --            (120,000)      (220,000)
       Increase in accounts payable and accrued expenses.......      340,000        141,000        482,000
       Increase in deferred revenue............................      --           2,108,000      2,805,000
                                                                 -----------    -----------    -----------
          Net cash (used in) provided by operating
            activities.........................................   (3,799,000)       656,000        803,000
                                                                 -----------    -----------    -----------
Cash flows from investing activities:
  Purchases of marketable securities...........................      --          (9,052,000)       --
  Proceeds from sale or maturity of marketable securities......      --           4,250,000      4,302,000
  Additions to property and equipment..........................     (168,000)      (495,000)    (2,292,000)
                                                                 -----------    -----------    -----------
          Net cash (used in) provided by investing
            activities.........................................     (168,000)    (5,297,000)     2,010,000
                                                                 -----------    -----------    -----------
Cash flows from financing activities:
  Proceeds from bridge financing--related party................    1,700,000        700,000        --
  Principal payments of capital lease obligations..............     (110,000)      (381,000)      (737,000)
  Proceeds from issuance of mandatorily redeemable convertible
     preferred stock, net......................................      --           6,885,000        --
  Proceeds from issuance of common stock.......................      --               1,000     31,521,000
  Capital contribution from ArQule Partners, L.P. .............    2,100,000        --             --
  Proceeds from sale-leaseback transactions....................      107,000        --             --
                                                                 -----------    -----------    -----------
          Net cash provided by financing activities............    3,797,000      7,205,000     30,784,000
                                                                 -----------    -----------    -----------
Net (decrease) increase in cash and cash equivalents...........     (170,000)     2,564,000     33,597,000
Cash and cash equivalents, beginning of period.................      595,000        425,000      2,989,000
                                                                 -----------    -----------    -----------
Cash and cash equivalents, end of period.......................  $   425,000    $ 2,989,000    $36,586,000
                                                                 ===========    ===========    ===========
</TABLE>
    
 
SUPPLEMENTAL DISCLOSURE OF NON-CASH INVESTING AND FINANCING ACTIVITIES:
 
     Capital lease obligations of $935,000, $503,000 and $2,178,000, were
incurred in 1994, 1995 and 1996, respectively, when the Company entered into
leases for various machinery and equipment, furniture and fixtures, and
leasehold improvements.
 
     During 1995, the Company converted $2,400,000 of bridge loans into
1,920,000 shares of Series A convertible preferred stock (Note 8). In addition,
during 1996, the Company converted $142,000 of interest relating to the bridge
loans into 113,429 shares of Series A convertible preferred stock.
 
     During 1996, 12,439,897 shares of Series A and Series B preferred stock
were converted into 6,219,948 shares of common stock, in connection with the
Company's initial public offering of common stock (Note 9). In addition, 234,992
shares of common stock were issued in connection with the cashless exercise of
outstanding warrants.
 
SUPPLEMENTAL DISCLOSURE OF CASH FLOW INFORMATION:
 
     During 1994, 1995 and 1996, the Company paid approximately $98,000,
$254,000 and $190,000, respectively, for interest.
 
   The accompanying notes are an integral part of these financial statements.
 
                                       F-6
<PAGE>   56
 
                                  ARQULE, INC.
 
                         NOTES TO FINANCIAL STATEMENTS
 
1.  ORGANIZATION AND NATURE OF OPERATIONS
 
   
     ArQule, Inc. (the "Company") is engaged in the discovery, development and
production of novel chemical compounds for the pharmaceutical, biotechnology and
agrichemical industries. Its operations are focused on the integration of
combinatorial chemistry, structure-guided rational drug design and other
proprietary technologies which automate the process of chemical synthesis to
produce arrays of small organic chemical compounds used to generate and optimize
drug development candidates.
    
 
   
     In May 1993 and in connection with the formation of ArQule Partners L.P.
(the "Partnership"), Legomer Technologies, Inc. ("LTI"), formerly Molecular
Recognition Technologies, Inc., a company owned by the two founding limited
partners in the Partnership, contributed to the Partnership all rights and
interests in certain LTI patented technology (the "Technology") in exchange for
a 0.5% general partner ownership position. The Company was legally incorporated
on December 30, 1993 to carry on the operations of the Partnership. Immediately
following the incorporation of the Company, the Partnership transferred
substantially all of its assets, liabilities and patented technology (the
"Operating Assets"), having an aggregate net book value of $771,000, to the
Company in exchange for 1,500 shares of the Company's $0.01 par value common
stock, representing all of the Company's then outstanding common stock. Because
of the related party nature of these transactions, the Operating Assets and
Technology transfers have been accounted for as transfers of assets between
entities under common control. Accordingly, the accompanying financial
statements include the assets, liabilities and results of operations of the
Company at historical amounts as if the transfers occurred at the inception of
the Partnership.
    
 
     Amounts which reflect the funding of the Partnership's operations prior to
the conversion of certain shares of the Company's common stock into Series A
preferred stock (Note 9) are reflected as paid-in capital in the accompanying
balance sheet and as capital contributed by ArQule Partners L.P. in the
statements of changes in redeemable preferred stock and stockholders' equity
(deficit) and of cash flows. Such funding totaled $2,100,000 of cash for the
year ended December 31, 1994, and was comprised of aggregate investments in
general partnership interests of $20,000 and limited partnership interests of
$2,080,000.
 
2.  SUMMARY OF SIGNIFICANT ACCOUNTING POLICIES
 
     Significant accounting policies followed in the preparation of these
financial statements are as follows:
 
  Cash Equivalents and Marketable Securities
 
     The Company considers all highly liquid investments purchased with an
original maturity of three months or less to be cash equivalents. The Company
invests its available cash primarily in money market mutual funds and U.S.
government and other investment grade debt securities which have strong credit
ratings. These investments are subject to minimal credit and market risks. The
Company specifically identifies securities for purposes of determining gains and
losses on the sale of cash equivalents and short-term investments. At December
31, 1996 and 1995, the Company has classified its investments as
available-for-sale as defined in Statement of Financial Accounting Standards
("SFAS") No. 115.
 
  Fair Value of Financial Instruments
 
     At December 31, 1995 and 1996, the Company's financial instruments consist
of cash, cash equivalents, marketable securities, accounts receivable, notes
receivable from related party, accounts
 
                                       F-7
<PAGE>   57
 
                                  ARQULE, INC.
 
                  NOTES TO FINANCIAL STATEMENTS -- (CONTINUED)
 
payable and accrued expenses and mandatorily redeemable convertible preferred
stock. The carrying amount of these instruments approximate their fair values.
 
  Property and Equipment
 
     Property and equipment are recorded at cost and depreciated using the
straight-line method over their estimated useful lives. Assets under capital
leases and leasehold improvements are amortized over the shorter of their
estimated useful lives or the term of the respective leases by use of the
straight-line method. Maintenance and repair costs are expensed as incurred.
 
  Revenue Recognition
 
     Compound development revenue relates to revenue from significant
collaborative agreements (Note 3) and from licensing of compound arrays. Revenue
from collaborative agreements relates to the delivery of compounds and to
compound development work and is recognized using the percentage of completion
method. The application of this revenue recognition method is dependent on the
contractual arrangement of either compound delivery or development. Accordingly,
revenue is recognized on the proportional achievement of deliveries against a
compound delivery schedule or as development labor is expended against a total
research and development labor plan. Payments received under these arrangements
prior to the completion of the related work are recorded as deferred revenue.
Revenue from licensing of compound arrays with no additional obligations is
recognized upon delivery of the compound array. License option fees represent
payments made to the Company for a right to evaluate and negotiate the terms of
potential licensing arrangements and are recognized as revenue as the options
are granted, as the Company has no further obligations and as payments are
nonrefundable.
 
  Cost of Revenue
 
     Cost of revenue represents the actual costs incurred in connection with
performance pursuant to collaborative agreements and the costs incurred to
produce compound arrays. These costs consist primarily of payroll and
payroll-related costs, supplies and overhead expenses.
 
  Stock Compensation
 
     Options granted to employees and directors are accounted for in accordance
with Accounting Principles Board ("APB") No. 25, "Accounting for Stock Issued to
Employees". The Company has adopted the disclosure requirements of SFAS No. 123,
"Accounting for Stock Based Compensation." Options granted to nonemployees are
accounted for using the fair value method and are recognized as compensation
expense over their respective vesting periods.
 
  Unaudited Pro Forma Net Loss Per Share
 
     Pro forma net loss per share is determined by dividing the net loss by the
weighted average number of common stock and common stock equivalents outstanding
during the period, assuming the conversion of all convertible preferred stock
which occurred upon the closing of the Company's initial public offering as
described in Note 9.
 
     Common stock equivalents, although anti-dilutive, issued at prices below
the offering price per share during the twelve month period preceding the
initial filing of the Registration Statement have been included in the
calculation of unaudited pro forma net loss per share using the treasury stock
method and the initial public offering price of $12.00 per share as if
outstanding for all periods presented through June 30, 1996.
 
                                       F-8
<PAGE>   58
 
                                  ARQULE, INC.
 
                  NOTES TO FINANCIAL STATEMENTS -- (CONTINUED)
 
     Historical net loss per share has not been presented as the Series A
convertible preferred stock would have been omitted from the weighted average
shares outstanding as it is anti-dilutive and was issued more than twelve months
prior to the initial public offering.
 
  Use of Estimates
 
     The preparation of financial statements in conformity with generally
accepted accounting principles requires management to make estimates and
assumptions that affect the reported amounts of assets and liabilities and
disclosure of contingent assets and liabilities at the date of the financial
statements and the reported amounts of revenues and expenses during the
reporting period. Actual results could differ from these estimates.
 
  Reclassifications
 
     Certain reclassifications have been made to the 1994 and 1995 financial
statements to conform to the 1996 presentation. These reclassifications had no
effect on the net loss for 1994 and 1995.
 
3.  SIGNIFICANT AGREEMENTS
 
     The Company has entered into a number of license, research and development
agreements (the "Agreements") with certain corporate collaborators. One
Agreement was entered into with Solvay Duphar B.V. ("Solvay"), a related party
(Note 9). Revenue related to the Solvay Agreement is included in compound
development revenue--related party. Under the terms of these Agreements, the
Company will provide a certain number of compounds per year and has granted the
right to screen these compounds against targets to identify biological activity
(an "Active Compound") and will provide research and development services. The
collaborators have the right to enter into an exclusive, worldwide license (the
"License") for any Active Compound identified. The initial terms of these
Agreements generally range from two to five years during which period the
collaborators make payments to the Company for technology access, delivery of
compounds and for its research and development services. In exchange for a
License, the Company will receive milestone payments during product development
and royalty payments based on the sales of the product. Solvay also has a right
which expires on December 31, 1997 to license certain of the Company's
technologies on a nonexclusive basis for internal use only. Deferred revenue
represents payments made to the Company in advance for technology access,
delivery of compounds and research and development pursuant to these Agreements.
At December 31, 1995, $100,000 of the deferred revenue amount is from a related
party.
 
     Under the terms of material transfer agreements with biotechnology
companies (the "biotech collaborators"), the Company has granted the biotech
collaborator the nonexclusive, royalty-free license to test certain compound
arrays supplied by the Company. Upon identification of an active compound, the
Company will negotiate a joint drug development program with the biotech
collaborator to develop the compound, provided the Company has not previously
licensed the compound. Under the collaboration agreements with these joint drug
development programs, the Company and the biotech collaborator will each bear
the costs and expenses of their respective activities. Proceeds received on
sales or a third party license of the jointly developed compound will first
reimburse development costs incurred by each party on a pro rata basis. After
all such reimbursements have been made, the remaining proceeds will be split
evenly between the parties.
 
                                       F-9
<PAGE>   59
 
                                  ARQULE, INC.
 
                  NOTES TO FINANCIAL STATEMENTS -- (CONTINUED)
 
4.  CASH EQUIVALENTS AND MARKETABLE SECURITIES
 
     The fair market value of cash equivalents was $2,688,000 and $36,126,000 at
December 31, 1995 and 1996, respectively. At December 31, 1995 and 1996, all of
the Company's cash equivalents were held in money market funds.
 
     The following is a summary of the fair market value of available-for-sale
marketable securities held by the Company at December 31, 1995 and 1996:
 
<TABLE>
<CAPTION>
                                                                          DECEMBER 31,
                                                                     -----------------------
                                                       MATURITY         1995          1996
                                                      -----------    ----------     --------
    <S>                                               <C>            <C>            <C>
    U.S. Government obligations.....................   1-5 years     $3,786,000     $500,000
    U.S. Government obligations.....................  5-10 years      1,016,000           --
                                                                     ----------     --------
                                                                     $4,802,000     $500,000
                                                                     ==========     ========
</TABLE>
 
     At December 31, 1995 and 1996, marketable securities are carried at fair
market value, which approximates amortized cost. All of the Company's marketable
securities are classified as current at December 31, 1996 as these funds are
highly liquid and are available to meet working capital needs and to fund
current operations. Gross unrealized gains and losses at December 31, 1995 and
1996 and realized gains and losses on sales of securities for the years ended
December 31, 1995 and 1996 were not significant.
 
5.  PROPERTY AND EQUIPMENT
 
     Property and equipment consist of the following:
 
<TABLE>
<CAPTION>
                                                       ESTIMATED
                                                         USEFUL            DECEMBER 31,
                                                          LIFE       -------------------------
                                                        (YEARS)         1995           1996
                                                       ----------    ----------     ----------
    <S>                                                <C>           <C>            <C>
    Machinery and equipment..........................     3-7        $1,839,000     $4,350,000
    Leasehold improvements...........................      5            656,000      2,628,000
    Furniture and fixtures...........................      7             72,000        178,000
    Construction-in-progress.........................      --           124,000          5,000
                                                                     ----------     ----------
                                                                      2,691,000      7,161,000
    Less--Accumulated depreciation and amortization..............       697,000      1,868,000
                                                                     ----------     ----------
                                                                     $1,994,000     $5,293,000
                                                                     ==========     ==========
</TABLE>
 
     Assets held under capital leases at December 31, 1995 consisted of
$1,438,000 of machinery and equipment and $485,000 of leasehold improvements. At
December 31, 1996, assets held under capital leases consisted of $3,162,000 of
machinery and equipment, $832,000 of leasehold improvements and $107,000 of
furniture and fixtures. Accumulated amortization of these assets totaled
$554,000 and $1,305,000 at December 31, 1995 and 1996, respectively. For the
years ended December 31, 1994, 1995 and 1996, amortization expense related to
assets held under capital lease obligations was $163,000, $300,000 and $751,000,
respectively.
 
                                      F-10
<PAGE>   60
 
                                  ARQULE, INC.
 
                  NOTES TO FINANCIAL STATEMENTS -- (CONTINUED)
 
6.  NOTES RECEIVABLE FROM RELATED PARTIES
 
     Notes receivable from related parties consist of the following:
 
<TABLE>
<CAPTION>
                                                                         DECEMBER 31,
                                                                     ---------------------
                                                                       1995         1996
                                                                     --------     --------
    <S>                                                              <C>          <C>
    Note receivable due from an officer of the Company, due in full
      on November 3, 1997..........................................  $ 63,000     $ 63,000
    Note receivable due from the same officer of the Company,
      payable in four equal annual installments commencing on
      November 2, 1996, principal due on each installment date will
      be forgiven so long as the officer is employed by the Company
      on the installment date, secured by the officer's beneficial
      interest in 48,000 shares of common stock of the Company.....   120,000       90,000
    Note receivable due from another officer of the Company,
      payable in three equal annual installments commencing on
      October 16, 1997, secured by shares of common stock of the
      Company issuable to the officer upon the exercise of
      options......................................................     --         250,000
                                                                     --------     --------
                                                                      183,000      403,000
    Less--Current portion..........................................    93,000      176,000
                                                                     --------     --------
                                                                     $ 90,000     $227,000
                                                                     ========     ========
</TABLE>
 
     Interest on the notes receivable from related parties accrues on the unpaid
principal and interest at the lowest applicable federal rate of interest as
published by the Internal Revenue Service (6.3% at December 31, 1996). Interest
due on the notes at December 31, 1995 and 1996 totaling $15,000 and $6,000,
respectively, is included in prepaid expenses and other current assets.
 
7.  ACCOUNTS PAYABLE AND ACCRUED EXPENSES
 
     Accounts payable and accrued expenses include the following:
 
<TABLE>
<CAPTION>
                                                                        DECEMBER 31,
                                                                   -----------------------
                                                                     1995          1996
                                                                   --------     ----------
    <S>                                                            <C>          <C>
    Accounts payable.............................................  $369,000     $  485,000
    Accrued professional fees....................................   176,000        469,000
    Other accrued expenses.......................................   224,000        155,000
                                                                   --------     ----------
                                                                   $769,000     $1,109,000
                                                                   ========     ==========
</TABLE>
 
8.  BRIDGE FINANCING--RELATED PARTY
 
     During 1994 and 1995, the Company received $1,700,000 and $700,000,
respectively under bridge financing arrangements with certain stockholders. In
connection with this financing, the Company issued unsecured promissory notes
and on November 2, 1995, the Company and the stockholders agreed to convert the
principal of these notes into 1,960,000 shares of Series A convertible preferred
stock. At December 31, 1995, interest payable relating to these bridge
financings was $142,000. In April 1996, the Company and the stockholders
converted the interest payable into an additional 113,429 shares of Series A
convertible preferred stock. In 1996, all outstanding shares of Series A
convertible preferred stock were converted into shares of common stock upon the
closing of the Company's initial public offering (Note 9).
 
     As partial consideration for the promissory notes, the Company issued
warrants to purchase 240,000 shares of the Company's common stock. In connection
with the Company's initial public
 
                                      F-11
<PAGE>   61
 
                                  ARQULE, INC.
 
                  NOTES TO FINANCIAL STATEMENTS -- (CONTINUED)
 
offering, the Company issued 234,992 shares of common stock upon the cashless
exercise of these warrants.
 
     The proceeds from the bridge financings were allocated to the notes and to
the warrants based on management's estimate of their relative fair values and of
the then-current market interest rate of 12%. This resulted in $132,000 and
$57,000 being ascribed to the warrants in 1994 and 1995, respectively, which was
recorded as additional paid-in-capital and as a discount to the face value of
the notes. The discount was amortized over the period from issuance to
conversion into Series A convertible preferred stock. The amortization of debt
discount totaled $25,000 and $164,000 for the years ended December 31, 1994 and
1995, respectively, and is included in interest expense.
 
9.  MANDATORILY REDEEMABLE CONVERTIBLE PREFERRED STOCK AND CONVERTIBLE PREFERRED
STOCK
 
     On November 18, 1994, the Partnership (the sole stockholder of the Company
as of that date) exchanged 563,972 shares of common stock of the Company for
Partnership interests held by certain employees and consultants. The Partnership
also contributed 140,528 shares of common stock to the Company for future
issuance pursuant to the Equity Incentive Plan (Note 11). The Company
immediately retired these contributed shares and reserved 140,528 shares of
common stock for issuance pursuant to the Equity Incentive Plan. The
stockholders of the Company approved the issuance of 8,591,000 shares of Series
A convertible preferred stock to the Partnership in exchange for the remaining
4,295,500 shares of common stock held by the Partnership. Upon the exchange of
preferred stock, the Company retired the related shares of common stock.
 
     On November 5, 1995, as part of a collaborative agreement (Note 3), the
Company sold to Solvay Duphar B.V. ("Solvay") 1,800,000 shares of Series B
preferred stock which resulted in net proceeds to the Company of $6,885,000. In
April 1996, the Company issued to Solvay an additional 15,468 shares of Series B
preferred stock in connection with the conversion of the bridge financing
interest into Series A preferred stock (Note 8) to maintain the original,
agreed-upon ownership percentage.
 
     At December 31, 1995, the Company had 15,000,000 shares of convertible
preferred stock authorized. Upon the closing of the Company's initial public
offering on October 16, 1996 (Note 10), all outstanding shares of Series A and
Series B preferred stock automatically converted into 6,219,948 shares of common
stock, and the number of authorized shares of preferred stock was reduced to
1,000,000 shares.
 
10.  COMMON STOCK
 
     On October 4, 1996, the Company effected a 1-for-2 reverse stock split on
the common stock of the Company. Accordingly, all common share and per share
data have been restated to give retroactive effect to the stock split for all
periods presented.
 
     In October and November 1996, the Company completed its initial public
offering of 2,875,000 shares of common stock. Proceeds to the Company, net of
issuance costs, amounted to $31,521,000. In connection with its initial public
offering, the stockholders approved an amendment to the Company's Certificate of
Incorporation to increase the number of authorized common shares to 30,000,000.
 
     At December 31, 1996, the Company has 2,203,453 shares of its common stock
reserved for issuance upon the exercise of options.
 
  Stock Restriction Agreements
 
     At December 31, 1996, the Company had outstanding 520,922 shares of common
stock issued pursuant to the Equity Incentive Plan (Note 11) which are subject
to stock restriction agreements
 
                                      F-12
<PAGE>   62
 
                                  ARQULE, INC.
 
                  NOTES TO FINANCIAL STATEMENTS -- (CONTINUED)
 
whereby the stockholder automatically forfeits to the Company the unvested
portion of shares of common stock in the event of termination of their
employment with the Company. All such forfeited shares shall immediately be
retired by the Company. Shares subject to this agreement vest over a four year
period, either monthly or annually. At December 31, 1996, the aggregate number
of unvested common shares is 277,903. Each stock restriction agreement may be
terminated at the election of the Company.
 
11.  EQUITY INCENTIVE AND STOCK PURCHASE PLANS
 
   
     During 1994, the stockholders approved the 1994 Amended and Restated Equity
Incentive Plan (the "Equity Incentive Plan"). During 1996, the stockholders
approved an amendment to increase the number of shares of common stock available
for awards under the Equity Incentive Plan to 3,200,000. All shares will be
awarded at the discretion of a Committee of the Board of Directors (the
"Committee") in a variety of stock-based forms including stock options and
restricted stock. Pursuant to the Equity Incentive Plan, incentive stock options
may not be granted at less than the fair market value of the Company's common
stock at the date of the grant, and the option term may not exceed ten years.
For holders of 10% or more of the Company's voting stock, options may not be
granted at less than 110% of the fair market value of the common stock at the
date of the grant, and the option term may not exceed five years. Stock
appreciation rights granted in tandem with an option shall have an exercise
price not less than the exercise price of the related option.
    
 
     Subject to the restrictions above, the Committee is authorized to designate
the options, awards, and purchases under the Equity Incentive Plan, the number
of shares covered by each option, award and purchase, and the related terms,
exercise dates, prices and methods of payment.
 
   
     In 1996, the stockholders approved, the 1996 Director Stock Option Plan
(the "1996 Director Plan") for nonemployee directors. Under this plan, eligible
directors are automatically granted once a year, at the annual meeting of
stockholders of the Company, options to purchase 3,500 shares of common stock
which are exercisable on the date of grant. Upon initial election of an eligible
director, options to purchase 7,500 shares of common stock will be granted which
will become exercisable in three equal annual installments commencing on the
date of the Company's next annual stockholders' meeting held after the date of
grant. All options granted pursuant to the 1996 Director Plan have a term of ten
years with exercise prices equal to fair market value on the date of grant.
Through December 31, 1996, options to purchase 22,500 shares of common stock
have been granted under this plan. A maximum of 125,000 shares of common stock
of the Company is reserved for issuance in accordance with the terms of this
plan, of which 102,500 are available for future grant.
    
 
   
     The Company applies APB No. 25 and related interpretations in accounting
for employee grants under the Equity Incentive Plan and the 1996 Director Plan
(collectively the "Plans"). For the three years ended December 31, 1996, no
compensation expense has been recognized under the Plans for employee grants.
Had compensation cost been determined based on the estimated value of options at
the grant date consistent with the provisions of SFAS No. 123, the Company's pro
forma net loss and pro forma net loss per share would have been as follows:
    
 
<TABLE>
<CAPTION>
                                                                         YEAR ENDED
                                                                        DECEMBER 31,
                                                                  -------------------------
                                                                     1995          1996
                                                                  -----------   -----------
    <S>                                                           <C>           <C>
    Pro forma net loss.........................................   $(2,254,000)  $(3,186,000)
    Pro forma net loss per share...............................         (0.33)        (0.41)
</TABLE>
 
   
     During 1996, the Company issued 140,000 options to certain consultants and
members of its scientific advisory board under the Equity Incentive Plan. The
estimated value of these options totaled
    
 
                                      F-13
<PAGE>   63
 
                                  ARQULE, INC.
 
                  NOTES TO FINANCIAL STATEMENTS -- (CONTINUED)
 
$709,000, was recorded as deferred compensation and is being amortized as
compensation expense over the vesting period of the options.
 
     For the purposes of pro forma disclosure, the estimated value of each
employee and nonemployee option grant was calculated on the date of grant using
the Black-Scholes option-pricing model with the following assumptions: no
dividend yield for both years; 45% volatility for nonemployee grants in both
years and employee grants subsequent to the initial filing of the Registration
Statement in connection with the Company's initial public offering; no
volatility for employee grants prior to the initial public offering; risk-free
interest rates ranging from 5.20% to 7.10% and expected lives ranging from 3 to
6 years for options granted during both years.
 
     Option activity under the Plans for the three years ended December 31, 1996
was as follows:
 
<TABLE>
<CAPTION>
                                                                                   WEIGHTED
                                                                                   AVERAGE
                                                                      NUMBER       EXERCISE
                             STOCK OPTIONS                           OF SHARES      PRICE
    ---------------------------------------------------------------  ---------     --------
    <S>                                                              <C>           <C>
    Granted........................................................       2,500      $ 0.02
                                                                     ----------
    Outstanding at December 31, 1994...............................       2,500      $ 0.02
    Granted........................................................     298,500      $ 0.17
                                                                     ----------
    Outstanding at December 31, 1995...............................     301,000      $ 0.17
    Granted........................................................   1,096,420      $ 4.55
    Exercised......................................................        (625)     $ 0.02
    Cancelled......................................................      (1,875)     $ 0.02
                                                                     ----------
    Outstanding at December 31, 1996...............................   1,394,920      $ 3.62
                                                                     ==========
    Exercisable at December 31, 1996...............................     149,611      $ 0.50
                                                                     ==========
    Weighted average estimated value of options granted during the
      year ended December 31, 1996.................................  $     1.49
                                                                     ==========
</TABLE>
 
     The following table summarizes information about options outstanding at
December 31, 1996:
 
<TABLE>
<CAPTION>
                                                                  OPTIONS OUTSTANDING
                                                      -------------------------------------------
                                                                          WEIGHTED
                                                          NUMBER           AVERAGE       WEIGHTED
                                                      OUTSTANDING AT      REMAINING      AVERAGE
                                                       DECEMBER 31,      CONTRACTUAL     EXERCISE
                RANGE OF EXERCISE PRICES                   1996             LIFE          PRICE
    ------------------------------------------------  --------------     -----------     --------
    <S>                                               <C>                <C>             <C>
          $0.02.....................................        50,000       8.3 years..      $ 0.02
           0.20.....................................       248,500       8.6 years..        0.20
     0.80 - 1.20....................................       477,420       9.1 years..        0.81
           2.40.....................................        27,500       9.4 years..        2.40
           6.00.....................................       395,000       9.5 years..        6.00
    10.25 - 12.00...................................       196,500       9.8 years..       11.04
                                                         ---------
                                                         1,394,920
                                                         =========
</TABLE>
 
                                      F-14
<PAGE>   64
 
                                  ARQULE, INC.
 
                  NOTES TO FINANCIAL STATEMENTS -- (CONTINUED)
 
   
<TABLE>
<CAPTION>
                                                                      OPTIONS EXERCISABLE
                                                                   -------------------------
                                                                      NUMBER
                                                                   EXERCISABLE      WEIGHTED
                                                                        AT          AVERAGE
                                                                   DECEMBER 31,     EXERCISE
                      RANGE OF EXERCISE PRICES                         1996          PRICE
    -------------------------------------------------------------  ------------     --------
    <S>                                                            <C>              <C>
         $0.02...................................................      12,500        $ 0.02
          0.20...................................................      59,625          0.20
          0.80...................................................      77,486          0.80
                                                                      -------
                                                                      149,611
                                                                      =======
</TABLE>
    
 
   
     At December 31, 1996, restricted common stock purchased pursuant to the
Equity Incentive Plan totaled 520,922 shares (Note 10), and there were 1,306,033
shares available for future grant under the Equity Incentive Plan.
    
 
  Stock Purchase Plan
 
     In 1996, the stockholders adopted the 1996 Employee Stock Purchase Plan
(the "Purchase Plan"). This plan enables eligible employees to exercise rights
to purchase the Company's common stock at 85% of the fair market value of the
stock on the date the right was granted or the date the right is exercised,
whichever is lower. Rights to purchase shares under the Purchase Plan are
granted by the Board of Directors. The rights are exercisable during a period
determined by the Board of Directors; however, in no event will the period be
longer than twenty-seven months. The Purchase Plan is available to substantially
all employees, subject to certain limitations. The Company has reserved 120,000
shares of common stock for purchases under the Purchase Plan. At December 31,
1996, no shares have been purchased pursuant to the Purchase Plan.
 
12.  INCOME TAXES
 
     The benefit (provision) for income taxes was as follows:
 
<TABLE>
<CAPTION>
                                                            YEAR ENDED DECEMBER 31,
                                                  -------------------------------------------
                                                     1994            1995            1996
                                                  -----------     -----------     -----------
    <S>                                           <C>             <C>             <C>
    Deferred tax benefit:
      Federal...................................  $ 1,420,000     $   794,000     $   886,000
      State.....................................      338,000         246,000         347,000
                                                  -----------     -----------     -----------
                                                    1,758,000       1,040,000       1,233,000
    Deferred tax asset valuation allowance......   (1,758,000)     (1,040,000)     (1,233,000)
                                                  -----------     -----------     -----------
                                                  $   --          $   --          $   --
                                                  ===========     ===========     ===========
</TABLE>
 
     The Company's deferred tax assets consist of the following:
 
<TABLE>
<CAPTION>
                                                                       DECEMBER 31,
                                                                ---------------------------
                                                                   1995            1996
                                                                -----------     -----------
    <S>                                                         <C>             <C>
    Preoperating costs capitalized for tax purposes...........  $   416,000     $   370,000
    Net operating loss carryforwards..........................    2,590,000       3,906,000
    Tax credit carryforwards..................................      272,000         311,000
    Book depreciation in excess of tax........................      106,000          30,000
                                                                -----------     -----------
    Gross deferred tax assets.................................    3,384,000       4,617,000
    Deferred tax asset valuation allowance....................   (3,384,000)     (4,617,000)
                                                                -----------     -----------
                                                                $   --          $   --
                                                                ===========     ===========
</TABLE>
 
                                      F-15
<PAGE>   65
 
                                  ARQULE, INC.
 
                  NOTES TO FINANCIAL STATEMENTS -- (CONTINUED)
 
     The Company has provided a full valuation allowance for the deferred tax
assets as the realization of these future benefits is not sufficiently assured
as of the end of each related year. If the Company achieves profitability, the
deferred tax assets will be available to offset future income tax liabilities
and expense.
 
     At December 31, 1996, the Company has federal net operating loss
carryforwards and tax credit carryforwards available to reduce future taxable
income and tax liabilities, respectively, which expire as follows:
 
<TABLE>
<CAPTION>
                                                                     NET          RESEARCH AND
                                                                  OPERATING        DEVELOPMENT
                             YEAR OF                                LOSS           TAX CREDIT
                            EXPIRATION                          CARRYFORWARDS     CARRYFORWARDS
    ----------------------------------------------------------  -------------     -------------
    <S>                                                         <C>               <C>
      2009....................................................   $4,320,000        $ 84,000
      2010....................................................    2,181,000          52,000
      2011....................................................    3,319,000          16,000
                                                                 ----------        --------
                                                                 $9,820,000        $152,000
                                                                 ==========        ========
</TABLE>
 
     Under the Internal Revenue Code, certain substantial changes in the
Company's ownership could result in an annual limitation on the amount of net
operating loss and tax credit carryforwards which can be utilized in future
years.
 
     A reconciliation between the amounts of reported income tax benefit and the
amount determined by applying the U.S. federal statutory rate of 35% for 1994,
1995 and 1996 to pre-tax loss is as follows:
 
<TABLE>
<CAPTION>
                                                            YEAR ENDED DECEMBER 31,
                                                  -------------------------------------------
                                                     1994            1995            1996
                                                  -----------     -----------     -----------
    <S>                                           <C>             <C>             <C>
    Income tax benefit at statutory rate........  $ 1,472,000     $   788,000     $ 1,048,000
    State tax benefit, net of federal benefit...      252,000         135,000         180,000
    Research and investment tax credits.........      139,000         133,000          53,000
    Other.......................................     (105,000)        (16,000)        (48,000)
                                                  -----------     -----------     -----------
                                                    1,758,000       1,040,000       1,233,000
    Increase in valuation allowance.............   (1,758,000)     (1,040,000)     (1,233,000)
                                                  -----------     -----------     -----------
                                                  $   --          $   --          $   --
                                                  ===========     ===========     ===========
</TABLE>
 
                                      F-16
<PAGE>   66
 
                                  ARQULE, INC.
 
                  NOTES TO FINANCIAL STATEMENTS -- (CONTINUED)
 
13.  COMMITMENTS AND CONTINGENCY
 
  Leases
 
     The Company leases facilities and equipment under noncancelable operating
and capital leases. The future minimum lease commitments under these leases are
as follows:
 
<TABLE>
<CAPTION>
                            YEAR ENDING                           OPERATING       CAPITAL
                            DECEMBER 31,                            LEASES         LEASES
    ------------------------------------------------------------  ----------     ----------
    <S>                                                           <C>            <C>
       1997.....................................................  $  541,000     $1,343,000
       1998.....................................................     520,000      1,058,000
       1999.....................................................     458,000        697,000
       2000.....................................................     373,000        102,000
       2001.....................................................     148,000         --
                                                                  ----------     ----------
    Total minimum lease payments................................  $2,040,000      3,200,000
                                                                  ==========
    Less--Amount representing interest..........................                    334,000
                                                                                 ----------
    Present value of minimum lease payments.....................                 $2,866,000
                                                                                 ==========
</TABLE>
 
     The Company has a lease line agreement with a financial institution (the
"Lessor") for $8,500,000 of which approximately $4,884,000 was available for
future leases at December 31, 1996. The term for each lease under the agreement
is forty-two months, commencing on the purchase date of the asset, and the lease
bears interest at a rate determined by the Lessor at the transaction date.
During 1994, the Company sold and leased back approximately $107,000 in
machinery and equipment, furniture and fixtures and office equipment from the
Lessor.
 
     Rent expense under noncancelable operating leases was approximately
$91,000, $163,000 and $283,000 for the years ended December 31, 1994, 1995 and
1996, respectively.
 
  Employment Agreements
 
     The Company entered into an employment agreement with an officer who is
also a member of the board of directors. This agreement provides that if his
employment is terminated without cause, the officer is entitled to receive up to
six months' salary. The Company also entered into an employment agreement with
another officer. This agreement provides that if his employment is terminated
without cause during the first year of the agreement, the officer is entitled to
receive up to six months' salary.
 
  Contingency
 
     In October 1996, the Company received a letter from two individuals who
have asserted that they are entitled to compensation from certain of the
Company's stockholders and/or the Company equal to approximately five percent of
the equity interest in the Company. The Company believes that there are
meritorious defenses against such claims and intends to contest them vigorously;
however, they are currently unable to estimate the outcome of this matter,
including the range of potential loss, if any.
 
                                      F-17
<PAGE>   67
 
================================================================================
 
     NO DEALER, SALESPERSON OR OTHER PERSON HAS BEEN AUTHORIZED TO GIVE ANY
INFORMATION OR TO MAKE ANY REPRESENTATIONS OTHER THAN THOSE CONTAINED IN THIS
PROSPECTUS AND, IF GIVEN OR MADE, SUCH INFORMATION OR REPRESENTATIONS MUST NOT
BE RELIED UPON AS HAVING BEEN AUTHORIZED BY THE COMPANY OR THE UNDERWRITERS.
THIS PROSPECTUS DOES NOT CONSTITUTE AN OFFER TO SELL OR A SOLICITATION OF AN
OFFER TO BUY THE COMMON STOCK TO ANY PERSON IN ANY JURISDICTION IN WHICH SUCH
OFFER OR SOLICITATION WOULD BE UNLAWFUL OR TO ANY PERSON TO WHOM IT IS UNLAWFUL.
NEITHER THE DELIVERY OF THIS PROSPECTUS NOR ANY OFFER OR SALE MADE HEREUNDER
SHALL, UNDER ANY CIRCUMSTANCES, CREATE ANY IMPLICATION THAT THERE HAS BEEN NO
CHANGE IN THE AFFAIRS OF THE COMPANY OR THAT THE INFORMATION CONTAINED HEREIN IS
CORRECT AS OF ANY TIME SUBSEQUENT TO THE DATE HEREOF.
 
                               ------------------
 
                               TABLE OF CONTENTS
 
   
<TABLE>
<CAPTION>
                                             PAGE
                                             ----
<S>                                          <C>
Prospectus Summary.........................    3
Risk Factors...............................    6
The Company................................   13
Use of Proceeds............................   13
Dividend Policy............................   13
Price Range of Common Stock................   14
Capitalization.............................   14
Dilution...................................   15
Selected Financial Data....................   16
Management's Discussion and Analysis of
  Financial Condition and Results of
  Operations...............................   17
Business...................................   20
Management.................................   34
Certain Transactions.......................   40
Principal and Selling Stockholders.........   42
Description of Capital Stock...............   44
Shares Eligible for Future Sale............   45
Underwriting...............................   47
Legal Matters..............................   48
Experts....................................   48
Available Information......................   48
Index to Financial Statements..............  F-1
</TABLE>
    
 
 
================================================================================
================================================================================
   
                                2,000,000 SHARES
    
 
                                  ARQULE, INC.

                                 [ARQULE LOGO]

                                  COMMON STOCK
 
   
                            ------------------------
    
                                   PROSPECTUS
                            ------------------------
 
   
                               HAMBRECHT & QUIST
    
 
                            OPPENHEIMER & CO., INC.
 
                      VECTOR SECURITIES INTERNATIONAL, INC.
   
                                           , 1997
    
 
   
================================================================================
    
<PAGE>   68
 
                                    PART II
 
                     INFORMATION NOT REQUIRED IN PROSPECTUS
 
ITEM 13.  OTHER EXPENSES OF ISSUANCE AND DISTRIBUTION
 
     The expenses to be borne by the Company in connection with this offering
are as follows:
 
<TABLE>
            <S>                                                         <C>
            SEC registration fee......................................  $ 13,330
            Nasdaq listing fee........................................    17,500
            NASD filing fee...........................................     4,899
            Blue Sky fees and expenses................................    10,000
            Printing and engraving expenses...........................    80,000
            Accounting fees and expenses..............................    40,000
            Legal fees and expenses...................................   100,000
            Transfer agent and registrar fees.........................     3,500
            Miscellaneous expenses....................................     5,771
                                                                        --------
                      Total...........................................  $275,000
                                                                        ========
</TABLE>
 
     All of the above figures, except the SEC registration fee and NASD filing
fee, are estimates.
 
ITEM 14.  INDEMNIFICATION OF DIRECTORS AND OFFICERS
 
     Section 145 of the Delaware General Corporation Law grants the Company the
power to indemnify each person who was or is a party or is threatened to be made
a party to any threatened, pending or completed action, suit or proceeding,
whether civil, criminal, administrative or investigative by reason of the fact
that he is or was a director, officer, employee or agent of the Company, or is
or was serving at the request of the Company as a director, officer, employee or
agent of another corporation, partnership, joint venture, trust or other
enterprise, against expenses (including attorneys' fees), judgements, fines and
amounts paid in settlement actually and reasonably incurred by him in connection
with such action, suit or proceeding if he acted in good faith and in a manner
he reasonably believed to be in or not opposed to the best interests of the
Company, and with respect to any criminal action or proceeding, had no
reasonable cause to believe his conduct was unlawful, provided, however, no
indemnification shall be made in connection with any proceeding brought by or in
the right of the Company where the person involved is adjudged to be liable to
the Company except to the extent approved by a court. Article V of the Company's
Amended and Restated By-laws provides that the Company shall, to extent legally
permitted, indemnify each person who was or is a party or is threatened to be
made a party to any threatened, pending or completed action, suit or proceeding
by reason of the fact that he is or was, or has agreed to become, a director or
officer of the Company, or is or was serving, or has agreed to serve, at the
request of the Company, as a director, officer or trustee of, or in a similar
capacity with, another corporation, partnership, joint venture, trust or other
enterprise. The indemnification provided for in Article V is expressly not
exclusive of any other rights to which those seeking indemnification may be
entitled under any law, agreement or vote of stockholders or disinterested
directors or otherwise, and shall inure to the benefit of the heirs, executors
and administrators of such persons. Article V also provides that the Company
shall have the power to purchase and maintain insurance on behalf of any person
who is or was a director, officer, employee or agent of the Company, or is or
was serving at the request of the Company, as a director, officer or trustee of,
or in a similar capacity with, another corporation, partnership, joint venture,
trust or other enterprise, against any liability asserted against and incurred
by such person in any such capacity.
 
     Pursuant to Section 102(b)(7) of the Delaware General Corporation Laws,
Section 7 of Article FIFTH of the Company's Restated Certificate eliminates a
director's personal liability for monetary damages to the Company and its
stockholders for breaches of fiduciary duty as a director, except in
circumstances involving a breach of a director's duty of loyalty to the Company
or its stockholders,
 
                                      II-1
<PAGE>   69
 
acts or omissions not in good faith, intentional misconduct, knowing violations
of the law, self-dealing or the unlawful payment of dividends or repurchase of
stock.
 
ITEM 15.  RECENT SALES OF UNREGISTERED SECURITIES
 
     Since June 1, 1993, the Company has issued and sold the following
securities, in each case in reliance on an exemption from required registration
pursuant to Section 4(2) of the Securities Act:
 
     In December 1993, in exchange for the transfer to the Company of
substantially all of the assets and liabilities of the Partnership, the Company
issued 1,500 shares of its Common Stock to the Partnership.
 
     Commencing in March 1995, the Company has granted employees and consultants
options under its Amended and Restated 1994 Equity Incentive Plan, which options
have a ten-year term and are exercisable at a price equal to fair market value
on the date of grant, as determined in good faith by the Board of Directors. As
of December 31, 1996, options for 1,372,420 shares of the Company's Common Stock
were outstanding. As of such date, an option for 625 shares of Common Stock had
been exercised at $0.02 per share.
 
     In addition, from inception through December 31, 1996, the Company made
grants of an aggregate of 520,922 shares of Common Stock to certain employees
and consultants of the Company. Such shares are subject to repurchase rights
held by the Company and were sold at fair market value on the date of grant.
 
     In November 1994, the Company declared and paid a stock dividend of
3,332.33 shares of its Common Stock on each outstanding share of Common Stock
held as of October 17, 1994. Pursuant to a Plan of Recapitalization, the
Partnership surrendered an aggregate of 4,295,500 outstanding shares of Common
Stock (after giving effect to such stock dividend) for shares of Series A
Convertible Preferred Stock of the Company which were converted into an equal
number of shares of Common Stock concurrently with the Company's initial public
offering.
 
     During the period from August 1994 through February 1995, certain
stockholders of the Company made a series of Bridge Loans to the Company for an
aggregate of $2,400,000 in exchange for promissory notes and warrants to
purchase an aggregate of 240,000 shares of Common Stock, which warrants were
exercised concurrently with the effective date of the Company's initial public
offering. In November 1995, the Bridge Loans were converted to shares of Series
A Preferred Stock, which were converted into 960,000 shares of Common Stock
concurrently with the closing of the Company's initial public offering.
 
     In November 1995, the Company issued 1,800,000 shares of Series B Preferred
Stock to Physica B.V., which were converted into 900,000 shares of Common Stock
concurrently with the closing of the Company's initial public offering, for cash
at the purchase price of $3.89 per share.
 
     In April 1996, all accrued interest outstanding on the Bridge Loans through
November 1995 was converted into shares of Series A Preferred Stock, which were
converted into 56,714 shares of Common Stock concurrently with the closing of
the Company's initial public offering. In April 1996, the Company also issued
shares of Series B Preferred Stock to Physica B.V., which converted into 7,734
shares of Common Stock concurrently with the closing of the Company's initial
public offering, in consideration of Physica B.V.'s waiver of its anti-dilution
rights under the Company's Amended and Restated Certificate of Incorporation and
its right of first refusal with respect to such shares of Series A Preferred
Stock.
 
                                      II-2
<PAGE>   70
 
ITEM 16.
 
(A) EXHIBITS
 
                                 EXHIBIT INDEX
 
   
<TABLE>
<CAPTION>
EXHIBIT NO.                                      DESCRIPTION
- -----------   ---------------------------------------------------------------------------------
<S>           <C>
 1.1          Form of Underwriting Agreement. Filed herewith.
 3.1++        Amended and Restated Certificate of Incorporation of the Company.
 3.2          Amended and Restated By-laws of the Company. Filed as Exhibit 3.5 to the
              Company's Registration Statement on Form S-1 (File No. 333-11105) and
              incorporated herein by reference.
 4.1          Specimen Common Stock Certificate. Filed as Exhibit 4.1 to the Company's
              Registration Statement on Form S-1 (File No. 333-11105) and incorporated herein
              by reference.
 5.1++        Opinion of Palmer & Dodge LLP.
10.1*         Amended and Restated 1994 Equity Incentive Plan, as amended through October 17,
              1994. Filed as Exhibit 10.1 to the Company's Registration Statement on Form S-1
              (File No. 333-11105) and incorporated herein by reference.
10.2*         1996 Employee Stock Purchase Plan. Filed as Exhibit 10.2 to the Company's
              Registration Statement on Form S-1 (File No. 333-11105) and incorporated herein
              by reference.
10.3*         1996 Director Stock Option Plan. Filed as Exhibit 10.3 to the Company's
              Registration Statement on Form S-1 (File No. 333-11105) and incorporated herein
              by reference.
10.4          Form of Indemnification Agreement between the Company and its directors. Such
              agreements are materially different only as to the signing directors and the
              dates of execution. Filed as Exhibit 10.4 to the Company's Registration Statement
              on Form S-1 (File No. 333-11105) and incorporated herein by reference.
10.5          Investors' Rights Agreement among the Company and certain stockholders of the
              Company dated November 2, 1995. Filed as Exhibit 10.5 to the Company's
              Registration Statement on Form S-1 (File No. 333-11105) and incorporated herein
              by reference.
10.6          Lease Agreement dated September 29, 1993 between the Company and Beautyrest
              Property, Inc. and WRB, Inc. Filed as Exhibit 10.6 to the Company's Registration
              Statement on Form S-1 (File No. 333-11105) and incorporated herein by reference.
10.7          Lease Agreement, dated July 27, 1995, between the Company and Cummings Properties
              Management, Inc. as amended. Filed as Exhibit 10.7 to the Company's Registration
              Statement on Form S-1 (File No. 333-11105) and incorporated herein by reference.
10.8*         Employment Agreement effective as of January 2, 1996, between the Company and
              Eric B. Gordon. Filed as Exhibit 10.8 to the Company's Registration Statement on
              Form S-1 (File No. 333-11105) and incorporated herein by reference.
10.9*         Employment Agreement effective as of July 9, 1996, between the Company and James
              R. Fitzgerald, Jr. Filed as Exhibit 10.9 to the Company's Registration Statement
              on Form S-1 (File No. 333-11105) and incorporated herein by reference.
10.10*        Promissory Note dated November 2, 1995 between Dr. Joseph C. Hogan, Jr. and the
              Company. Filed as Exhibit 10.10 to the Company's Registration Statement on Form
              S-1 (File No. 333-11105) and incorporated herein by reference.
10.11*        Pledge Agreement dated November 2, 1995 between Dr. Joseph C. Hogan, Jr. and the
              Company. Filed as Exhibit 10.11 to the Company's Registration Statement on Form
              S-1 (File No. 333-11105) and incorporated herein by reference.
10.12*        Promissory Note and Pledge Agreement dated July 9, 1996 between Eric B. Gordon
              and the Company. Filed as Exhibit 10.12 to the Company's Registration Statement
              on Form S-1 (File No. 333-11105) and incorporated herein by reference.
10.13*        Promissory Note dated November 4, 1993 between Dr. Joseph C. Hogan, Jr. and the
              Company. Filed as Exhibit 10.13 to the Company's Registration Statement on Form
              S-1 (File No. 333-11105) and incorporated herein by reference.
</TABLE>
    
 
                                      II-3
<PAGE>   71
 
   
<TABLE>
<CAPTION>
EXHIBIT NO.                                      DESCRIPTION
- -----------   ---------------------------------------------------------------------------------
<S>           <C>
10.14+        Research, Development and License Agreement between the Company and Solvay Duphar
              B.V. dated November 2, 1995. Filed as Exhibit 10.14 to the Company's Registration
              Statement on Form S-1 (File No. 333-11105) and incorporated herein by reference.
10.15+        Research & Development and License Agreement between the Company and Abbott
              Laboratories dated June 15, 1995, as amended. Filed as Exhibit 10.15 to the
              Company's Registration Statement on Form S-1 (file No. 333-11105) and
              incorporated herein by reference.
10.16+        Research & Development Agreement between the Company and Pharmacia Biotech AB
              dated March 10, 1995, as amended. Filed as Exhibit 10.16 to the Company's
              Registration Statement on Form S-1 (File No. 333-11105) and incorporated herein
              by reference.
10.17+        Option Agreement between the Company and Pharmacia Biotech AB dated March 10,
              1995, as amended. Filed as Exhibit 10.17 to the Company's Registration Statement
              on Form S-1 (File No. 333-11105) and incorporated herein by reference.
10.18*        Adoption Agreement for Fidelity Management and Research Company (the Company's
              401(k) plan). Filed as Exhibit 10.18 to the Company's Registration Statement on
              Form S-1 (File No. 333-11105) and incorporated herein by reference.
10.19         Research and License Agreement between the Company and Roche Bioscience dated
              September 13, 1996. Filed as Exhibit 10.19 to the Company's Registration
              Statement on Form S-1 (File No. 333-11105) and incorporated herein by reference.
10.20+        Array Delivery and Testing Agreement between the Company and Monsanto Company
              dated as of December 23, 1996. Filed herewith.
10.21+++      Amendment No. 2 to Research & Development License Agreement between the Company
              and Abbot Laboratories dated as of December 24, 1996.
10.22++       Lease Agreement, dated December 20, 1996 between the Company and Cummings
              Property Management, Inc.
11.1++        Statement re computation of unaudited pro forma net loss per share.
23.1          Consent of Price Waterhouse LLP. Filed herewith.
23.2          Consent of Palmer & Dodge LLP. Included in the opinion filed as Exhibit 5.1.
24.1++        Power of attorney.
27.1++        Financial Data Schedule.
</TABLE>
    
 
- ---------------
* Indicates a management contract or compensatory plan.
 
+ Certain confidential material contained in the document has been omitted and
  filed separately, with the Securities and Exchange Commission pursuant to Rule
  406 of the Securities Act of 1933, as amended.
 
   
++ Previously filed.
    
 
(B) FINANCIAL STATEMENT SCHEDULE
 
<TABLE>
<CAPTION>
                                                                                        PAGE
                                                                                        ----
<S>                                                                                     <C>
II Valuation and Qualifying Accounts and Reserves.....................................  S-1
</TABLE>
 
ITEM 17.  UNDERTAKINGS
 
     (a) Insofar as indemnification for liabilities arising under the Securities
Act of 1933 may be permitted to directors, officers and controlling persons of
the Registrant pursuant to the provisions described under "Item
14--Indemnification of Directors and Officers" above, or otherwise, the
Registrant has been advised that in the opinion of the Securities and Exchange
Commission such indemnification is against public policy as expressed in the Act
and is, therefore, unenforceable. In the event that a claim for indemnification
against such liabilities (other than the payment by the Registrant of expenses
incurred or paid by a director, officer or controlling person of the Registrant
in
 
                                      II-4
<PAGE>   72
 
the successful defense of any action, suit or proceeding) is asserted by such
director, officer or controlling person in connection with the securities being
registered, the Registrant will, unless in the opinion of its counsel the matter
has been settled by controlling precedent, submit to a court of appropriate
jurisdiction the question whether such indemnification by it is against public
policy as expressed in the Act and will be governed by the final adjudication of
such issue.
 
     (b) The undersigned Registrant hereby undertakes that:
 
          (1) For purposes of determining any liability under the Securities
     Act, the information omitted from the form of prospectus filed as part of
     this Registration Statement in reliance upon Rule 430A and contained in a
     form of prospectus filed by the Registrant pursuant to Rule 424(b)(1) or
     (4) or 497(h) under the Securities Act shall be deemed to be part of this
     Registration Statement as of the time it was declared effective.
 
          (2) For the purpose of determining any liability under the Securities
     Act, each post-effective amendment that contains a form of prospectus shall
     be deemed to be a new registration statement relating to the securities
     offered therein, and the offering of such securities at that time shall be
     deemed to be the initial bona fide offering thereof.
 
     (c) The undersigned Registrant hereby undertakes to provide to the
Underwriters at the closing specified in the underwriting agreement,
certificates in such denominations and registered in such names as required by
the Underwriters to permit prompt delivery to each purchaser.
 
                                      II-5
<PAGE>   73
 
                                   SIGNATURES
 
   
     Pursuant to the requirements of the Securities Act of 1933, the Registrant
certifies that it has duly caused this Registration Statement to be signed on
its behalf by the undersigned, thereunto duly authorized, in the Town of
Medford, Commonwealth of Massachusetts, on April 3, 1997.
    
 
                                          ARQULE, INC.
 
   
                                          By:                  *
    
                                            ------------------------------------
                                            Eric B. Gordon
                                            President, and Chief Executive
                                              Officer
 
   
     Pursuant to the requirements of the Securities Act of 1933, this
Registration Statement has been signed below by the following persons in the
capacities and on the dates indicated.
    
 
   
<TABLE>
<CAPTION>
             SIGNATURE                                TITLE                        DATE
- -----------------------------------    -----------------------------------    ---------------
<C>                                    <S>                                    <C>
 
                 *                     President, Chief Executive Officer     April 3, 1997
- -----------------------------------    and Director (Principal Executive
          Eric B. Gordon               Officer)
 
                 *                     Vice President, Chief Financial        April 3, 1997
- -----------------------------------    Officer and Treasurer (Principal
     James R. Fitzgerald, Jr.          Financial Officer and Principal
                                       Accounting Officer)
 
                 *                     Director                               April 3, 1997
- -----------------------------------
          Stephen M. Dow
 
                 *                     Chairman of the Board, Senior Vice     April 3, 1997
- -----------------------------------    President of Research and
       Joseph C. Hogan, Jr.            Development, Chief Scientific
                                       Officer and Director
 
                 *                     Director                               April 3, 1997
- -----------------------------------
          Adrian de Jonge
 
                 *                     Director                               April 3, 1997
- -----------------------------------
         Allan R. Ferguson
 
*By: LYNNETTE C. FALLON
      -----------------------------
        Lynnette C. Fallon
         Attorney-in-fact
</TABLE>
    
 
                                      II-6
<PAGE>   74
 
                                                                     SCHEDULE II
 
                                  ARQULE, INC.
 
                 VALUATION AND QUALIFYING ACCOUNTS AND RESERVES
 
<TABLE>
<CAPTION>
                                                                  CHARGED
                                                 BALANCE AT      TO COSTS      CHARGED TO     DEDUCTIONS     BALANCE AT
                                                BEGINNING OF        AND          OTHER           AND           END OF
                 DESCRIPTION                       PERIOD        EXPENSES       ACCOUNTS      WRITE-OFFS       PERIOD
- ----------------------------------------------  ------------     ---------     ----------     ----------     ----------
<S>                                             <C>              <C>           <C>            <C>            <C>
Deferred tax asset valuation allowance
    Year ended December 31, 1994..............   $  586,000      1,758,000        --             --          $2,344,000
    Year ended December 31, 1995..............    2,344,000      1,040,000        --             --          3,384,000
    Year ended December 31, 1996..............    3,384,000      1,233,000        --             --          4,617,000
</TABLE>
 
                                       S-1
<PAGE>   75
 
                                 EXHIBIT INDEX
 
   
<TABLE>
<CAPTION>
EXHIBIT NO.                                      DESCRIPTION
- -----------   ---------------------------------------------------------------------------------
<S>           <C>
 1.1          Form of Underwriting Agreement. Filed herewith.
 3.1++        Amended and Restated Certificate of Incorporation of the Company.
 3.2          Amended and Restated By-laws of the Company. Filed as Exhibit 3.5 to the
              Company's Registration Statement on Form S-1 (File No. 333-11105) and
              incorporated herein by reference.
 4.1          Specimen Common Stock Certificate. Filed as Exhibit 4.1 to the Company's
              Registration Statement on Form S-1 (File No. 333-11105) and incorporated herein
              by reference.
 5.1++        Opinion of Palmer & Dodge LLP.
10.1*         Amended and Restated 1994 Equity Incentive Plan, as amended through October 17,
              1994. Filed as Exhibit 10.1 to the Company's Registration Statement on Form S-1
              (File No. 333-11105) and incorporated herein by reference.
10.2*         1996 Employee Stock Purchase Plan. Filed as Exhibit 10.2 to the Company's
              Registration Statement on Form S-1 (File No. 333-11105) and incorporated herein
              by reference.
10.3*         1996 Director Stock Option Plan. Filed as Exhibit 10.3 to the Company's
              Registration Statement on Form S-1 (File No. 333-11105) and incorporated herein
              by reference.
10.4          Form of Indemnification Agreement between the Company and its directors. Such
              agreements are materially different only as to the signing directors and the
              dates of execution. Filed as Exhibit 10.4 to the Company's Registration Statement
              on Form S-1 (File No. 333-11105) and incorporated herein by reference.
10.5          Investors' Rights Agreement among the Company and certain stockholders of the
              Company dated November 2, 1995. Filed as Exhibit 10.5 to the Company's
              Registration Statement on Form S-1 (File No. 333-11105) and incorporated herein
              by reference.
10.6          Lease Agreement dated September 29, 1993 between the Company and Beautyrest
              Property, Inc. and WRB, Inc. Filed as Exhibit 10.6 to the Company's Registration
              Statement on Form S-1 (File No. 333-11105) and incorporated herein by reference.
10.7          Lease Agreement, dated July 27, 1995, between the Company and Cummings Properties
              Management, Inc. as amended. Filed as Exhibit 10.7 to the Company's Registration
              Statement on Form S-1 (File No. 333-11105) and incorporated herein by reference.
10.8*         Employment Agreement effective as of January 2, 1996, between the Company and
              Eric B. Gordon. Filed as Exhibit 10.8 to the Company's Registration Statement on
              Form S-1 (File No. 333-11105) and incorporated herein by reference.
10.9*         Employment Agreement effective as of July 9, 1996, between the Company and James
              R. Fitzgerald, Jr. Filed as Exhibit 10.9 to the Company's Registration Statement
              on Form S-1 (File No. 333-11105) and incorporated herein by reference.
10.10*        Promissory Note dated November 2, 1995 between Dr. Joseph C. Hogan, Jr. and the
              Company. Filed as Exhibit 10.10 to the Company's Registration Statement on Form
              S-1 (File No. 333-11105) and incorporated herein by reference.
10.11*        Pledge Agreement dated November 2, 1995 between Dr. Joseph C. Hogan, Jr. and the
              Company. Filed as Exhibit 10.11 to the Company's Registration Statement on Form
              S-1 (File No. 333-11105) and incorporated herein by reference.
10.12*        Promissory Note and Pledge Agreement dated July 9, 1996 between Eric B. Gordon
              and the Company. Filed as Exhibit 10.12 to the Company's Registration Statement
              on Form S-1 (File No. 333-11105) and incorporated herein by reference.
10.13*        Promissory Note dated November 4, 1993 between Dr. Joseph C. Hogan, Jr. and the
              Company. Filed as Exhibit 10.13 to the Company's Registration Statement on Form
              S-1 (File No. 333-11105) and incorporated herein by reference.
10.14+        Research, Development and License Agreement between the Company and Solvay Duphar
              B.V. dated November 2, 1995. Filed as Exhibit 10.14 to the Company's Registration
              Statement on Form S-1 (File No. 333-11105) and incorporated herein by reference.
</TABLE>
    
<PAGE>   76
 
   
<TABLE>
<CAPTION>
EXHIBIT NO.                                      DESCRIPTION
- -----------   ---------------------------------------------------------------------------------
<S>           <C>
10.15+        Research & Development and License Agreement between the Company and Abbott
              Laboratories dated June 15, 1995, as amended. Filed as Exhibit 10.15 to the
              Company's Registration Statement on Form S-1 (file No. 333-11105) and
              incorporated herein by reference.
10.16+        Research & Development Agreement between the Company and Pharmacia Biotech AB
              dated March 10, 1995, as amended. Filed as Exhibit 10.16 to the Company's
              Registration Statement on Form S-1 (File No. 333-11105) and incorporated herein
              by reference.
10.17+        Option Agreement between the Company and Pharmacia Biotech AB dated March 10,
              1995, as amended. Filed as Exhibit 10.17 to the Company's Registration Statement
              on Form S-1 (File No. 333-11105) and incorporated herein by reference.
10.18*        Adoption Agreement for Fidelity Management and Research Company (the Company's
              401(k) plan). Filed as Exhibit 10.18 to the Company's Registration Statement on
              Form S-1 (File No. 333-11105) and incorporated herein by reference.
10.19         Research and License Agreement between the Company and Roche Bioscience dated
              September 13, 1996. Filed as Exhibit 10.19 to the Company's Registration
              Statement on Form S-1 (File No. 333-11105) and incorporated herein by reference.
10.20+        Array Delivery and Testing Agreement between the Company and Monsanto Company
              dated as of December 23, 1996. Filed herewith.
10.21+++      Amendment No. 2 to Research & Development License Agreement between the Company
              and Abbot Laboratories dated as of December 24, 1996.
10.22++       Lease Agreement, dated December 20, 1996 between the Company and Cummings
              Property Management, Inc.
11.1++        Statement re computation of unaudited pro forma net loss per share.
23.1          Consent of Price Waterhouse LLP. Filed herewith.
23.2          Consent of Palmer & Dodge LLP. Included in the opinion filed as Exhibit 5.1.
24.1++        Power of attorney.
27.1++        Financial Data Schedule.
</TABLE>
    
 
- ---------------
* Indicates a management contract or compensatory plan.
 
+ Certain confidential material contained in the document has been omitted and
  filed separately, with the Securities and Exchange Commission pursuant to Rule
  406 of the Securities Act of 1933, as amended.
 
   
++ Previously filed.
    

<PAGE>   1

                                  ARQULE, INC.

                                2,000,000 SHARES(1)

                                  COMMON STOCK

                             UNDERWRITING AGREEMENT
                             


                                                                  April __, 1997

HAMBRECHT & QUIST LLC
OPPENHEIMER & CO., INC.
VECTOR SECURITIES INTERNATIONAL, INC.
c/o Hambrecht & Quist LLC
One Bush Street
San Francisco, CA 94104

Ladies and Gentlemen:

         ArQule, Inc., a Delaware corporation (herein called the Company),
proposes to issue and sell 1,632,500 shares of its authorized but unissued
Common Stock, $.01 par value (herein called the Common Stock), and the
stockholders of the Company named in SCHEDULE II hereto (herein collectively
called the Selling Securityholders) propose to sell an aggregate of 367,500
shares of Common Stock of the Company (said shares of Common Stock being herein
called the Underwritten Stock). The Company proposes to grant to the
Underwriters (as hereinafter defined) an option to purchase up to 300,000
additional shares of Common Stock (herein called the Option Stock and with the
Underwritten Stock herein collectively called the Stock). The Common Stock is
more fully described in the Registration Statement and the Prospectus
hereinafter mentioned.

         The Company and the Selling Securityholders severally hereby confirm
the agreements made with respect to the purchase of the Stock by the several
underwriters, for whom you are acting, named in SCHEDULE I hereto (herein
collectively called the Underwriters, which term shall also include any
underwriter purchasing Stock pursuant to Section 3(b) hereof). You represent and
warrant that you have been authorized by each of the other Underwriters to enter
into this Agreement on its behalf and to act for it in the manner herein
provided.

         1. REGISTRATION STATEMENT. The Company has filed with the Securities
and Exchange Commission (herein called the Commission) a registration statement
on Form S-1 (No. 333-22945), including the related preliminary prospectus, for
the registration under the Securities Act of 1933, as amended (herein called the
Securities Act) of the Stock. Copies of such registration statement and of each
amendment thereto, if any, including the related preliminary prospectus (meeting
the requirements of Rule 430A of the rules and regulations of 

- -----------------
(1)   Plus an option to purchase from the Company up to 300,000 additional 
      shares to cover over-allotments.


<PAGE>   2
                                      -2-

the Commission) heretofore filed by the Company with the Commission have been
delivered to you and are identical to the electronically transmitted copies
thereof filed with the Commission pursuant to the Commission's Electronic Data
Gathering, Analysis and Retrieval System (herein called EDGAR), except to the
extent permitted by Regulation S-T.

         The term Registration Statement as used in this Agreement shall mean
such registration statement, including all exhibits and financial statements,
all information omitted therefrom in reliance upon Rule 430A and contained in
the Prospectus referred to below, in the form in which it became effective, and
any registration statement filed pursuant to Rule 462(b) of the rules and
regulations of the Commission with respect to the Stock (herein called a Rule
462(b) registration statement), and, in the event of any amendment thereto after
the effective date of such registration statement (herein called the Effective
Date), shall also mean (from and after the effectiveness of such amendment) such
registration statement as so amended (including any Rule 462(b) registration
statement). The term Prospectus as used in this Agreement shall mean the
prospectus relating to the Stock first filed with the Commission pursuant to
Rule 424(b) and Rule 430A (or if no such filing is required, as included in the
Registration Statement) and, in the event of any supplement or amendment to such
prospectus after the Effective Date, shall also mean (from and after the filing
with the Commission of such supplement or the effectiveness of such amendment)
such prospectus as so supplemented or amended. The term Preliminary Prospectus
as used in this Agreement shall mean each preliminary prospectus included in
such registration statement prior to the time it becomes effective. For the
purposes of this Agreement, all references to the Registration Statement, any
Preliminary Prospectus, the Prospectus or any amendment or supplement to any of
the foregoing shall be deemed to include the copy filed with the Commission
pursuant to EDGAR.

         The Registration Statement has been declared effective under the
Securities Act, and no post-effective amendment to the Registration Statement
has been filed as of the date of this Agreement. The Company has caused to be
delivered to you copies of each Preliminary Prospectus and has consented to the
use of such copies for the purposes permitted by the Securities Act.

         2.       REPRESENTATIONS AND WARRANTIES OF THE COMPANY AND THE SELLING 
SECURITYHOLDERS.

         (a) The Company hereby represents and warrants as follows:

         (i)      The Company has been duly incorporated and is validly existing
    as a corporation in good standing under the laws of the jurisdiction of its
    incorporation, has full corporate power and authority to own or lease its
    properties and conduct its business as described in the Registration
    Statement and the Prospectus and as being conducted, and is duly qualified
    as a foreign corporation and in good standing in all jurisdictions in which
    the character of the property owned or leased or the nature of the business
    transacted by it makes qualification necessary (except where the failure to
    be so qualified would not have a material adverse effect on the business,
    properties, financial condition or results of operations of the Company).


<PAGE>   3
                                      -3-


         (ii)     Since the respective dates as of which information is given in
    the Registration Statement and the Prospectus, there has not been any
    material adverse change, or any development for which the Company has a
    reasonable basis to believe may result in a prospective material adverse
    change, in the business, properties, financial condition or results of
    operations of the Company, whether or not arising from transactions in the
    ordinary course of business, other than as set forth in the Registration
    Statement and the Prospectus, and since such dates, except in the ordinary
    course of business, the Company has not entered into any material
    transaction not referred to in the Registration Statement and the
    Prospectus.

         (iii)    The Registration Statement and the Prospectus comply, and on
    the Closing Date (as hereinafter defined) and any later date on which Option
    Stock is to be purchased, the Prospectus will comply as to form, in all
    material respects, with the provisions of the Securities Act and the rules
    and regulations of the Commission thereunder. On the Effective Date, the
    Registration Statement did not contain any untrue statement of a material
    fact and did not omit to state any material fact required to be stated
    therein or necessary in order to make the statements therein not misleading;
    on the Effective Date, the Prospectus did not and, on the Closing Date and
    any later date on which Option Stock is to be purchased, will not, contain
    any untrue statement of a material fact or omit to state any material fact
    necessary in order to make the statements therein, in the light of the
    circumstances under which they were made, not misleading; and each of the
    Prospectus and any amendments or supplements thereto delivered to you for
    use in connection with the offering of the Stock is identical to the
    electronically transmitted copies thereof filed with the Commission pursuant
    to EDGAR, except to the extent permitted by Regulation S-T; provided,
    however, that none of the representations and warranties in this
    subparagraph (c) shall apply to statements in, or omissions from, the
    Registration Statement or the Prospectus made in reliance upon and in
    conformity with information herein or otherwise furnished in writing to the
    Company by or on behalf of the Underwriters expressly for use in the
    Registration Statement or the Prospectus.

         (iv)     The Stock is duly and validly authorized, will be, when issued
    and sold to the Underwriters as provided herein, duly and validly issued,
    fully paid and nonassessable and conforms to the description thereof in the
    Prospectus. No further approval or authority of the stockholders or the
    Board of Directors of the Company will be required for the issuance and sale
    of the Stock as contemplated herein.

         (v)      The Stock to be sold by the Company has been duly authorized
    for listing on the Nasdaq National Market, subject to official notice of
    issuance. The Stock to be sold by the Selling Securityholders is listed and
    duly admitted to trading on the Nasdaq National Market.

         (vi)     Except as set forth in the Prospectus, to the best of the
   Company's knowledge, the Company now holds, and on the Closing Date and any
   later date on which Option Stock is to be purchased will hold, all material
   licenses, certificates and permits from state, federal and other regulatory
   authorities which are necessary for the conduct of the business of the
   Company as currently conducted; the Company is not in violation of its
   corporate charter or by-laws, or in default in the performance or observance
   of any provision of any obligation, agreement, covenant or condition
   contained in any contract, indenture, mortgage, loan 



<PAGE>   4
                                      -4-

    agreement, joint venture or other agreement or instrument which is an
    exhibit to the Registration Statement and to which it is a party or by which
    it or any of its properties is bound or, to the best of the Company's
    knowledge, in violation of any law, order, rule, regulation, writ,
    injunction or decree of any government, governmental instrumentality or
    court, domestic or foreign statute or any order, rule or regulation of any
    court or governmental agency or body having jurisdiction over the Company or
    over the properties of the Company, which violation or default would have a
    Material Adverse Effect.

         (vii)    The Company owns, or possesses adequate rights to use and
   sublicense, all patents, patent rights, inventions, trade secrets, licenses,
   know-how, proprietary techniques, including processes, trademarks, service
   marks, trade names, copyrights and other intellectual property described or
   referred to in the Registration Statement and the Prospectus as owned or used
   by it or, except as set forth in the Prospectus, which are necessary for the
   conduct of its business as now conducted and as described in the Registration
   Statement and the Prospectus. All such patents, patent rights, licenses,
   trademarks, service marks and copyrights are (i) valid and enforceable and
   (ii) not being infringed by any third parties which infringement could,
   whether singly or in the aggregate, materially and adversely affect the
   business, properties, operations, condition (financial or otherwise), results
   of operations, income or business prospects of the Company, as presently
   being conducted or as proposed to be conducted in the Prospectus. Except as
   set forth in the Prospectus, the Company has no knowledge of, nor has it
   received any notice of, infringement of or conflict with asserted rights of
   others with respect to any patents, patent rights, inventions, trade secrets,
   licenses, know-how, proprietary techniques, including processes and
   substances, trademarks, service marks, trade names, copyrights or other
   intellectual property which, singly or in the aggregate, is, or is reasonably
   likely to be, the subject of an unfavorable decision, ruling or finding that
   could have a material adverse effect on the business, properties, financial
   condition or results of operations of the Company.

         (viii)   The authorized and outstanding shares of capital stock of the
   Company are as set forth in the Prospectus under the caption "Description of
   Capital Stock" provided that the outstanding shares shall have increased by
   the number of shares as have been issued after December 31, 1996 and prior to
   the Closing Date pursuant to the exercise of options granted under the
   Company's Amended and Restated 1994 Equity Incentive Plan and the 1996
   Employee Stock Purchase Plan and the 1996 Director Stock Option Plan (herein
   called the Option Plans). The Company has no subsidiaries. On the Closing
   Date the capital stock of the Company will conform to the description thereof
   in the Registration Statement under the caption "Description of Capital
   Stock". There are no outstanding options, warrants or other rights granted to
   or by the Company to purchase shares of Common Stock or other securities of
   the Company, or any subsidiary, other than as set forth herein or described
   in the Prospectus. To the best knowledge of the Company, no such option,
   warrant or other right has been granted to any person, the exercise of which
   would cause such person to own more than five percent of the Common Stock
   outstanding immediately after the offering other than as described in the
   Prospectus. No person or entity holds a right to require or participate in a
   registration under the Securities Act of shares of Common Stock of the
   Company which right has not been waived by the holder thereof as of the date
   hereof with respect to the registration of shares pursuant to the
   Registration Statement. Except as set forth in the Prospectus, no person
   holds a right to require registration under the Securities Act of shares of
   Common Stock of the Company at any other 


<PAGE>   5
                                      -5-

    time. Except for rights terminating upon the consummation of the offering of
    the Stock, no person or entity has a right of first refusal or participation
    with respect to the sale of shares of the Stock by the Company.

         (ix)     The financial statements of the Company, together with related
   notes and schedules as set forth in the Registration Statement, present
   fairly the financial position, results of operations and cash flows of the
   Company at the indicated dates and for the indicated periods. Such financial
   statements have been prepared in accordance with generally accepted
   accounting principles consistently applied throughout the periods involved,
   and all adjustments necessary for a fair presentation of results for such
   periods have been made. The summary financial and other data included in the
   Registration Statement present fairly the information shown therein and have
   been compiled on a basis consistent with the financial statements presented
   therein.

         (x)      Price Waterhouse LLP, which has certified certain of the
    financial statements filed with the Commission as part of the Registration
    Statement, are independent public accountants as required by the Securities
    Act and the Rules and Regulations thereunder.

         (xi)     The Company confirms as of the date hereof that it is in
   compliance with all provisions of Section 1 of laws of Florida, Chapter
   92-198, An Act Relating to Disclosure of Doing Business with Cuba, and the
   Company further agrees that if it commences engaging in business with the
   government of Cuba or with any person or affiliate located in Cuba after the
   date the Registration Statement becomes or has become effective with the
   Commission or with the Florida Department of Banking and Finance (the
   "Department"), whichever date is later, or if the information reported or
   incorporated by reference in the Prospectus, if any, concerning the Company's
   business with Cuba or with any person or affiliate located in Cuba changes in
   any material way, the Company will provide the Department notice of such
   business or change, as appropriate, in a form acceptable to the Department.

         (xii)    The Company is familiar with the Investment Company Act of
    1940, as amended, and has in the past conducted its affairs in such a manner
    to ensure that the Company was not and is not an "investment company" or a
    company "controlled" by an "investment company" within the meaning of the
    Investment Company Act of 1940, as amended, and the rules and regulations
    thereunder.

         (xiii)   Except as set forth in the Prospectus, there are no legal or
governmental proceedings pending to which the Company is a party or to which any
property or assets of the Company is the subject which, if determined adversely
to the Company, might have a material adverse effect on the business,
properties, financial conditions or results of operations of the Company; and to
the best of the Company's knowledge, except as set forth in the Prospectus, no
such proceedings are threatened or contemplated by governmental authorities or
threatened by others.

         (b)      Each of the Selling Securityholders, severally and not 
jointly, hereby represents and warrants as follows:


<PAGE>   6
                                      -6-

                  (i)      The Selling Securityholder has good and marketable
    title to all of the shares of Stock to be sold by such Selling
    Securityholder hereunder, free and clear of all liens, encumbrances,
    restrictions on transfer (other than the restrictions imposed by any
    "lock-up" agreements contemplated herein), equities, security interests and
    claims whatsoever, with full right and authority to deliver the same
    hereunder, subject in the case of each Selling Securityholder, to the rights
    of the Company, as Custodian (herein called the Custodian), and that upon
    the delivery of and payment for such shares of the Stock hereunder, the
    several Underwriters will receive good and marketable title thereto, free
    and clear of all liens, encumbrances, restrictions on transfer, equities,
    security interests and claims whatsoever.

                  (ii)     Certificates in negotiable form for the shares of the
    Stock to be sold by such Selling Securityholder have been placed in custody
    under a Custody Agreement and Power of Attorney (hereinafter called the
    Custody Agreement) for delivery under this Agreement with the Custodian;
    such Selling Securityholder specifically agrees that the shares of the Stock
    represented by the certificates so held in custody for such Selling
    Securityholder are subject to the interests of the several Underwriters and
    the Company, that the arrangements made by such Selling Securityholder for
    such custody, including the Power of Attorney provided for in such Custody
    Agreement, are to that extent irrevocable, and that the obligations of such
    Selling Securityholder with respect to the shares of Stock to be sold shall
    not be terminated by any act of such Selling Securityholder or by operation
    of law, whether by the death or incapacity of such Selling Securityholder
    (or, in the case of a Selling Securityholder that is not an individual, the
    dissolution or liquidation of such Selling Securityholder) or the occurrence
    of any other event; if any such death, incapacity, dissolution, liquidation
    or other such event should occur before the delivery of such shares of the
    Stock hereunder, certificates for such shares of the Stock shall be
    delivered by the Custodian in accordance with the terms and conditions of
    this Agreement as if such death, incapacity, dissolution, liquidation or
    other event had not occurred, regardless of whether the Custodian shall have
    received notice of such death, incapacity, dissolution, liquidation or other
    event.

         (c)      Each of Joseph C. Hogan, Jr., Gregory Petsko, Ph.D., Dagmar
    Ringe, Ph.D. and William R. Roush, Ph.D., in their capacity as Selling
    Securityholders, severally and not jointly, represents and warrants that the
    representations and warranties of the Company set forth in subparagraph
    (iii) of paragraph 2(a) above are true and correct and that, to their
    knowledge, the representations and warranties of the Company set forth in
    subparagraphs (i) and (ii) and (iv)-(xii) of paragraph 2(a) above are true
    and correct.

         (d)      Robert Dishman, in his capacity as a Selling Securityholder,
    represents and warrants that the information furnished by him to the Company
    for inclusion in the Registration Statement and Prospectus, consisting of
    the information provided by him in the section of the Prospectus called
    "Principal and Selling Stockholders," do not contain any untrue statement of
    a material fact and do not omit to state any material fact required to be
    stated therein or necessary in order to make the statements therein not
    misleading.


<PAGE>   7
                                      -7-


         3.       PURCHASE OF THE STOCK BY THE UNDERWRITERS.

         (a)      On the basis of the representations and warranties and subject
to the terms and conditions herein set forth, the Company agrees to issue and
sell 1,632,500 shares of the Underwritten Stock to the several Underwriters,
each Selling Securityholder agrees to sell to the several Underwriters the
number of shares of the Underwritten Stock set forth in SCHEDULE II opposite the
name of such Selling Securityholder, and each of the Underwriters agrees to
purchase from the Company and the Selling Securityholders the respective
aggregate number of shares of Underwritten Stock set forth opposite its name in
SCHEDULE I. The price at which such shares of Underwritten Stock shall be sold
by the Company and the Selling Securityholders and purchased by the several
Underwriters shall be $_____ per share. The obligation of each Underwriter to
each of the Company and the Selling Securityholders shall be to purchase from
each of the Company and the Selling Securityholders that number of shares of the
Underwritten Stock which represents the same proportion of the total number of
shares of the Underwritten Stock to be sold by each of the Company and the
Selling Securityholders pursuant to this Agreement as the number of shares of
the Underwritten Stock set forth opposite the name of such Underwriter in
SCHEDULE I hereto represents of the total number of shares of the Underwritten
Stock to be purchased by all Underwriters pursuant to this Agreement, as
adjusted by you in such manner as you deem advisable to avoid fractional shares.
In making this Agreement, each Underwriter is contracting severally and not
jointly; except as provided in paragraphs (b) and (c) of this Section 3, the
agreement of each Underwriter is to purchase only the respective number of
shares of the Underwritten Stock specified in SCHEDULE I.

         (b)      If for any reason one or more of the Underwriters shall fail
or refuse (otherwise than for a reason sufficient to justify the termination of
this Agreement under the provisions of Section 8 or 9 hereof) to purchase and
pay for the number of shares of the Stock agreed to be purchased by such
Underwriter or Underwriters, the Company or the Selling Securityholders shall
immediately give notice thereof to you, and the non-defaulting Underwriters
shall have the right within 24 hours after the receipt by you of such notice to
purchase, or procure one or more other Underwriters to purchase, in such
proportions as may be agreed upon between you and such purchasing Underwriter or
Underwriters and upon the terms herein set forth, all or any part of the shares
of the Stock which such defaulting Underwriter or Underwriters agreed to
purchase. If the non-defaulting Underwriters fail so to make such arrangements
with respect to all such shares and portion, the number of shares of the Stock
which each non-defaulting Underwriter is otherwise obligated to purchase under
this Agreement shall be automatically increased on a pro rata basis to absorb
the remaining shares and portion which the defaulting Underwriter or
Underwriters agreed to purchase; provided, however, that the non-defaulting
Underwriters shall not be obligated to purchase the shares and portion which the
defaulting Underwriter or Underwriters agreed to purchase if the aggregate
number of such shares of the Stock exceeds 10% of the total number of shares of
the Stock which all Underwriters agreed to purchase hereunder. If the total
number of shares of the Stock which the defaulting Underwriter or Underwriters
agreed to purchase shall not be purchased or absorbed in accordance with the two
preceding sentences, the Company and the Selling Securityholders shall have the
right, within 24 hours next succeeding the 24-hour period above referred to, to
make arrangements with other underwriters or purchasers satisfactory to you for
purchase of such shares and portion on the 

<PAGE>   8
                                      -8-

terms herein set forth. In any such case, either you or the Company and the
Selling Securityholders shall have the right to postpone the Closing Date
determined as provided in Section 5 hereof for not more than seven business days
after the date originally fixed as the Closing Date pursuant to said Section 5
in order that any necessary changes in the Registration Statement, the
Prospectus or any other documents or arrangements may be made. If neither the
non-defaulting Underwriters nor the Company and the Selling Securityholders
shall make arrangements within the 24-hour periods stated above for the purchase
of all the shares of the Stock which the defaulting Underwriter or Underwriters
agreed to purchase hereunder, this Agreement shall be terminated without further
act or deed and without any liability on the part of the Company or the Selling
Securityholders to any non-defaulting Underwriter and without any liability on
the part of any non-defaulting Underwriter to the Company or the Selling
Securityholders. Nothing in this paragraph (b), and no action taken hereunder,
shall relieve any defaulting Underwriter from liability in respect of any
default of such Underwriter under this Agreement.

         (c)      On the basis of the representations, warranties and covenants
herein contained and subject to the terms and conditions herein set forth, the
Company hereby grants an option to the several Underwriters to purchase the
Option Stock at the same price per share as the Underwriters shall pay for the
Underwritten Stock. Said option may be exercised only to cover over-allotments
in the sale of the Underwritten Stock by the Underwriters and may be exercised
in whole or in part at any time (but not more than once) on or before the
thirtieth day after the date of this Agreement upon written or telegraphic
notice by you to the Company setting forth the aggregate number of shares of the
Option Stock as to which the several Underwriters are exercising the option.
Delivery of certificates for the shares of Option Stock, and payment therefor,
shall be made as provided in Section 5 hereof. The number of shares of the
Option Stock to be purchased by each Underwriter shall be the same percentage of
the total number of shares of the Option Stock to be purchased by the several
Underwriters as such Underwriter is purchasing of the Underwritten Stock, as
adjusted by you in such manner as you deem advisable to avoid fractional shares.

         4.       OFFERING BY UNDERWRITERS.

         (a)      The terms of the initial public offering by the Underwriters
of the Stock to be purchased by them shall be as set forth in the Prospectus.
The Underwriters may from time to time change the public offering price after
the closing of the initial public offering and increase or decrease the
concessions and discounts to dealers as they may determine.

         (b)      The information set forth in the last paragraph on the front
cover page, the first two paragraphs on the inside front cover and under
"Underwriting" in the Registration Statement, any Preliminary Prospectus and the
Prospectus relating to the Stock filed by the Company (insofar as such
information relates to the Underwriters) constitutes the only information
furnished by the Underwriters to the Company for inclusion in the Registration
Statement, any Preliminary Prospectus, and the Prospectus, and you on behalf of
the respective Underwriters represent and warrant to the Company that the
statements made therein are correct.



<PAGE>   9
                                      -9-

         5.       DELIVERY OF AND PAYMENT FOR THE STOCK.

         (a)      Delivery of certificates for the shares of the Underwritten
Stock and the Option Stock (if the option granted by Section 3(c) hereof shall
have been exercised not later than 7:00 A.M., San Francisco time, on the date
two business days preceding the Closing Date), and payment therefor, shall be
made at the office of Palmer & Dodge LLP, One Beacon Street, Boston, MA 02108,
at 7:00 a.m., San Francisco time, on the third business day after the date of
this Agreement, or at such time on such other day, not later than seven full
business days after such third business day, as shall be agreed upon in writing
by the Company, the Selling Securityholders and you. The date and hour of such
delivery and payment (which may be postponed as provided in Section 3(b) hereof)
are herein called the Closing Date.

         (b)      If the option granted by Section 3(c) hereof shall be
exercised after 7:00 a.m., San Francisco time, on the date two business days
preceding the Closing Date, delivery of certificates for the shares of Option
Stock, and payment therefor, shall be made at the office of Palmer & Dodge LLP,
One Beacon Street, Boston, MA 02108, at 7:00 a.m., San Francisco time, on the
third business day after the exercise of such option.

         (c)      Payment for the Stock purchased from the Company shall be made
to the Company or its order, and payment for the Stock purchased from the
Selling Securityholders shall be made to the Custodian, for the account of the
Selling Securityholders, in each case by wire transfer or one or more certified
or official bank check or checks in same day funds. Such payment shall be made
upon delivery of certificates for the Stock to you for the respective accounts
of the several Underwriters against receipt therefor signed by you. Certificates
for the Stock to be delivered to you shall be registered in such name or names
and shall be in such denominations as you may request at least one business day
before the Closing Date, in the case of Underwritten Stock, and at least one
business day prior to the purchase thereof, in the case of the Option Stock.
Such certificates will be made available to the Underwriters for inspection,
checking and packaging at the offices of Lewco Securities Corporation, 2
Broadway, New York, New York 10004 on the business day prior to the Closing Date
or, in the case of the Option Stock, by 3:00 p.m., New York time, on the
business day preceding the date of purchase.

         It is understood that you, individually and not on behalf of the
Underwriters, may (but shall not be obligated to) make payment to the Company
and the Selling Securityholders for shares to be purchased by any Underwriter
whose check shall not have been received by you on the Closing Date or any later
date on which Option Stock is purchased for the account of such Underwriter. Any
such payment by you shall not relieve such Underwriter from any of its
obligations hereunder.


         6.       FURTHER AGREEMENTS OF THE COMPANY AND THE SELLING 
SECURITYHOLDERS. Each of the Company and, to the extent set forth in subsections
(i) and (l), the Selling Securityholders respectively covenants and agrees as
follows:

         (a)      The Company will (i) to the extent necessary prepare and
timely file with the Commission under Rule 424(b) a Prospectus containing
information previously omitted at the 


<PAGE>   10
                                      -10-

time of effectiveness of the Registration Statement in reliance on Rule 430A and
(ii) not file any amendment to the Registration Statement or supplement to the
Prospectus of which you shall not previously have been advised and furnished
with a copy or to which you shall have reasonably objected in writing or which
is not in compliance with the Securities Act or the rules and regulations of the
Commission.

         (b)    The Company will promptly notify each Underwriter in the event 
of (i) the request by the Commission for amendment of the Registration
Statement or for supplement to the Prospectus or for any additional
information, (ii) the issuance by the Commission of any stop order suspending
the effectiveness of the Registration Statement, (iii) the institution or
notice of intended institution of any action or proceeding for that purpose,
(iv) the receipt by the Company of any notification with respect to the
suspension of the qualification of the  Stock for sale in any jurisdiction, or
(v) the receipt by it of notice of the initiation or threatening of any
proceeding for such purpose. The Company and the Selling Securityholders will
make every reasonable effort to prevent the issuance of such a stop order and,
if such an order shall at any time be issued, to obtain the withdrawal thereof
at the earliest possible moment.

         (c)    The Company will (i) on or before the Closing Date, deliver to 
you a signed copy of the Registration Statement as originally filed and of each
amendment thereto filed prior to the time the Registration Statement becomes
effective and, promptly upon the filing thereof, a signed copy of each
post-effective amendment, if any, to the Registration Statement (together with,
in each case, all exhibits thereto unless previously furnished to you) and will
also deliver to you, for distribution to the Underwriters, a sufficient number
of additional conformed copies of each of the foregoing (but without exhibits)
so that one copy of each may be distributed to each Underwriter, (ii) as
promptly as possible deliver to you and send to the several Underwriters, at
such office or offices as you may designate, as many copies of the Prospectus as
you may reasonably request, and (iii) thereafter from time to time during the
period in which a prospectus is required by law to be delivered by an
Underwriter or dealer, likewise send to the Underwriters as many additional
copies of the Prospectus and as many copies of any supplement to the Prospectus
and of any amended prospectus, filed by the Company with the Commission, as you
may reasonably request for the purposes contemplated by the Securities Act. The
Registration Statement, the Prospectus and any amendments or supplements thereto
furnished to you will be identical to the electronically transmitted copies
thereof filed with the Commission pursuant to EDGAR, except to the extent
permitted by Regulation S-T.

         (d)    If at any time during the period in which a prospectus is 
required by law to be delivered by an Underwriter or dealer any event relating 
to or affecting the Company, or of which the Company shall be advised in 
writing by you, shall occur as a result of which it is necessary, in the 
opinion of counsel for the Company or of counsel for the Underwriters, to
supplement or amend the Prospectus in order to make the Prospectus not
misleading in the light of the circumstances existing at the time it is
delivered to a purchaser of the Stock, the Company will forthwith prepare and
file with the Commission a supplement to the Prospectus or an amended
prospectus so that the Prospectus as so supplemented or amended will not
contain any untrue statement of a material fact or omit to state any material
fact necessary in order to make the statements therein, in the light of the
circumstances existing at the time such Prospectus is delivered to such
purchaser, not misleading. If, after the initial public offering of the Stock
by 


<PAGE>   11
                                      -11-

the Underwriters and during such period, the Underwriters shall propose to vary
the terms of offering thereof by reason of changes in general market conditions
or otherwise, you will advise the Company in writing of the proposed variation,
and, if in the opinion either of counsel for the Company or of counsel for the
Underwriters such proposed variation requires that the Prospectus be
supplemented or amended, the Company will forthwith prepare and file with the
Commission a supplement to the Prospectus or an amended prospectus setting forth
such variation. The Company authorizes the Underwriters and all dealers to whom
any of the Stock may be sold by the several Underwriters to use the Prospectus,
as from time to time amended or supplemented, in connection with the sale of the
Stock in accordance with the applicable provisions of the Securities Act and the
applicable rules and regulations thereunder for such period.

         (e)     Prior to the filing thereof with the Commission, the Company
will submit to you, for your information, a copy of any post-effective amendment
to the Registration Statement and any supplement to the Prospectus or any
amended prospectus proposed to be filed.

         (f)     The Company will cooperate, when and as requested by you, in
the qualification of the Stock for offer and sale under the securities or blue
sky laws of such jurisdictions as you may designate and, during the period in
which a prospectus is required by law to be delivered by an Underwriter or
dealer, in keeping such qualifications in good standing under said securities or
blue sky laws; provided, however, that the Company shall not be obligated to
file any general consent to service of process or to qualify as a foreign
corporation in any jurisdiction in which it is not so qualified. The Company
will, from time to time, prepare and file such statements, reports, and other
documents as are or may be required to continue such qualifications in effect
for so long a period as you may reasonably request for distribution of the
Stock.

         (g)     During a period of five years commencing with the date hereof,
the Company will furnish to you, and to each Underwriter who may so request in
writing, copies of all periodic and special reports, documents or statements
furnished to stockholders of the Company or filed with the Commission. If
applicable, any such document furnished to you will be identical to the
electronically transmitted copy thereof filed with the Commission pursuant to
EDGAR, except to the extent permitted by Regulation S-T.

         (h)     Not later than the 45th day following the end of the fiscal
quarter first occurring after the first anniversary of the Effective Date, the
Company will make generally available to its stockholders an earnings statement
in accordance with Section 11(a) of the Securities Act and Rule 158 thereunder.

         (i)     The Company agrees to pay all costs and expenses incident to
the performance of the obligations of the Company and the Selling
Securityholders under this Agreement, including all costs and expenses incident
to (i) the preparation, printing and filing with the Commission and the National
Association of Securities Dealers, Inc. ("NASD") of the Registration Statement,
any Preliminary Prospectus and the Prospectus, (ii) the furnishing to the
Underwriters of copies of any Preliminary Prospectus and of the several
documents required by paragraph (c) of this Section 6 to be so furnished, (iii)
the photocopying of this Agreement and related documents delivered to the
Underwriters, (iv) the preparation, printing and filing of all supplements and
amendments to the Prospectus referred to in paragraph (d) of this Section 6, (v)
the furnishing to 

<PAGE>   12
                                      -12-

you and the Underwriters of the reports and information referred to in paragraph
(g) of this Section 6 and (vi) the printing and issuance of stock certificates,
including the transfer agent's fees. Each of the Selling Securityholders will
pay any transfer taxes incident to the transfer to the Underwriters of the
shares of Stock being sold by such Selling Securityholder.

         (j)    The Company agrees to reimburse you, for the account of the 
several Underwriters, for fees and related disbursements (including counsel
fees and disbursements and cost of printing memoranda for the Underwriters)
paid by or for the account of the Underwriters or their counsel in
qualifying the Stock under state securities or blue sky laws and in the review
of the offering by the NASD.

         (k)    The provisions of paragraphs (i) and (j) of this Section are
intended to relieve the Underwriters from the payment of the expenses and costs
which the Company hereby agrees to pay and shall not affect any agreement which
the Company and the Selling Securityholders may make, or may have made, for the
sharing of any such expenses and costs.

         (l)    The Company and each of the Selling Securityholders hereby 
agrees that, without the prior written consent of Hambrecht & Quist LLC on 
behalf of the Underwriters, it will not, for a period of 90 days following the
effective date of the Registration Statement, (i) sell, offer, contract to
sell, make any  short sale, pledge, transfer or otherwise dispose of, directly
or indirectly, any shares of Common Stock (including any stock appreciation
right or similar right with an exercise or conversion privilege at a price
related to, or derived from the market price of the Common Stock) or any
securities convertible into or exchangeable or exercisable for shares of Common
Stock owned directly by the undersigned or with respect to which the
undersigned has the power of disposition (including, without limitation, shares
of Common Stock which the undersigned may be deemed to beneficially own in
accordance with the rules and regulations promulgated under the Securities and
Exchange Act of 1934, as amended), or (ii) engage in any hedging transaction
with respect to any shares of Common Stock that may have an impact on the
market price of the Common Stock,, whether any such transaction is to be
settled by delivery of Common Stock or such other securities, in cash or
otherwise. The foregoing sentence shall not apply to (A) the sale of Stock to
be sold to the Underwriters pursuant to this Agreement, (B) the issuance of
shares of Common Stock issued by the Company upon the exercise of options
granted under the Option Plans, and (C) the grant of options to purchase Common
Stock under the Option Plans.

         (m)    If at any time during the 25-day period after the Registration
Statement becomes effective any rumor, publication or event relating to or
affecting the Company shall occur as a result of which in your reasonable
opinion the market price for the Stock has been or is likely to be materially
affected (regardless of whether such rumor, publication or event necessitates a
supplement to or amendment of the Prospectus), the Company will, after written
notice from you advising the Company to the effect set forth above, forthwith
prepare, consult with you concerning the substance of, and disseminate a press
release or other public statement, reasonably satisfactory to you, responding to
or commenting on such rumor, publication or event.


<PAGE>   13
                                      -13-

         (n)      The Company will in the future conduct its affairs in such a
manner to ensure that the Company will not be an "investment company" or a
company "controlled" by an "investment company" within the meaning of the
Investment Company Act of 1940, as amended, and the rules and regulations
thereunder.

         7.       INDEMNIFICATION AND CONTRIBUTION.

         (a)      Subject to the provisions of paragraph (f) of this Section 7,
the Company and the Selling Securityholders jointly and severally agree to
indemnify and hold harmless each Underwriter and each person (including each
partner or officer thereof) who controls any Underwriter within the meaning of
Section 15 of the Securities Act from and against any and all losses, claims,
damages or liabilities, joint or several, to which such indemnified parties or
any of them may become subject under the Securities Act, the Securities Exchange
Act of 1934, as amended (herein called the Exchange Act), or the common law or
otherwise, and the Company and the Selling Securityholders jointly and severally
agree to reimburse each such Underwriter and controlling person for any legal or
other expenses (including, except as otherwise hereinafter provided, reasonable
fees and disbursements of a single counsel for all indemnified parties) incurred
by the respective indemnified parties in connection with defending against any
such losses, claims, damages or liabilities or in connection with any
investigation or inquiry of, or other proceeding which may be brought against,
the respective indemnified parties, in each case arising out of or based upon
(i) any untrue statement or alleged untrue statement of a material fact
contained in the Registration Statement (including the Prospectus as part
thereof and any Rule 462(b) registration statement) or any post-effective
amendment thereto (including any Rule 462(b) registration statement) or the
omission or alleged omission to state therein a material fact required to be
stated therein or necessary to make the statements therein not misleading, or
(ii) any untrue statement or alleged untrue statement of a material fact
contained in any Preliminary Prospectus or the Prospectus (as amended or as
supplemented if the Company shall have filed with the Commission any amendment
thereof or supplement thereto) or the omission or alleged omission to state
therein a material fact necessary in order to make the statements therein, in
the light of the circumstances under which they were made, not misleading;
provided, however, that (1) the indemnity agreements of the Company and the
Selling Securityholders contained in this paragraph (a) shall not apply to any
such losses, claims, damages, liabilities or expenses if such statement or
omission was made in reliance upon and in conformity with information furnished
as herein stated or otherwise furnished in writing to the Company by or on
behalf of any Underwriter for use in any Preliminary Prospectus or the
Registration Statement or the Prospectus or any such amendment thereof or
supplement thereto, (2) the indemnity agreement contained in this paragraph (a)
with respect to any Preliminary Prospectus shall not inure to the benefit of any
Underwriter from whom the person asserting any such losses, claims, damages,
liabilities or expenses purchased the Stock which is the subject thereof (or to
the benefit of any person controlling such Underwriter) if at or prior to the
written confirmation of the sale of such Stock a copy of the Prospectus (or the
Prospectus as amended or supplemented) was not sent or delivered to such person
and the untrue statement or omission of a material fact contained in such
Preliminary Prospectus was corrected in the Prospectus (or the Prospectus as
amended or supplemented) unless the failure is the result of noncompliance by
the Company with paragraph (c) of Section 6 hereof, and (3) Robert Dishman, in
his capacity as a Selling Securityholder, shall only be liable under this
paragraph with respect to information pertaining to Mr. Dishman 

<PAGE>   14
                                      -14-


furnished by or on behalf of Mr. Dishman expressly for use in any Preliminary
Prospectus or the Registration Statement or the Prospectus or any such amendment
thereof or supplement thereto. The indemnity agreements of the Company and the
Selling Securityholders contained in this paragraph (a) and the representations
and warranties of the Company and the Selling Securityholders contained in
Section 2 hereof shall remain operative and in full force and effect regardless
of any investigation made by or on behalf of any indemnified party and shall
survive the delivery of and payment for the Stock.

         (b)    Each Underwriter severally agrees to indemnify and hold harmless
the Company, each of its officers who signs the Registration Statement on his
own behalf or pursuant to a power of attorney, each of its directors, each of
the Selling Securityholders, each other Underwriter and each person (including
each partner or officer thereof) who controls the Company, any such other
Underwriter or any such Selling Securityholders, within the meaning of Section
15 of the Securities Act from and against any and all losses, claims, damages or
liabilities, joint or several, to which such indemnified parties or any of them
may become subject under the Securities Act, the Exchange Act, or the common law
or otherwise and to reimburse each of them for any legal or other expenses
(including, except as otherwise hereinafter provided, reasonable fees and
disbursements of a single counsel for all indemnified parties) incurred by the
respective indemnified parties in connection with defending against any such
losses, claims, damages or liabilities or in connection with any investigation
or inquiry of, or other proceeding which may be brought against, the respective
indemnified parties, in each case arising out of or based upon (i) any untrue
statement or alleged untrue statement of a material fact contained in the
Registration Statement (including the Prospectus as part thereof and any Rule
462(b) registration statement) or any post-effective amendment thereto
(including any Rule 462(b) registration statement) or the omission or alleged
omission to state therein a material fact required to be stated therein or
necessary to make the statements therein not misleading or (ii) any untrue
statement or alleged untrue statement of a material fact contained in the
Prospectus (as amended or as supplemented if the Company shall have filed with
the Commission any amendment thereof or supplement thereto) or the omission or
alleged omission to state therein a material fact necessary in order to make the
statements therein, in the light of the circumstances under which they were
made, not misleading, if such statement or omission was made in reliance upon
and in conformity with information furnished as herein stated or otherwise
furnished in writing to the Company by or on behalf of such indemnifying
Underwriter for use in the Registration Statement or the Prospectus or any such
amendment thereof or supplement thereto. The indemnity agreement of each
Underwriter contained in this paragraph (b) shall remain operative and in full
force and effect regardless of any investigation made by or on behalf of any
indemnified party and shall survive the delivery of and payment for the Stock.

         (c)    Each party indemnified under the provision of paragraphs (a) and
(b) of this Section 7 agrees that, upon the service of a summons or other
initial legal process upon it in any action or suit instituted against it or
upon its receipt of written notification of the commencement of any
investigation or inquiry of, or proceeding against, it in respect of which
indemnity may be sought on account of any indemnity agreement contained in such
paragraphs, it will promptly give written notice (herein called the Notice) of
such service or notification to the party or parties from whom indemnification
may be sought hereunder. No indemnification provided for in such paragraphs
shall be available to any party who shall fail so to give the Notice if the
party to 
<PAGE>   15

                                      -15-

whom such Notice was not given was unaware of the action, suit, investigation,
inquiry or proceeding to which the Notice would have related and was prejudiced
by the failure to give the Notice, but the omission so to notify such
indemnifying party or parties of any such service or notification shall not
relieve such indemnifying party or parties from any liability which it or they
may have to the indemnified party for contribution or otherwise than on account
of such indemnity agreement. Any indemnifying party shall be entitled at its own
expense to participate in the defense of any action, suit or proceeding against,
or investigation or inquiry of, an indemnified party. Any indemnifying party
shall be entitled, if it so elects within a reasonable time after receipt of the
Notice by giving written notice (herein called the Notice of Defense) to the
indemnified party, to assume (alone or in conjunction with any other
indemnifying party or parties) the entire defense of such action, suit,
investigation, inquiry or proceeding, in which event such defense shall be
conducted, at the expense of the indemnifying party or parties, by counsel
chosen by such indemnifying party or parties and reasonably satisfactory to the
indemnified party or parties; provided, however, that (i) if the indemnified
party or parties reasonably determine that there may be a conflict between the
positions of the indemnifying party or parties and of the indemnified party or
parties in conducting the defense of such action, suit, investigation, inquiry
or proceeding or that there may be legal defenses available to such indemnified
party or parties different from or in addition to those available to the
indemnifying party or parties, then counsel for the indemnified party or parties
shall be entitled to conduct the defense to the extent reasonably determined by
such counsel to be necessary to protect the interests of the indemnified party
or parties and (ii) in any event the indemnified party or parties shall be
entitled to have counsel chosen by such indemnified party or parties participate
in, but not conduct, the defense. If, within a reasonable time after receipt of
the Notice, an indemnifying party gives a Notice of Defense and the counsel
chosen by the indemnifying party or parties is reasonably satisfactory to the
indemnified party or parties(it being agreed that Palmer & Dodge LLP is
satisfactory), the indemnifying party or parties will not be liable under
paragraphs (a) through (c) of this Section 7 for any legal or other expenses
subsequently incurred by the indemnified party or parties in connection with the
defense of the action, suit, investigation, inquiry or proceeding, except that
(A) the indemnifying party or parties shall bear the, legal and other expenses
incurred in connection with the conduct of the defense as referred to in clause
(i) of the proviso to the preceding sentence and (B) the indemnifying party or
parties shall bear such other expenses as it or they have authorized to be
incurred by the indemnified party or parties. If, within a reasonable time after
receipt of the Notice, no Notice of Defense has been given, the indemnifying
party or parties shall be responsible for any legal or other expenses incurred
by the indemnified party or parties in connection with the defense of the
action, suit, investigation, inquiry or proceeding.

         (d)    If the indemnification provided for in this Section 7 is
unavailable or insufficient to hold harmless an indemnified party under
paragraph (a) or (b) of this Section 7, then each indemnifying party, in lieu of
indemnifying such indemnified party, shall contribute to the amount paid or
payable by such indemnified party as a result of the losses, claims, damages or
liabilities referred to in paragraph (a) or (b) of this Section 7 (i) in such
proportion as is appropriate to reflect the relative benefits received by each
indemnifying party from the offering of the Stock or (ii) if the allocation
provided by clause (i) above is not permitted by applicable law, in such
proportion as is appropriate to reflect not only the relative benefits referred
to in clause (i) above but also the relative fault of each indemnifying party in
connection with the 


<PAGE>   16
                                      -16-

statements or omissions that resulted in such losses, claims, damages or
liabilities, or actions in respect thereof, as well as any other relevant
equitable considerations. The relative benefits received by the Company and the
Selling Securityholders on the one hand and the Underwriters on the other shall
be deemed to be in the same respective proportions as the total net proceeds
from the offering of the Stock received by the Company and the Selling
Securityholders and the total underwriting discount received by the
Underwriters, as set forth in the table on the cover page of the Prospectus,
bear to the aggregate public offering price of the Stock. Relative fault shall
be determined by reference to, among other things, whether the untrue or alleged
untrue statement of a material fact or the omission or alleged omission to state
a material fact relates to information supplied by each indemnifying party and
the parties' relative intent knowledge, access to information and opportunity to
correct or prevent such untrue statement or omission.

         The parties agree that it would not be just and equitable if
contributions pursuant to this paragraph (d) were to be determined by pro rata
allocation (even if the Underwriters were treated as one entity for such
purpose) or by any other method of allocation which does not take into account
the equitable considerations referred to in the first sentence of this paragraph
(d). The amount paid by an indemnified party as a result of the losses, claims,
damages or liabilities, or actions in respect thereof, referred to in the first
sentence of this paragraph (d) shall be deemed to include any legal or other
expenses reasonably incurred by such indemnified party in connection with
investigating, preparing to defend or defending against any action or claim
which is the subject of this paragraph (d). Notwithstanding the provisions of
this paragraph (d), no Underwriter shall be required to contribute any amount in
excess of the underwriting discount applicable to the Stock purchased by such
Underwriter. No person guilty of fraudulent misrepresentation (within the
meaning of Section 11(f) of the Securities Act) shall be entitled to
contribution from any person who was not guilty of such fraudulent
misrepresentation. The Underwriters' obligations in this paragraph (d) to
contribute are several in proportion to their respective underwriting
obligations and not joint.

         Each party entitled to contribution agrees that upon the service of a
summons or other initial legal process upon it in any action instituted against
it in respect of which contribution may be sought, it will promptly give written
notice of such service to the party or parties from whom contribution may be
sought, but the omission so to notify such party or parties of any such service
shall not relieve the party from whom contribution may be sought from any
obligation it may have hereunder or otherwise (except as specifically provided
in paragraph (c) of this Section 7).

         (e)    Neither the Company nor the Selling Securityholders will, 
without the prior written consent of each Underwriter, settle or compromise or 
consent to the entry of any judgment in any pending or threatened claim,
action, suit or proceeding in respect of which indemnification may be sought
hereunder (whether or not such Underwriter or any person who controls such
Underwriter within the  meaning of Section 15 of the Securities Act or Section
20 of the Exchange Act is a party to such claim, action, suit or proceeding)
unless such settlement compromise or consent includes an unconditional release
of such Underwriter and each such controlling person from all liability arising
out of such claim, action, suit or proceeding.

<PAGE>   17
                                      -17-


         (f)      Except for the liability of each Selling Securityholder under
such Selling Securityholder's representations and warranties contained in
subparagraphs (b)(i) and (b)(ii) of Section 2 hereof, which liability shall not
be limited, the liability of each Selling Securityholder (other than Robert
Dishman) under such Selling Securityholder's representations and warranties
contained in paragraph (c) of Section 2 hereof, the liability of Robert Dishman
under his representations and warranties contained in paragraph (d) of Section 2
hereof, and, as to all Selling Securityholders, liability under the indemnity
and reimbursement agreements contained in the provisions of this Section 7 and
Section 11 hereof, shall be limited to an amount equal to the proceeds of the
sale of the stock received by such Selling Securityholder from the Underwriters.
provided, however, no Selling Securityholder shall be required to provide
indemnification hereunder until such Underwriter seeking indemnification shall
have first exhausted all remedies against the Company. The Company and the
Selling Securityholders may agree, as among themselves and without limiting the
rights of the Underwriters under this Agreement, as to the respective amounts of
such liability for which they each shall be responsible.

         8.       TERMINATION. This Agreement may be terminated by you at any
time prior to the Closing Date by giving written notice to the Company if after
the date of this Agreement trading in the Common Stock shall have been
suspended, or if there shall have occurred (i) the engagement in hostilities or
an escalation of major hostilities by the United States or the declaration of
war or a national emergency by the United States on or after the date hereof,
(ii) any outbreak of hostilities or other national or international calamity or
crisis or change in economic or political conditions if the effect of such
outbreak, calamity, crisis or change in economic or political conditions in the
financial markets of the United States would, in the Underwriters' reasonable
judgment, make the offering or delivery of the Stock impracticable, (iii)
suspension of trading in securities generally or a material adverse decline in
value of securities generally on the New York Stock Exchange, the American Stock
Exchange, or The Nasdaq Stock Market or limitations on prices (other than
limitations on hours or numbers of days of trading) for securities on either
such exchange or system, (iv) the enactment, publication, decree or other
promulgation of any federal or state statute, regulation, rule or order of, or
commencement of any proceeding or investigation by, any court, legislative body,
agency or other governmental authority which in the Underwriters' reasonable
opinion materially and adversely affects or will materially or adversely affect
the business or operations of the Company, (v) declaration of a banking
moratorium by either federal or New York State authorities or (vi) the taking of
any action by any federal, state or local government or agency in respect of its
monetary or fiscal affairs which in the Underwriters' reasonable opinion has a
material adverse effect on the securities markets in the United States. If this
Agreement shall be terminated pursuant to this Section 8, there shall be no
liability of the Company or the Selling Securityholders to the Underwriters and
no liability of the Underwriters to the Company or the Selling Securityholders;
provided, however, that in the event of any such termination the Company agrees
to indemnify and hold harmless the Underwriters from all actual, accountable,
out-of-pocket costs and expenses incident to the performance of the obligations
of the Company and the Selling Securityholders under this Agreement, including
all actual, accountable, out-of-pocket costs and expenses referred to in
paragraphs (i) and (j) of Section 6 hereof.

<PAGE>   18
                                      -18-

         9.     CONDITIONS OF UNDERWRITERS' OBLIGATIONS. The obligations of
the several Underwriters to purchase and pay for the Stock shall be subject to
the performance by the Company and by the Selling Securityholders of all their
respective obligations to be performed hereunder at or prior to the Closing Date
or any later date on which Option Stock is to be purchased, as the case may be,
and to the following further conditions:

         (a)    The Registration Statement shall have become effective; and no 
stop order suspending the effectiveness thereof shall have been issued and no
proceedings therefor shall be pending or threatened by the Commission.

         (b)    The legality and sufficiency of the sale of the Stock hereunder 
and the validity and form of the certificates representing the Stock,
all corporate proceedings and other legal matters incident to the foregoing,
and the form of the Registration Statement and of the Prospectus (except as to
the financial statements contained therein), shall have been approved at or
prior to the Closing Date by Testa, Hurwitz & Thibeault, LLP, counsel for the
Underwriters.

         (c)    You shall have received from Palmer & Dodge LLP, counsel for the
Company and the Selling Securityholders, an opinion, addressed to the
Underwriters and dated the Closing Date, covering the matters set forth in Annex
A hereto, and if Option Stock is purchased at any date after the Closing Date,
additional opinions from each such counsel, addressed to the Underwriters and
dated such later date, confirming that the statements expressed as of the
Closing Date in such opinions remain valid as of such later date.

         (d)    You shall have received from Pennie & Edmonds, patent counsel 
for the Company, an opinion, addressed to the Underwriters and dated the Closing
Date, to the effect that they serve a patent counsel to the Company with respect
to the issued patents, pending and contemplated patent applications, trade
secrets and the proprietary technology that the Company owns or has rights to,
and covering the matters set forth in Annex B hereto, and if Option Stock is
purchased at any date after the Closing Date, additional opinions from such
counsel, addressed to the Underwriters and dated such later date, confirming
that the statements expressed as of the Closing Date, in such opinion remain
valid as of such later date.

         (e)    You shall be satisfied that (i) as of the Effective Date, the
statements made in the Registration Statement and the Prospectus were true and
correct in all material respects and neither the Registration Statement nor the
Prospectus omitted to state any material fact required to be stated therein or
necessary in order to make the statements therein, respectively, not misleading,
(ii) since the Effective Date, no event has occurred which should have been set
forth in a supplement or amendment to the Prospectus which has not been set
forth in such a supplement or amendment, (iii) since the respective dates as of
which information is given in the Registration Statement in the form in which it
originally became effective and the Prospectus contained therein, there has not
been any material adverse change or any development involving a prospective
material adverse change in or affecting the business, properties, financial
condition or results of operations of the Company, whether or not arising from
transactions in the ordinary course of business, and, since such dates, except
in the ordinary course of business, the Company has not entered into any
material transaction not referred to in the Registration Statement in the form
in which it originally became effective and the Prospectus contained therein,
(iv) the 

<PAGE>   19
                                      -19-


Company has no material contingent obligations which are not disclosed in the
Registration Statement and the Prospectus, (v) there are no pending or
threatened legal proceedings to which the Company is a party or of which
property of the Company is the subject which are material and which are not
disclosed in the Registration Statement and the Prospectus, (vi) there are no
franchises, contracts, leases or other documents which are required to be filed
as exhibits to the Registration Statement which have not been filed as required,
(vii) the representations and warranties of the Company and the Selling
Securityholders herein are true and correct in all material respects as of the
Closing Date and the Company and each of the Selling Securityholders have
complied with each obligation which is required to be performed on his or its
part at or prior to the Closing Date or any later date on which Option Stock is
to be purchased, as the case may be, and (viii) there has not been any material
change in the market for securities in general or in political, financial or
economic conditions from those reasonably foreseeable that would render it
impracticable in your reasonable judgment to make a public offering of the
Stock, or a material adverse change in market levels for securities in general
(or those of companies such as the Company in particular) or financial or
economic conditions which render it inadvisable to proceed.

         (f) You shall have received on the Closing Date and on any later date
on which Option Stock is purchased a certificate, dated the Closing Date or such
later date, as the case may be, and signed by the Chief Executive Officer,
President and the Chief Financial Officer of the Company, stating that the
respective signers of said certificate have carefully examined the Registration
Statement in the form in which it originally became effective and the Prospectus
contained therein and any supplements or amendments thereto, and that the
statements included in clauses (i) through (vii) of paragraph (e) of this
Section 9 are true and correct.

         (g) You shall have received from Price Waterhouse LLP a letter or
letters, addressed to the Underwriters and dated the Closing Date and any later
date on which Option Stock is purchased, confirming that they are independent
public accountants with respect to the Company within the meaning of the
Securities Act and the applicable published rules and regulations thereunder and
based upon the procedures described in their letter delivered to you
concurrently with the execution of this Agreement (herein called the Original
Letter), but carried out to a date not more than five business days prior to the
Closing Date or such later date on which Option Stock is purchased (i)
confirming, to the extent true, that the statements and conclusions set forth in
the Original Letter are accurate as of the Closing Date or such later date, as
the case may be, and (ii) setting forth any revisions and additions to the
statements and conclusions set forth in the Original Letter which are necessary
to reflect any changes in the facts described in the Original Letter since the
date of the Original Letter or to reflect the availability of more recent
financial statements, data or information. The letters shall not disclose any
change, or any development involving a prospective change, in or affecting the
business or properties of the Company or any of its subsidiaries which, in your
sole judgment makes it impractical or inadvisable to proceed with the public
offering of the Stock or the purchase of the Option Stock as contemplated by the
Prospectus.

         (h) You shall have received from Price Waterhouse LLP a letter stating
that their review of the Company's system of internal accounting controls, to
the extent they deemed necessary in establishing the scope of their examination
of the Company's financial statements as 

<PAGE>   20
                                      -20-

of December 31, 1996, did not disclose any weakness in internal controls that
they considered to be material weaknesses.

         (i)      You shall have received on the Closing Date (and, with respect
to the Selling Securityholders listed in SCHEDULE II, any later date on which
Option Stock is purchased from such Selling Securityholders) a certificate from
or on behalf of each Selling Securityholder stating that:

                  (i)      The representations and warranties made by such 
Selling Securityholder herein are true or correct in all material respects on
the Closing Date; and

                  (ii)     Such Selling Securityholder has complied with each
obligation which is required to be performed on his or its part at or prior to
the Closing Date.

         (j)      You shall have been furnished evidence in usual written or
telegraphic form from the appropriate authorities of the several jurisdictions,
or other evidence satisfactory to you, of the qualification referred to in
paragraph (f) of Section 6 hereof.

         (k)      Prior to the Closing Date, the Stock to be issued and sold by
the Company shall have been duly authorized for listing by the Nasdaq National
Market upon official notice of issuance.

         (l)      On or prior to the Closing Date, you shall have received from
all directors, officers, Selling Securityholders and beneficial holders of more
than 5% of the outstanding Common Stock, agreements, in form reasonably
satisfactory to Hambrecht & Quist LLC, stating that without the prior written
consent of Hambrecht & Quist LLC on behalf of the Underwriters, such person or
entity will not, for a period of 90 days after the effective date of the
Registration Statement, (i) sell, offer, contract to sell, make any short sale,
pledge, transfer or otherwise dispose of, directly or indirectly, any shares of
Common Stock (including any stock appreciation right or similar right with an
exercise or conversion privilege at a price related to, or derived from the
market price of the Common Stock) or any securities convertible into or
exchangeable or exercisable for shares of Common Stock owned directly by the
undersigned or with respect to which the undersigned has the power of
disposition (including, without limitation, shares of Common Stock which the
undersigned may be deemed to beneficially own in accordance with the rules and
regulations promulgated under the Securities and Exchange Act of 1934, as
amended), or (ii) engage in any hedging transaction with respect to any shares
of Common Stock that may have an impact on the market price of the Common Stock,
whether any such transaction is to be settled by delivery of Common Stock or
such other securities, in cash or otherwise.

         All the agreements, opinions, certificates and letters mentioned above
or elsewhere in this Agreement shall be deemed to be in compliance with the
provisions hereof only if Testa, Hurwitz & Thibeault, LLP, counsel for the
Underwriters, shall be reasonably satisfied that they comply in form and scope.

         In case any of the conditions specified in this Section 9 shall not be
fulfilled, this Agreement may be terminated by you by giving notice to the
Company and to the Selling 

<PAGE>   21
                                      -21-


Securityholders. Any such termination shall be without liability of the Company
or the Selling Securityholders to the Underwriters and without liability of the
Underwriters to the Company or the Selling Securityholders; provided, however,
that (i) in the event of such termination, the Company agrees to indemnify and
hold harmless the Underwriters from all actual, accountable, out-of-pocket costs
and expenses incident to the performance of the obligations of the Company and
the Selling Securityholders under this Agreement, including all actual,
accountable, out-of-pocket costs and expenses referred to in paragraphs (i) and
(j) of Section 6 hereof, and (ii) if this Agreement is terminated by you because
of any refusal, inability or failure on the part of the Company or the Selling
Securityholders to perform any agreement herein, to fulfill any of the
conditions herein, or to comply with any provision hereof other than by reason
of a default by any of the Underwriters, the Company will reimburse the
Underwriters severally upon demand for all actual, accountable, out-of-pocket
expenses (including reasonable fees and disbursements of counsel) that shall
have been incurred by them in connection with the transactions contemplated
hereby.

         10. CONDITIONS OF THE OBLIGATION OF THE COMPANY AND THE SELLING
SECURITYHOLDERS. The obligation of the Company and the Selling Securityholders
to deliver the Stock shall be subject to the conditions that (a) the
Registration Statement shall have become effective and (b) no stop order
suspending the effectiveness thereof shall be in effect and no proceedings
therefor shall be pending or threatened by the Commission.

         In case either of the conditions specified in this Section 10 shall not
be fulfilled, this Agreement may be terminated by the Company and the Selling
Securityholders by giving notice to you. Any such termination shall be without
liability of the Company and the Selling Securityholders to the Underwriters and
without liability of the Underwriters to the Company or the Selling
Securityholders; provided, however, that in the event of any such termination
the Company agrees to indemnify and hold harmless the Underwriters from all
actual, accountable, out-of-pocket costs and expenses incident to the
performance of the obligations of the Company and the Selling Securityholders
under this Agreement including all actual, accountable, out-of-pocket costs and
expenses referred to in paragraphs (i) and (j) of Section 6 hereof.

         11. REIMBURSEMENT OF CERTAIN EXPENSES. In addition to their other
obligations under Section 7 of this Agreement (and subject, in the case of a
Selling Securityholder, to the provisions of paragraph (f) of Section 7), the
Company and the Selling Securityholders hereby jointly and severally agree to
reimburse on a quarterly basis the Underwriters for all reasonable legal and
other expenses incurred in connection with investigating or defending any claim,
action, investigation, inquiry or other proceeding arising out of or based upon
any statement or omission, or any alleged statement or omission, described in
paragraph (a) of Section 7 of this Agreement, notwithstanding the absence of a
judicial determination as to the propriety and enforceability of the obligations
under this Section 11 and the possibility that such payments might later be held
to be improper; PROVIDED, HOWEVER, that (i) to the extent any such payment is
ultimately held to be improper, the persons receiving such payments shall
promptly refund them and (ii) such persons shall provide to the Company, upon
request, reasonable assurances of their ability to effect any refund, when and
if due.
<PAGE>   22
                                      -22-


         12. PERSONS ENTITLED TO BENEFIT OF AGREEMENT. This Agreement shall
inure to the benefit of the Company, the Selling Securityholders and the several
Underwriters and, with respect to the provisions of Section 7 hereof, the
several parties (in addition to the Company, the Selling Securityholders and the
several Underwriters) indemnified under the provisions of said Section 7, and
their respective personal representatives, successors and assigns. Nothing in
this Agreement is intended or shall be construed to give to any other person,
firm or corporation any legal or equitable remedy or claim under or in respect
of this Agreement or any provision herein contained. The term "successors and
assigns" as herein used shall not include any purchaser, as such, of any of the
Stock from any of the several Underwriters.

         13. NOTICES. Except as otherwise provided herein, all communications
hereunder shall be in writing or by telegraph and, if to the Underwriters, shall
be mailed, telecopied or delivered to Hambrecht & Quist LLC, One Bush Street,
San Francisco, California 94104; and if to the Company, shall be mailed,
telecopied or delivered to it at its office, 200 Boston Avenue, Medford, MA
02155, Attention: Chief Executive Officer; and if to the Selling
Securityholders, shall be mailed, telegraphed or delivered to the Selling
Securityholders in care of the Custodian at the address of the Company set forth
above. All notices given by telecopy shall be promptly confirmed by letter.

         14. DEFAULT BY SELLING SECURITYHOLDERS. If on any Closing Date any
Selling Securityholder fails to sell the Stock which such Selling Securityholder
has agreed to sell on such date as set forth in SCHEDULE II hereto, the Company
agrees that it will sell or arrange for the sale of that number of shares of
Common Stock to the Underwriters which represents the shares of Stock which such
Selling Securityholder has failed to so sell, as set forth in Schedule II
hereto, or such fewer number of shares as may be requested by the Underwriters.

         15. MISCELLANEOUS. The reimbursement indemnification and contribution
agreements contained in this Agreement and the representations, warranties and
covenants in this Agreement shall remain in full force and effect regardless of
(a) any termination of this Agreement, (b) any investigation made by or on
behalf of any Underwriter or controlling person thereof, or by or on behalf of
the Company or the Selling Securityholders or their respective directors or
officers, and (c) delivery and payment for the Stock under this Agreement;
PROVIDED. HOWEVER, that if this Agreement is terminated prior to the Closing
Date, the provisions of paragraphs (l) and (m) of Section 6 hereof shall be of
no further force or effect.

         This Agreement may be executed in two or more counterparts, each of
which shall be deemed an original, but all of which together shall constitute
one and the same instrument.

         This Agreement shall be governed by, and construed in accordance with,
the laws of the State of California.


<PAGE>   23
                                      -23-

         Please sign and return to the Company the enclosed duplicates of this
letter, whereupon this letter will become a binding agreement among the Company
and the several Underwriters in accordance with its terms.

                                Very Truly Yours,

                                ARQULE, INC.


                                By: ____________________________________________
                                    Eric B. Gordon
                                    President and Chief Executive Officer




                                SELLING SECURITYHOLDERS LISTED ON 
                                SCHEDULE II HERETO:



                                By: ____________________________________________
                                    Attorney-in-Fact


The foregoing Agreement is hereby 
confirmed and accepted as of the date 
first above written.

HAMBRECHT & QUIST LLC
OPPENHEIMER & CO., INC.
VECTOR SECURITIES INTERNATIONAL, INC.
By: Hambrecht & Quist LLC


By: ____________________________
    Managing Director

Acting on behalf of the several 
Underwriters, including themselves, 
named in Schedule I hereto.
         ----------


<PAGE>   24





<TABLE>
                                   SCHEDULE I

                                  UNDERWRITERS
<CAPTION>


                                                                  NUMBER OF
                                                                  SHARES OF
                                                             UNDERWRITTEN STOCK
                      UNDERWRITERS                             TO BE PURCHASED
                      ------------                             ---------------

<S>                                                            <C>
Hambrecht & Quist LLC...................................
Oppenheimer & Co., Inc..................................
Vector Securities International, Inc....................
</TABLE>




<PAGE>   25






                                  SCHEDULE II

                            SELLING SECURITYHOLDERS




                                                             NUMBER OF SHARES OF
                                                              UNDERWRITTEN STOCK
           NAME OF SELLING SECURITYHOLDERS                        TO BE SOLD
           -------------------------------                        ----------


<PAGE>   26






                                     ANNEX A

                     Matters to be Covered in the Opinion of
             Counsel for the Company and the Selling Securityholders


         1.       The Company has been duly incorporated and is validly existing
as a corporation in good standing under the laws of the State of Delaware and is
duly qualified to do business and is in good standing as a foreign corporation
in the Commonwealth of Massachusetts. The Company has all corporate power and
authority necessary to own or hold its properties and conduct the business in
which it is presently engaged.

         2.       The Company's authorized capitalization consists of 30,000,000
shares of Common Stock, $.01 par value per share, and 1,000,000 shares of
Preferred Stock, $0.01 par value per share. All of the issued and outstanding
shares of capital stock of the Company have been, and the shares of the Stock
being delivered on the date hereof, upon issuance and delivery and payment
therefor in the manner described in the Underwriting Agreement, will be, duly
and validly authorized and issued, fully paid and non-assessable with no
personal liability attaching to the ownership thereof. The statements made in
the Prospectus under the caption "Description of Capital Stock," insofar as they
purport to constitute summaries of the terms of the Company's capital stock
(including the Stock), constitute accurate summaries of the terms of such
capital stock in all material respects and fairly present in all material
respects the information called for with respect thereto by Item 202 of
Regulation S-K promulgated by the Commission.

         3.       There are no preemptive or other rights to subscribe for or to
purchase or rights of first refusal or participation with respect to any shares
of Common Stock pursuant to the Company's charter or by-laws or any agreement or
other instrument known to us. Except as described in the Prospectus and as
provided in the Company charter and by-laws, there are no restrictions upon the
voting or transfer of any shares of Common Stock pursuant to any agreement or
other instrument known to us.

         4.       To our knowledge, but without inquiry into the dockets of any 
court, commission, regulatory body, administrative agency or other government
body, and except as set forth in the Prospectus, there are no legal or
governmental proceedings pending to which the Company or any of its subsidiaries
is a party or to which any property or assets of the Company or any of its
subsidiaries is subject which, if determined adversely to the Company or any of
its subsidiaries, are reasonably likely to have a material adverse effect on the
business or prospects of the Company and its subsidiaries taken as a whole and,
to our knowledge, except as set forth in the Prospectus, no such proceedings are
threatened by governmental authorities or by others.

         5.       The Registration Statement has been declared effective under 
the Securities Act and, to our knowledge, no stop order suspending the
effectiveness of the Registration Statement has been issued and no proceeding
for that purpose is pending or threatened by the Commission.

<PAGE>   27


         6.       The Registration Statement and the Prospectus and any further 
amendments or supplements thereto made by the Company prior to the date hereof
(other than the financial statements, financial and statistical information, pro
forma financial information and related schedules and notes thereto, as to which
we express no opinion) comply as to form in all material respects with the
requirements of the Securities Act and the Rules and Regulations. In passing
upon the form of such documents, we have not independently verified and are not
passing upon, and have assumed the correctness and completeness of, the
statements made therein.

         7.       To our knowledge, there are no contracts or other documents
that are required to be described in the Prospectus or filed as exhibits to the
Registration Statement by the Securities Act or by the Rules and Regulations
that have not been described or filed as exhibits to the Registration Statement.

         8.       The Company has full right, power, and authority to execute 
and deliver the Underwriting Agreement and to perform its obligations
thereunder; and all corporate action required to be taken for the due and proper
authorization, issuance, sale and delivery of the Common Stock to be sold by the
Company under the Underwriting Agreement and the consummation of the
transactions contemplated thereby to be effected by the Company have been duly
and validly taken by the Company.

         9.       The Underwriting Agreement has been duly authorized, executed,
and delivered by the Company.

         10.      The Underwriting Agreement has been duly executed and
delivered by or on behalf of each of the Selling Securityholders and the Custody
Agreement between the Selling Securityholders and the Company, as Custodian, and
the Power of Attorney referred to in such Custody Agreement have been duly
executed and delivered by each of the Selling Securityholders.

         11.      To such counsel's knowledge each Selling Securityholder has 
full legal right, power and authority, and any approval required by law (other
than any approval required by the applicable federal or state securities and
Blue Sky laws) to sell, assign, transfer and deliver the Stock to be sold by him
in the manner provided in the Underwriting Agreement and the Custody Agreement.

         12.      Upon delivery to the Underwriters of a certificate 
representing the Stock that is being sold by each Selling Securityholder under
the Underwriting Agreement and payment for such Stock by the Underwriters, each
Underwriter will acquire all of the rights of such Selling Securityholder in
such Stock, and each Underwriter will also acquire such Stock free of any
"adverse claim" (within the meaning of Section 8-302(2) of the Uniform
Commercial Code).

         13.      The issuance and sale of the shares of Stock being delivered
on the date hereof by the Company and the Selling Securityholders, the
compliance by the Company and each Selling Securityholder with all of the
provisions of the Underwriting Agreement and the consummation of the
transactions contemplated thereby will not conflict with or result in a breach
or violation of 

<PAGE>   28


any of the terms or provisions of, or constitute a default, an event of default,
or an event which, with notice or lapse of time or both, would constitute a
default or event of default under, any indenture, mortgage, deed of trust, loan
agreement, or other agreement or instrument filed as an exhibit to the
Registration Statement, nor will such actions result in any violation of the
provisions of the charter or by-laws of the Company or any material statute,
order, rule or regulation or, to our knowledge, any judgment, order or decree of
any court or governmental agency or body having jurisdiction over the Company or
any of its properties or assets, except for such conflicts, breaches, violations
and defaults as are not reasonably likely, individually or in the aggregate, to
have (a) a material adverse effect on the business or prospects of the Company;
or (b) any adverse effect on the consummation of the transactions contemplated
by the Underwriting Agreement. Except for the registration of the Stock under
the Securities Act, and such consents, approvals, authorizations, registrations,
or qualifications as may be required under the Exchange Act and applicable state
or foreign securities laws in connection with the purchase and distribution of
the Stock by the underwriters thereof, no consent, approval, authorization or
order of, or filing or registration with, any such court or governmental agency
or body is required for the issuance and sale of the shares of Stock being
delivered on the date hereof by the Company and the Selling Securityholders, the
compliance by the Company and the Selling Securityholders with all of the
provisions of the Underwriting Agreement or the consummation of the transactions
contemplated thereby.

         14.      To our knowledge, except as described under the caption 
"Shares Eligible for Future Sale -- Registration Rights" in the Preliminary
Prospectus there are no contracts, agreements or understandings in effect on the
date hereof between the Company and any person granting such person the right to
require the Company to file a registration statement under the Securities Act
with respect to any securities of the Company owned or to be owned by such
person or to require the Company to include such securities in the Registration
Statement or in any other registration statement filed by the Company under the
Securities Act.

         15.      The Stock issued and sold by the Company will be accepted for 
listing by The Nasdaq National Market upon official notice of issuance of the
shares by the Company to The Nasdaq National Market.

         In connection with the preparation of the Registration Statement and
the Prospectus, we have participated in conferences with officers and
representatives of the Company and the independent accountants of the Company,
at which conferences we have made inquiries of such persons and others and
discussed the contents of the Registration Statement and the Prospectus. While
the limitations inherent in the independent verification of factual matters and
the character of determinations involved in the registration process are such
that we are not passing upon and do not assume any responsibility for the
accuracy, completeness or fairness of the statements contained in the
Registration Statement or the Prospectus (except as specifically stated
elsewhere in this opinion), nothing has come to our attention that has caused us
to believe that the Registration Statement, as of its effective date, contained
any untrue statement of a material fact or omitted to state any material fact
required to be stated therein or necessary in order to make the statements
therein not misleading (except that we express no view or opinion with respect
to the financial statements and schedules or other financial and statistical
data included in the 

<PAGE>   29


Registration Statement), and nothing has come to our attention that has caused
us to believe that the Prospectus, as of its date and as of the Closing Date,
contained any untrue statement of a material fact or omitted to state any
material fact necessary in order to make the statements therein, in the light of
the circumstances under which they were made, not misleading (except that we
express no view or opinion with respect to the financial statements and
schedules or other financial and statistical data included in the Prospectus).


                          ----------------------------


         In rendering the foregoing opinion we may rely as to questions of law
not involving the laws of the United States, the Commonwealth of Massachusetts
and the State of Delaware upon opinions of local counsel satisfactory in form
and scope to counsel for the Underwriters. We are not, however, rendering any
opinion with respect to patents, trademarks or federal or state regulation of
healthcare products. Copies of any opinions so relied upon shall be delivered to
the Representatives and to counsel for the Underwriters and the foregoing
opinion shall also state that counsel knows of no reason the Underwriters are
not entitled to rely upon the opinions of such local counsel. In addition, we
may state that as to various questions of fact material to our opinion, we have
relied upon the representations made in or pursuant to the Underwriting
Agreement and upon certificates of officers of the Company.


<PAGE>   30





                                     ANNEX B

                     Matters to be Covered in the Opinion of
                         Patent Counsel for the Company


         1.       With respect to the U.S. patent and each of the U.S. patent
applications referred to in the Registration Statement which are listed in
Schedules ____, nothing has come to our attention which would cause us to
believe that the sections of the Registration Statement entitled "Risk Factors -
Dependence on Patents and Proprietary Rights"; and "Business - Patents and
Proprietary Rights", at the time the Registration Statement became effective,
contained any untrue statement of a material fact or omitted to state a material
fact required to be stated therein or necessary to make the statements therein,
not misleading.

         2.       With respect to the US. patent and each of the U.S. patent 
applications referred to in the Prospectus which are listed in Schedules ____,
nothing has come to our attention which would cause us to believe that the
sections of the Prospectus entitled "Risk Factors - Dependence on Patents and
Proprietary Rights"; and "Business - Patents and Proprietary Rights", as of its
date and as of the Closing Date, contain any untrue statement of material fact
or omit to state a material fact necessary to make the statements therein, in
light of the circumstances in which they were made, not misleading.

         3.       To the best of our knowledge, except as described in the 
Prospectus, and with the exception of proceedings before the U.S. Patent and
Trademark Office, there are no pending, or threatened, legal or governmental
proceedings relating to the U.S. patent or any of the U.S. patent applications
listed in Schedules ____.

         4.       To the best of our knowledge, except as described in the
Prospectus, the Company owns [the U.S. patent and each of the U.S. patent
applications referred to in the Prospectus that are listed in Schedules ____].

         5.       To the best of our knowledge, the Company has not received any
notice challenging the validity or enforceability of the U.S. patent listed in
Schedule ____.

         6.       While there can be no guarantee that any particular patent 
application will issue as a patent, each of the U.S. patent applications
referred to in the Prospectus which is listed in Schedules ____ was properly
filed, and is being properly and diligently prosecuted, in the U.S. Patent and
Trademark Office.

         7.       To the best of our knowledge, for each U.S. patent application
listed in Schedules ____, all information known to Pennie & Edmonds, to date, to
be "material to patentability", as defined in 37 C.F.R. ss. 1.56(b), has been
disclosed, or will be disclosed pursuant to 37 C.F.R. ss. 1.97, to the U.S.
Patent and Trademark Office.


<PAGE>   31

         8.       To the best of our knowledge, no claim, action, suit or 
proceeding is presently pending or threatened against the Company relating to
the potential infringement of, or conflict with, any patents of others. We have
no knowledge of any facts which would form a basis for the belief that there is
any infringement by others of the Company's U.S. patent.



<PAGE>   1










                      ARRAY DELIVERY AND TESTING AGREEMENT

                                     between

                                  ARQULE, INC.

                                       and

                                MONSANTO COMPANY













<PAGE>   2


                      ARRAY DELIVERY AND TESTING AGREEMENT


      This Agreement, dated as of December 23, 1996, is between ArQule, Inc.
("ArQule"), a Delaware corporation, and Monsanto Company ("Monsanto"), a
Delaware corporation.


                                R E C I T A L S
                                - - - - - - - -

      WHEREAS, ArQule has developed certain technology that has applications in
the discovery and development of compounds for use in agriculture and in planta;

      WHEREAS, Monsanto desires that ArQule apply its technologies to the
research and development of compounds with agricultural and in planta
applications for Monsanto; and

      WHEREAS, in exchange for payment by Monsanto of research funds, milestone
payments and royalties, ArQule is willing to provide compound arrays for
Monsanto testing and perform certain other compound development activities,
subject to the terms and conditions of this Agreement;

      NOW, THEREFORE, in consideration of the mutual covenants set forth in this
Agreement, the parties hereby agree as follows:


1.    Definitions.
      -----------

            "ACTIVE HOMOLOG" shall mean any ArQule Derivative Compound or
Monsanto Derivative Compound that exhibits substantial homology with an Active
ArQule Compound or Active Monsanto Compound, respectively, as determined by the
Research Committee.

            "ACTIVE ARQULE COMPOUND" shall mean any ArQule Compound or ArQule
Derivative Compound which exhibits confirmed significant functional activity
against a Target. The Research Committee shall establish the criteria for
"significant functional activity" at the time of selection of each Target.

            "ACTIVE COMPOUND" shall mean any Active ArQule Compound or Active 
Monsanto Compound.

            "ACTIVE MONSANTO COMPOUND" shall mean any Monsanto Compound or
Monsanto Derivative Compound which exhibits confirmed significant functional
activity against a Target. The Research Committee shall establish the criteria
for "significant functional activity" at the time of selection of each Target.

            "ADVANCED FIELD TRIALS" shall mean advanced testing trials conducted
by or for Monsanto in a manner representative of actual agricultural or
industrial practices including (i) determining the performance or safety of a
Licensed Compound or (ii) greenhouse, growth chamber or laboratory testing
including radio-labeled synthesis and associated testing, advanced toxicity,
environmental fate, and toxicity on non-target species including mammals and/or
assembling field information necessary to obtain an EUP.




<PAGE>   3


            "AGREEMENT" shall mean this Array Delivery and Testing Agreement,
together with Exhibit A and Exhibit B hereto.

            "ARQULE COMPOUND" shall mean any chemical molecule that is
synthesized by ArQule using its proprietary technology and provided by ArQule to
Monsanto under the Mapping Array(TM) Program or the Directed Array(TM) Program
as described below.

            "ARQULE DERIVATIVE COMPOUND" shall mean a Derivative Compound
synthesized by ArQule from an ArQule Compound under the Directed Array(TM)
Program described in Section 3.3.

            "ARQULE INTERNAL DISCOVERY PROGRAM" shall mean any testing or
screening activity performed by ArQule itself with the primary purpose of
determining the functional activity in the Field of ArQule Compounds or ArQule
Derivative Compounds, but shall not include any advanced field trials.

            "ARQULE PATENT RIGHTS" shall mean Patent Rights controlled or owned
by ArQule as of the Effective Date or during the Research Period, as set forth
in Section 5.1(b).

            "ARQULE TECHNOLOGY" shall mean all information and data which is
owned by or licensed by third parties to ArQule during the Research Program and
is necessary or useful to conduct the screening to discover Active Compounds and
Licensed Compounds or to develop, make, use, sell or seek regulatory approval in
any country to market a product containing a Licensed Compound; all to the
extent and only to the extent that ArQule now has or hereafter will have the
right to grant licenses, immunities or other rights thereunder.

            "ARRAY" shall mean a set of samples of structurally related chemical
compounds arranged in a format such as a microtiter screening plate or another
format as mutually agreed to by the Parties.

            "BASE RATE OF INTEREST" shall mean the base rate of interest charged
to its best commercial customers from time to time by the Bank of Boston or its
successor.

            "CHEMICAL THEME" shall mean the chemical or structural
characteristics shared by a group of compounds as determined by the Research
Committee pursuant to Section 2.2.

            "CONFIDENTIAL INFORMATION" shall have the meaning set forth in 
Section 8.1.

            "CONTRACT YEAR" shall mean each twelve (12) month fiscal year of the
Research Period, commencing on January 1 of each year and concluding twelve (12)
months thereafter.

            "DERIVATIVE COMPOUND" shall mean a chemical compound structurally
derived in one or more steps from another by a process of modification (either
through manipulation of a compound or synthesis from structural information
provided hereunder) or partial substitution of at least one component wherein at
least one structural feature is retained at each process step. The number of
intermediate steps or compounds is not relevant to the classification of a



                                       2
<PAGE>   4


compound as a Derivative Compound. A compound need not have structural
similarity to another compound in order to be classified as a Derivative
Compound.

            "DIRECTED ARRAY" shall mean an Array comprised of ArQule Derivative
Compounds synthesized by ArQule under the Directed Array(TM) Program described
in Section 3.3.

            "DIRECTED ARRAY(TM) PROGRAM" shall mean a Directed Array(TM) Program
conducted by ArQule as set forth in Section 3.3, with each Directed Array(TM)
Program consisting of multiple Arrays derived from one (1) Monsanto Compound, or
one (1) Monsanto Derivative Compound, or one (1) ArQule Compound, or one (1)
ArQule Derivative Compound.

            "DISCLOSING PARTY" shall mean that Party disclosing Confidential
Information to the other Party under Section 8.

            "EU" shall mean Austria, Belgium, Denmark, Finland, France, Germany,
Greece, Ireland, Italy, Luxembourg, Netherlands, Norway, Portugal, Spain,
Sweden, United Kingdom and such other countries that may be subsequently
admitted to or excluded from the EU.

            "EUP" shall mean an Experimental Use Permit.

            "EFFECTIVE DATE" shall mean the date of execution of this Agreement
by the Parties hereto, at which time this Agreement shall become effective.

            "EPA" shall mean the Environmental Protection Agency (or its foreign
equivalent responsible for approval of commercial use of Licensed Compounds as
defined in the Field).

            "EXPERIMENTAL USE PERMIT" shall mean a permit for field application
issued by the EPA prior to label approval.

            "EXTRAORDINARY EXPENSES" shall mean those unusual capital expenses
incurred by ArQule at the request of Monsanto which are not contemplated by the
original Research Plan executed by the Parties.

            "FIELD" shall mean the field of all agricultural and in planta
applications of any Licensed Compound.

            "JOINT PATENT RIGHTS" shall mean any Patent Rights that are jointly
owned by the Parties as of the Effective Date or during the Research Period, as
set forth in Section 5.1(c).

            "LICENSED COMPOUND" shall mean any Active Compound and Active
Homologs thereto with respect to which the Research Committee has elected to
conduct Preliminary Field Trials.

            "MAPPING ARRAY" shall mean an Array of ArQule Compounds synthesized
by ArQule under the Mapping Array(TM) Program.




                                       3
<PAGE>   5
 
           "MAPPING ARRAY(TM) PROGRAM" shall mean the Mapping Array(TM)
component of the Research Program.

            MATERIALS TRANSFER AGREEMENT shall mean that agreement the form of
which is attached as Exhibit B hereto.

            "MONSANTO COMPOUND" shall mean any chemical molecule provided by
Monsanto or its Primary Affiliates to ArQule under the Mapping Array(TM) Program
or the Directed Array(TM) Program.

            "MONSANTO DERIVATIVE COMPOUND " shall mean a Derivative Compound
synthesized by ArQule from a Monsanto Compound under the Directed Array(TM)
Program.

            "MONSANTO PATENT RIGHTS" shall mean Patent Rights controlled or
owned by Monsanto as of the Effective Date or during the Research Period, as set
forth in Section 5.1(a).

            "NET SALES" shall mean the aggregate Net Sales Price of 
Royalty-Bearing Products in any Royalty Period.

      .     "NET SALES PRICE" shall mean the gross amount received on sales by
Monsanto, its Secondary Affiliates and Sublicensees of Royalty-Bearing Products,
less the following amounts actually paid out by Monsanto, its Secondary
Affiliates or Sublicensees or credited against the amounts received by them from
the sale or distribution of Royalty-Bearing Product [        
                                                         ]*. In the event that
Monsanto, its Secondary Affiliates or Sublicensees receives non-monetary
consideration for any Royalty-Bearing Products, the Net Sales Price shall be
calculated based on the average price charged by Monsanto, its Secondary
Affiliates or Sublicensees for such Royalty-Bearing Products in the same
territory during the preceding Royalty Period less the items set forth in items
(i) through (iv) above.

            "PARTY" means ArQule or Monsanto or their respective Primary
Affiliates; "PARTIES" means ArQule and Monsanto and their respective Primary
Affiliates.

            "PATENT RIGHTS" shall mean all Valid Claims of all issued and
subsisting patents and reissues, reexaminations, extensions and supplementary
protection certificates thereof and all patent applications and any divisions,
continuations, or continuations-in-part thereof.

            "PRELIMINARY FIELD TRIALS" shall mean, with respect to any Licensed
Compound, preliminary testing first conducted by or for Monsanto to determine
efficacy conducted under anticipated use conditions, generally in an external
environment. Preliminary Field Trials does not include primary testing, which
includes greenhouse, growth chamber or laboratory testing 

* Confidential information omitted and filed with the Commission.

                                       4
<PAGE>   6


including associated testing for environmental fate, toxicity, and toxicity on
non-target species including mammals.

      .     "PRIMARY AFFILIATE" of a Party shall mean a corporation or other
 legal entity that owns, directly or indirectly, fifty percent (50%) or more of
the outstanding equity securities of a corporation which are entitled to vote in
the election of directors or a fifty percent (50%) or greater interest in the
net assets or profits of an entity which is not a corporation or any similar
type of control relationship.

            "PRODUCT TEAM" shall mean a group of Monsanto employees formed to
facilitate product development analysis following successful completion of
Advanced Field Trials.

            "RECEIVING PARTY" shall mean that Party receiving Confidential
Information under Section 8.1.

            "RESEARCH COMMITTEE"  shall have the meaning set forth in 
Section 2.1.

            "RESEARCH PERIOD" shall mean the period during which the applicable
aspect (Mapping Array(TM) Program or Directed Array(TM) Program) of the Research
Program remains in effect.

            "RESEARCH PROGRAM" shall mean, collectively, each of the Directed
Array(TM) Programs and the Mapping Array(TM) Program.

            "RESEARCH PLAN" shall mean a plan of research for the Directed
Array(TM) Program covering a minimum of a six-month period, which shall be
updated quarterly pursuant to Section 2.2 to reflect developments during the
previous three (3) months and extended for the subsequent three (3) months. A
form of the initial Research Plan shall be attached as EXHIBIT A to this
Agreement, and shall be executed by the Parties prior to March 1, 1997.

            "ROYALTY-BEARING PRODUCT" shall mean a commercial product containing
as one of its constituents (a) any Active ArQule Compound; (b) any ArQule
Derivative Compound; (c) any Monsanto Derivative Compound; or (d) any other
compound discovered or designed by Monsanto directly as a result of information
provided by ArQule to Monsanto under the Mapping Array(TM) Program or Directed
Array(TM) Program, which information forms the primary basis for such discovery
or development.

            "ROYALTY PERIOD" shall mean, with respect to each Royalty-Bearing
Product, every calendar quarter, or partial calendar quarter, commencing with
the first arms-length, commercial sale of such Royalty-Bearing Product in any
country and ending at the end of the quarter during which all Patent Rights
covering such Royalty-Bearing Product expire in the applicable country provided
that if there is no Valid Claim covering a Royalty Bearing Product at the end of
ten (10) years from the date of the first arms-length commercial sale in that
country of the applicable Licensed Product, then the Royalty Period shall be
deemed to have terminated for all purposes with respect to that Royalty-Bearing
Product in that country.


                                       5
<PAGE>   7



            "SECONDARY AFFILIATE" of a Party shall mean a corporation or other
legal entity that owns, directly or indirectly, twenty percent (20%) or more of
the outstanding equity securities of a corporation which are entitled to vote in
the election of directors or a twenty percent (20%) or greater interest in the
net assets or profits of an entity which is not a corporation or any similar
type of control relationship.

            "SUBLICENSEE" shall mean any third party (not including a Secondary
Affiliate) licensed by Monsanto to make, use (except where the implied right to
use accompanies the sale to the third party of any Royalty-Bearing Product by
Monsanto or its Secondary Affiliates or Sublicensees), sell, import, export,
advertise, promote and otherwise commercialize any Royalty-Bearing Product.

            "TARGET" shall mean any target within the Field selected by
Monsanto. A biological target used for purposes of toxicity testing shall be
deemed a Target within the Field.

            "VALID CLAIM" shall mean either (a) a claim of an issued and
subsisting patent that has not been held finally unenforceable or invalid by an
agency, court or other tribunal of competent jurisdiction in any unappealable or
unappealed decision the time for appeal of which has expired or (b) a claim of a
pending patent application that has not been abandoned or finally rejected
without the possibility of appeal or refiling.

            The above definitions are intended to encompass the defined terms in
both the singular and plural tenses.

2.    Management of Research Program.
      ------------------------------  

      2.1.  COMPOSITION OF RESEARCH COMMITTEE. The Parties hereby establish a
Research Committee comprised of four (4) members, with two (2) representatives
appointed by each Party. The initial members of the Research Committee shall be
as follows:

            ArQule Representatives              Monsanto Representatives
            ----------------------              ------------------------

            David Coffen, Ph.D.                 Eugene Logusch, Ph.D.

            David Casebier, Ph.D.                Scott Woodard, Ph.D.

A Party may change one or more of its representatives to the Research Committee
at any time upon notice to the other Party. Each Party will designate one of its
representatives as its team leader.

      2.2.  DUTIES OF THE RESEARCH COMMITTEE. The Research Committee shall
direct and administer the Research Program. With respect to each Directed
Array(TM) Program, the Research Committee shall specifically determine the
following: (i) the appropriate objectives of each Chemical Theme and/or Active
Compound to be submitted to the Directed Array(TM) Program; (ii) the appropriate
number and type of Chemical Themes to be submitted to the Directed Array(TM)
Program, subject to ArQule's right to exclude certain compounds as set forth in
Section 3.2.3 below; (iii) the appropriate number of compounds that ArQule
should generate in a Directed 



                                       6
<PAGE>   8

Array(TM) for a particular Chemical Theme; and (iv) the appropriate amount of
each compound in a Directed Array(TM) that ArQule should deliver to Monsanto for
further research and development. The scope of each Chemical Theme will be
determined on the basis of the following criteria: (i) the specific reaction or
reaction sequence used to combine members of two or more discrete chemical units
in which each chemical unit bears the functional group(s) required for the
specific reaction(s) that result in the combination of the chemical units; and
(ii) the extent to which a class of compounds is related by a recurring
structural motif associated with a particular biological activity. In addition,
the Research Committee shall (i) review test reports provided by Monsanto as to
the significant functional activity derived from testing each Mapping Array(TM)
and, based on such results, recommend to ArQule whether to develop Directed
Arrays(TM) for any Active ArQule Compound, (ii) determine, subject to
availability in the case of Active ArQule Compounds as provided in Section
3.2.3, whether any Active Compound and/or any Active Homolog thereto should be
designated as a Licensed Compound; (iii) determine and update the list of
Licensed Compounds; (iv) determine the allocation of the funding and personnel
resources to be contributed by the Parties under this Agreement; (v) revise and
extend the Research Plan each calendar quarter for the subsequent six (6) months
based on prior developments; and (vi) resolve matters involving scientific
questions.

      2.3.  MEETINGS OF THE RESEARCH COMMITTEE. The Research Committee shall
conduct monthly telephone conferences and shall prepare and deliver a brief
written report describing the significant issues and discussions that take place
during such telephone conferences. A representative of the Research Committee
jointly appointed by its members shall provide each member with five (5)
business days notice of the time of any such telephone conferences and the
proposed agenda with respect thereto, unless waived by all members. The Research
Committee shall meet at least once each quarter at the facilities of ArQule, or
at such other times and locations as the Research Committee determines. A
representative of the Research Committee jointly appointed by its members shall
provide each member with five (5) business days notice of the time and location
of meetings, unless such notice is waived by all members. If a designated
representative of a Party cannot attend any meeting of the Research Committee,
such Party may designate a different representative for that meeting without
notice to the other Party, and the substitute member will have full power to
vote on behalf of the permanent member. Except as otherwise provided in this
Section 2, all actions and decisions of the Research Committee will require the
unanimous consent of all of its members. If the Research Committee fails to
reach agreement upon any matter, the dispute will be resolved in accordance with
the procedures set forth in Section 12.5 below. Within ten (10) days following
each quarterly meeting of the Research Committee, the Research Committee shall
prepare and deliver, to both Parties, a written report describing the decisions
made, conclusions and actions agreed upon.

      2.4.  COOPERATION. Each Party agrees to provide the Research Committee
with information and documentation as reasonably required for the Research
Committee to fulfill its duties under this Agreement. In addition, each Party
agrees to make available its employees and consultants as reasonably requested
by the Research Committee. The Parties anticipate that members of the Research
Committee will communicate informally with each other and with employees and
consultants of the Parties on matters relating to the Directed Array(TM)
Program.

      2.5.  VISITS TO FACILITIES. Members of the Research Committee shall have
reasonable access to the facilities of each Party where activities under this
Agreement are in progress, but 








                                      7
<PAGE>   9

only during normal business hours and with reasonable prior notice. Each Party
shall bear its own expenses in connection with such site visits.

3.    Access Fee; Description of Programs.
      -----------------------------------

      3.1.  ACCESS FEE. In partial consideration for Monsanto's obtaining access
to ArQule's Mapping Array(TM) Program and Directed Array(TM) Program as provided
herein, Monsanto shall pay to ArQule a technology access fee equal to 
[         ]*, payable in [    ]* equal installments of [       ]* each, with the
first such payment to be made on the [         ]* and the remaining [     ]*
payments to be made on [                      ]*.

      3.2.  Mapping Array(TM) Program.
            -------------------------
 
            3.2.1. CONDUCT OF MAPPING ARRAY(TM) PROGRAM. During each Contract
Year, ArQule will supply Monsanto with Mapping Arrays(TM) containing
approximately [              ]* each of not less than [      ]* different ArQule
Compounds not included in any other Mapping Array(TM) supplied to Monsanto,
based on approximately [       ]* different Chemical Themes per year; provided,
however, that ArQule hereby agrees that the first Mapping Array(TM) containing
at least [      ]* ArQule Compounds to be delivered under this Agreement will be
shipped no later than [          ]*, and the difference between [        ]* and
the number of ArQule Compounds so delivered by [         ]* will be
delivered to Monsanto prior to [         ]*. Promptly upon its receipt of any
such Mapping Arrays, Monsanto shall commence testing of such Mapping Arrays(TM)
for activity against Targets. Upon the completion by Monsanto of its testing of
any such Mapping Arrays, Monsanto shall provide the Research Committee with
notice of the discovery of Active ArQule Compounds, together with relevant
information concerning the functional activity identified.

            3.2.2. TIMING OF DELIVERY. ArQule shall provide to Monsanto all
ArQule Compounds for screening in the Field pursuant to the Mapping Array(TM)
Program contemporaneously with the date of delivery of such compound to any
other third party Mapping Array(TM) partner for screening in the Field.

            3.2.3. MUTUAL DISCLOSURE. Initially, ArQule will identify the
Chemical Theme of each Mapping Array(TM) but not the structures of the
individual ArQule Compounds in the Mapping Arrays. Monsanto may screen the
Mapping Arrays(TM) against any Targets within the Field during the term of this
Agreement. Initially, Monsanto will not disclose the Targets screened. If
Monsanto detects any Active ArQule Compound in a Mapping Array(TM), ArQule will
disclose (a) the structure of each Active ArQule Compound and (b) the
structures, but not the locations in the Mapping Array(TM), of all other ArQule
Compounds in the Mapping Array(TM) and Monsanto will disclose (a) the identity
of the Target and (b) the level of activity. All such disclosed information
shall be treated as Confidential Information by the receiving Party. Monsanto
may subsequently request that the Research Committee designate such Active
ArQule Compound and up to five Active Homologs thereof as a Licensed Compound.
In such event, ArQule will promptly notify the Research Committee if, as of the
date of such request, any such Active ArQule Compound or such Active Homolog
thereof (i) has been licensed to a third party, (ii) is included in an existing
ArQule Internal Discovery Program and ArQule has previously notified Monsanto of
the inclusion of such compound in an ArQule Internal Discovery Program 


* Confidential information omitted and filed with the Commission.

                                       8
<PAGE>   10

pursuant to the terms of Section 3.2.6, or (iii) is included within a Directed
Array(TM) Program for a third party, in which case such Active ArQule Compound
or Active Homolog thereof may not be designated as a Licensed Compound. Unless
(i) the Active ArQule Compound or Active Homolog thereof has been licensed to a
third party in the Field, (ii) is included in an existing ArQule Internal
Discovery Program and ArQule has previously notified Monsanto of the inclusion
of such compound in an ArQule Internal Discovery Program pursuant to the terms
of Section 3.2.6, or (iii) is included within a Directed Array(TM) Program for a
third party in the Field, the Research Committee shall designate such Active
ArQule Compound and such Active Homologs thereof as a Licensed Compound.
Monsanto may, by written notice to ArQule given within thirty (30) days of the
determination by the Research Committee that any such Active ArQule Compound and
such Active Homologs thereof should properly be designated as a Licensed
Compound, elect to either (i) further develop any such Active ArQule Compound
and such Active Homologs thereof itself or through a third party, or (ii)
subject to the approval of the Research Committee, submit such Active ArQule
Compound to the Directed Array(TM) Program under Section 3.3.

            3.2.4. MAPPING ARRAY(TM) PROGRAM PAYMENTS. In consideration of the
performance by ArQule of the Mapping Array(TM) Program, Monsanto shall pay
ArQule a delivery fee equal to [                                   ]*, payable
[                              ]* days of [                               ]*
of [         ]* due for [                                          ]*
to be provided by ArQule in such [              ]*. Thereafter, Monsanto shall
make the following annual payment to ArQule [                                ]*
of such [                                                              ]*
due for that [                                                              ]*
remainder of the scheduled [                  ]*:

      Annual Payment =  [         ]* x (1 + CPI)

      Where CPI is a fraction, the numerator of which is the difference between
      the Consumer Price Index (CPI-U; U.S. City Average for all items; 1982-84
      = 100) as of the last month of the immediately preceding Contract Year and
      the Consumer Price Index as of the month immediately preceding the
      Effective Date and the denominator of which is the Consumer Price Index as
      of the month immediately preceding the Effective Date.

            3.2.5. TERM OF MAPPING ARRAY(TM) PROGRAM. The Mapping Array(TM)
Program shall commence on the Effective Date and continue for a period of five
(5) Contract Years, unless earlier terminated as provided in this Section 3.2.5
or Article 11 below; PROVIDED, HOWEVER, that upon six (6) months prior written
notice by Monsanto, the Mapping Array(TM) Program may be extended for up to two
(2) additional one-year periods. Monsanto may terminate the Mapping Array(TM)
Program at its discretion upon six (6) months written notice to ArQule at any
time subject to the payment by Monsanto of all amounts that would have been due
to ArQule during the entire term of this Agreement pursuant to the terms of
Sections 3.1 and 3.2.4 herein if the Mapping Array(TM) Program had not been so
terminated. Upon notice of termination, ArQule



* Confidential information omitted and filed with the Commission.

                                       9
<PAGE>   11

shall use reasonable efforts to complete the Mapping Array(TM) Programs then
underway in a reasonable and orderly fashion.

      3.2.6 ARQULE INTERNAL DISCOVERY PROGRAM. In the event ArQule shall
commence an Internal Discovery Program including a compound previously provided
to Monsanto pursuant to the Mapping Array(TM) Program, ArQule shall promptly
notify Monsanto of the location of each such compound within any Mapping
Array(TM) previously provided to Monsanto.

      3.3.  Directed Array(TM) Program.
            --------------------------
 
            3.3.1. DESCRIPTION OF DIRECTED ARRAY(TM) PROGRAM. Under the
direction of the Research Committee and in accordance with the Research Plan,
ArQule will synthesize multiple Directed Arrays(TM) of compounds derived from
(i) each Monsanto Compound provided to ArQule by Monsanto, or (ii) each Active
ArQule Compound provided by ArQule to Monsanto under the Mapping Array(TM)
Program and approved by the Research Committee for inclusion in the Directed
Array(TM) Program, subject to Section 3.3.2 below. The number of Chemical Themes
to be submitted to the Directed Array(TM) Program and the number of ArQule
Derivative Compounds to be produced per Chemical Theme will be determined by the
Research Committee. The Parties intend that ArQule will produce approximately
[                  ]* of each ArQule Derivative Compound in the Directed
Arrays, subject to the availability of the original Monsanto Compounds and/or
the ArQule Compounds; PROVIDED, HOWEVER that the amount of each ArQule
Derivative Compound that ArQule actually produces will ultimately be determined
by the Research Committee.

            3.3.2. COMPOUNDS EXCLUDED FROM THE DIRECTED ARRAY(TM) PROGRAM.
ArQule shall have the right, at any time Monsanto seeks to include any Active
ArQule Compound in any Directed Array(TM) Program, to exclude from such Directed
Array(TM) Program any Active ArQule Compound that is at that time included
within a Directed Array(TM) Program for a third party for development in the
Field.

            3.3.3. CONDUCT OF DIRECTED ARRAY(TM) PROGRAM. The Directed
Array(TM) Program shall be conducted in a good scientific manner and in
compliance with all applicable legal requirements. The conduct of the Directed
Array(TM) Program shall be the primary responsibility of ArQule with
participation by Monsanto. Monsanto shall propose Chemical Themes to the
Research Committee for inclusion in the Directed Array(TM) Program based on
either an Active ArQule Compound from the Mapping Array(TM) or an Active
Monsanto Compound. If the Research Committee approves the inclusion of the
proposed Chemical Theme, then Monsanto may either deliver to ArQule amounts of
the Active Monsanto Compound or the structural information sufficient for ArQule
to synthesize the Active Monsanto Compound. If ArQule is requested to synthesize
the Active Monsanto Compound, then Monsanto shall specify to ArQule the required
amount and purity of Monsanto Compounds for that Chemical Theme, as directed by
the Research Committee. ArQule shall thereupon diligently synthesize Directed
Arrays(TM) of ArQule Derivative Compounds or Monsanto Derivative Compounds, as
the case may be, in accordance with the Research Plan. Monsanto shall, in its
discretion, test all compounds in the Directed Arrays. The Parties shall
continue the procedure described in this Section 3.3.3 for each Active Compound
until the earliest to occur of (i) the determination by the Research Committee,
in accordance with Section 2.2, to designate any such Active Compound and any
Active 

* Confidential information omitted and filed with the Commission.

                                       10
<PAGE>   12

Homolog thereto as a Licensed Compound, (ii) the determination by the Research
Committee to cease further testing of such Active Compound, or (iii) the
termination of this Agreement in accordance with Section 11.

            3.3.4. Directed Array(TM) Program Payments.
                   -----------------------------------
  
                  (a)   DELIVERY FEE. In consideration of the performance by
ArQule of the Directed Array(TM) Program, Monsanto shall pay ArQule a delivery 
fee equal to [         ]* per Directed Array(TM) Program during [         ]*.
Thereafter, Monsanto shall make the following annual payment to ArQule during
[          ]*.

      Annual Payment =  [         ]* x (1 + CPI)

      Where CPI is a fraction, the numerator of which is the difference between
      the Consumer Price Index (CPI-U; U.S. City Average for all items; 1982-84
      = 100) as of the last month of the immediately preceding Contract Year and
      the Consumer Price Index as of the month immediately preceding the
      Effective Date and the denominator of which is the Consumer Price Index as
      of the month immediately preceding the Effective Date.

            (b)   EXPENSES. In addition to the amounts payable pursuant to
Section 3.3.4(a) above, Monsanto shall pay any and all Extraordinary Expenses of
ArQule, as required and approved in advance by the Research Committee.

      3.3.5. TERM OF DIRECTED ARRAY(TM) PROGRAM. The Directed Array(TM) Program
shall commence upon execution of the Research Plan by each of the team leaders
of Research Committee and continue for a period of five (5) Contract Years,
unless earlier terminated as provided in this Section 3.3.5 or Article 11 below;
PROVIDED, HOWEVER, that upon six (6) months prior written notice by Monsanto,
the Directed Array(TM) Program may be extended for up to two (2) additional
one-year periods. Monsanto may terminate the Directed Array(TM) Program at its
discretion upon six (6) months written notice to ArQule at any time subject to
the payment by Monsanto of all amounts that would have been due to ArQule during
the entire term of this Agreement pursuant to Section 3.3.4 herein if the
Directed Array(TM) Program had not been so terminated. Upon notice of
termination, ArQule shall use reasonable efforts to complete the Directed
Array(TM) Programs then underway in a reasonable and orderly fashion.



* Confidential information omitted and filed with the Commission.

                                       11
<PAGE>   13


4.    License Grants; Diligence.
      -------------------------

      4.1.  SCREENING LICENSES. ArQule hereby grants to Monsanto (a) a
nonexclusive, worldwide, royalty-free license (without the right to sublicense)
to test Mapping Arrays(TM) against Targets in the Field and to perform other
analytical work on the compounds in the Mapping Arrays(TM), and (b) an exclusive
(including to the exclusion of ArQule), worldwide, royalty-free license (without
the right to sublicense) to test any Directed Arrays(TM) for significant
functional activity against Targets in the Field and to perform other analytical
work on the compounds in the Directed Arrays(TM).

      4.2.  COMMERCIALIZATION LICENSES. Upon the identification by Monsanto of
any Active Compound and the determination by the Research Committee that such
Active Compound or any Active Homolog thereof should properly be designated as a
Licensed Compound, ArQule, without any further action, shall be deemed to have
granted to Monsanto, under ArQule Patent Rights, ArQule's interest in any Joint
Patent Rights and ArQule Technology, an exclusive (including to the exclusion of
ArQule), worldwide, royalty-bearing license (with the right to grant
sublicenses) (i) to develop (including the making of Derivative Compounds), have
developed, make, or have made Royalty-Bearing Products incorporating or using
any patent or other intellectual property rights of ArQule covering the
composition, manufacture or use of such Licensed Compound for use, distribution
and sale in the Field, and (ii) to distribute for sale and sell in the Field
Royalty-Bearing Products incorporating or using any patent or other intellectual
property rights of ArQule covering the composition, manufacture or use of such
Licensed Compound, and (iii) to use in the Field Royalty-Bearing Products
incorporating or using any patent or other intellectual property rights of
ArQule covering the composition, manufacture or use of such Licensed Compound.

      4.3.  TERMINATION OF LICENSES. The licenses granted to Monsanto by ArQule
pursuant to Sections 4.1 and 4.2 and the license granted to ArQule by Monsanto
pursuant to Section 4.8 shall continue in perpetuity unless this Agreement
terminates pursuant to Sections 11.2 or 11.3 or such licenses terminate pursuant
to section 4.4.

      4.4.  RETURN OF MATERIALS. Except as provided in Section 4.5 below,
Monsanto agrees to use reasonable commercial efforts to develop and market
Royalty-Bearing Products based on or incorporating any Licensed Compound, using
a level of effort consistent with that used for other Monsanto products having
similar commercial potential. Monsanto shall have the sole and absolute
discretion to make all decisions relating to the research, development,
marketing and other commercialization activities with respect to any Licensed
Compound or any Royalty-Bearing Product derived therefrom. In the event that
Monsanto takes no action to protect its intellectual property rights or further
develop any Licensed Compound for a period of ninety (90) days after the earlier
of (i) the time at which a milestone payment is due but has not been paid by
Monsanto, or (ii) the failure of Monsanto to continue with or initiate any
activity that could reasonably lead to a milestone payment as determined by the
Research Committee, then Monsanto shall so notify ArQule and ArQule shall have
the right, upon reasonable notice, to terminate any license granted to Monsanto
under Sections 4.1 or 4.2 with respect to such Licensed Compound.




                                       12
<PAGE>   14

      4.5.  COMMENCEMENT OF DILIGENCE. Notwithstanding anything to the contrary
in this Agreement, the Parties hereby agree that the diligence obligations
described in Section 4.4 shall not commence with respect to any Licensed
Compound that is included within a Directed Array(TM) Program until such time as
such Directed Array(TM) Program is completed.

      4.6.  LICENSE REQUIREMENTS. The Parties recognize and agree that Monsanto
does not and will not at any time need any license or other permission or
authorization from ArQule for any activities (including by way of example and
not limitation) making, using, offering for sale, selling and importing
concerning or involving any compound or composition or its manufacture or use
unless ArQule owns (to the exclusion of Monsanto) (i) ArQule Patent Rights, or
(ii) proprietary and confidential ArQule Technology covering such compound or
composition or its manufacture or use.

      4.7.  SCREENING OF ARQULE COMPOUNDS. During any Research Period, Monsanto
shall have the right, either directly or through Monsanto's Primary Affiliates
or third parties (including Secondary Affiliates who are not also Primary
Affiliates) selected by Monsanto, to perform such testing as Monsanto deems
appropriate on ArQule Compounds and ArQule Derivative Compounds received
hereunder, provided that, prior to delivering any ArQule Compounds or ArQule
Derivative Compounds to any such third party(including Secondary Affiliates who
are not also Primary Affiliates), Monsanto, ArQule and each such third
party(including Secondary Affiliates who are not also Primary Affiliates) enter
into a Materials Transfer Agreement substantially in the form of the attached
Exhibit B.

      4.8.  GRANT OF LICENSE TO ARQULE. Monsanto hereby grants to ArQule an
exclusive (including to the exclusion of Monsanto), worldwide, royalty-free
license (with the right to sublicense) to make, have made, use, sell, have sold,
import, export and distribute for sale outside of the Field compounds containing
or using any intellectual property rights of Monsanto covering the composition,
manufacture or use of Licensed Compounds.

      4.9   REVERSE ENGINEERING. Monsanto shall not attempt to reverse engineer,
or attempt to determine the structure of, any ArQule Compound in a Mapping
Array(TM) until the structure of such compound has been disclosed to Monsanto by
ArQule and Monsanto has disclosed to ArQule the identity of the Target and level
of activity, all pursuant to Section 3.2.3.

5.    Intellectual Property Rights.
      ----------------------------

      5.1.  Ownership of Patent Rights.
            --------------------------

            (a)   MONSANTO PATENT RIGHTS. Monsanto will solely own any Patent
      Rights applied for or obtained by either Party covering (i) Monsanto
      Compounds, or (ii) Monsanto Derivative Compounds, except, and only to the
      extent that ArQule can show that any such compounds were independently
      developed by ArQule employees who had no access to Monsanto Confidential
      Information or any information of ArQule developed or furthered as a
      result of this Agreement. The parties express no intent as to the
      ownership of Monsanto Compounds or Monsanto Derivative Compounds to the
      extent such compounds (i) were already within a Mapping Array(TM) Program
      before such compounds were proposed to be included in the Directed
      Array(TM) Program, or (ii) were





                                       13
<PAGE>   15


      under development by ArQule (including programs with academic
      collaborators or corporate partners) before such compound was proposed to
      be included in the Directed Array(TM) Program. Monsanto will solely own
      any Patent Rights filed by either Party covering Licensed Compounds.
      Monsanto will solely own any Patent Rights filed by either Party covering
      any method of making or using any ArQule Compound, ArQule Derivative
      Compound, Monsanto Compound or Monsanto Derivative Compound where such
      method is invented solely by Monsanto.

            (b)   ARQULE PATENT RIGHTS. ArQule will solely own any Patent Rights
      applied for or obtained by either Party covering (i) ArQule Compounds or
      ArQule Derivative Compounds not owned by Monsanto pursuant to 5.1(a), or
      (ii) any method of making or using any ArQule Compound, ArQule Derivative
      Compound, Monsanto Compound or Monsanto Derivative Compound where such
      method is invented solely by ArQule.

            (c)   JOINT PATENT RIGHTS. ArQule and Monsanto will jointly own any
      Patent Rights applied for or obtained by either Party covering any method
      of making or using any ArQule Compound, ArQule Derivative Compound,
      Monsanto Compound or Monsanto Derivative Compound where such method is
      invented jointly by Monsanto and ArQule.

      5.2.  MANAGEMENT OF JOINT PATENT RIGHTS. In the case of Joint Patent
Rights, Monsanto shall have all control over and shall bear all responsibility
for, and the expense of, the preparation, filing, prosecution, and maintenance
of any Joint Patent Rights claiming such inventions. Monsanto shall consult with
ArQule as to the preparation, filing, prosecution, and maintenance of such Joint
Patent Right reasonably prior to any deadline or action with the U.S. Patent &
Trademark Office or its foreign equivalent, and shall furnish to ArQule copies
of all relevant documents reasonably in advance of such consultation. In the
event that Monsanto desires to abandon such Joint Patent Right, or if Monsanto
later declines responsibility for such Joint Patent Right, Monsanto shall
provide reasonable prior written notice to ArQule of such intention to abandon
or decline responsibility, and ArQule shall have the right, at its expense, to
prepare, file, prosecute, and maintain such Joint Patent Rights.

      5.3.  COOPERATION OF THE PARTIES. Each Party agrees to cooperate fully in
the preparation, filing, and prosecution of any Patent Rights under this
Agreement. Such cooperation includes, but is not limited to:

                  (a) executing all papers and instruments, or requiring its
      employees or agents, to execute such papers and instruments, so as to
      effectuate the ownership of Patent Rights set forth in Section 5.1 above
      and to enable the other Party to apply for and to prosecute patent
      applications in any country;

                  (b) promptly informing the other Party of any matters coming
      to such Party's attention that may affect the preparation, filing, or
      prosecution of any such patent applications; and

                  (c) undertaking no actions that are potentially deleterious to
      the preparation, filing, or prosecution of such patent applications.




                                       14
<PAGE>   16


      5.4.  INFRINGEMENT BY THIRD PARTIES. ArQule and Monsanto shall each
promptly notify the other in writing of any alleged or threatened infringement
by a third party of any ArQule Patent Right, Monsanto Patent Right or Joint
Patent Right of which they become aware. The Parties shall consult concerning
the action(s) to be taken in connection with any such alleged or threatened
infringement.

6.    Ownership of Compounds.
      ----------------------

      All Monsanto Compounds, Monsanto Derivative Compounds, ArQule Compounds
and ArQule Derivative Compounds shall be owned in the same manner as the patent
rights to such compounds are owned as set forth in Article 5.

7.    Payments, Reports, and Records.
      ------------------------------

<TABLE>
      7.1.  MILESTONE PAYMENTS. In partial consideration of the rights granted
Monsanto under this Agreement, Monsanto shall pay ArQule the following amounts
within forty-five (45) days after each occurrence of the following milestones:
<CAPTION>

      Payment              Milestone
      -------              ---------

      <S>                  <C>     
      [         ]*         [                      ]*

      [         ]*         [                      ]*

      [         ]*         [                      ]*

      [         ]*         [                      ]*
 
      [         ]*         [                      ]*

      [         ]*         [                      ]*

- ----------
<FN>

(1). A single milestone payment will be made for each Active Compound along with
up to [five (5)] Active Homologs thereof as determined by the Research Committee.

</TABLE>

* Confidential information omitted and filed with the Commission.



                                       15
<PAGE>   17

Such milestone payments shall be non-refundable and shall not be credited
against royalties payable to ArQule under this Agreement. Monsanto shall
promptly notify ArQule of each occurrence of any of the foregoing milestones.

      7.2.  Royalties.
            ---------
 
      (a)   In consideration of the licenses granted to Monsanto hereunder,
Monsanto shall pay to ArQule a royalty of [         ]* of Net Sales of
Royalty-Bearing Products.

      (b)   No royalty shall accrue on sales among Monsanto, its Secondary
Affiliates and Sublicensees. Royalties shall only accrue on sales by Monsanto,
its Secondary Affiliates and Sublicensees to parties other than Monsanto, its
Secondary Affiliates and Sublicensees and shall be payable only once for any
given unit of Royalty-Bearing Product sold.

      7.3.  REPORTS AND PAYMENTS. Within thirty (30) days after the conclusion
of each Royalty Period, Monsanto shall deliver to ArQule a report containing the
following information:


                  (a)   gross sales of Royalty-Bearing Products by Monsanto, its
Secondary Affiliates and Sublicensees during the applicable Royalty Period in
each country of sale;

                  (b)   adjustments and calculation of Net Sales for the
applicable Royalty Period in each country of sale; and

                  (c)   total Net Sales in U.S. dollars, together with the
exchange rates used for conversion.

All such reports shall be maintained in confidence by ArQule. If no royalties
are due to ArQule for any reporting period, the report shall so state.
Concurrent with this report, Monsanto shall remit to ArQule any payment due for
the applicable Royalty Period using a method of payment mutually agreed to by
the Parties. All amounts payable to ArQule under this Section will first be
calculated in the currency of sale and then converted into U.S. dollars in
accordance with Section 7.4, and such amounts shall be paid without deduction,
except as required by law, of any withholding taxes, value-added taxes, or other
charges applicable to such payments.

      7.4.  INVOICES; PAYMENTS IN U.S. DOLLARS. With the exception of royalty
payments due under Section 7.2, ArQule shall submit invoices to Monsanto for
each payment due ArQule hereunder (including without limitation all payments due
pursuant to Sections 3.1, 3.2.4 and 3.3.4(a)), and Monsanto shall pay such
invoices within forty-five (45) days of receipt thereof. All payments due under
this Agreement shall, except as provided in Section 7.5 below, be payable in
United States dollars. Conversion of foreign currency to U.S. dollars shall be
made at the conversion rate existing in the United States (as reported in THE
WALL STREET JOURNAL) on the last working day of the calendar quarter preceding
the applicable calendar quarter. Such payments shall be without deduction of
exchange, collection, or other charges.


* Confidential information omitted and filed with the Commission.

                                       16
<PAGE>   18


      7.5.  PAYMENTS IN OTHER CURRENCIES. If by law, regulation, or fiscal
policy of a particular country, conversion into United States dollars or
transfer of funds of a convertible currency to the United States is restricted
or forbidden, Monsanto shall give ArQule prompt written notice of such
restriction, which notice shall satisfy the forty-five day payment deadline
described in Section 7.4. Monsanto shall pay any amounts due ArQule through
whatever lawful methods ArQule reasonably designates; provided, however, that if
ArQule fails to designate such payment method within forty-five (45) days after
ArQule is notified of the restriction, then Monsanto may deposit such payment in
local currency to the credit of ArQule in a recognized banking institution
selected by Monsanto and identified by written notice to ArQule, and such
deposit shall fulfill all obligations of Monsanto to ArQule with respect to such
payment.

      7.7.  RECORDS. Monsanto and its Secondary Affiliates shall maintain
complete and accurate records of Royalty-Bearing Products made, used or sold by
them or their Sublicensees under this Agreement, and any amounts payable to
ArQule in relation to such Royalty-Bearing Products, which records shall contain
sufficient information to permit ArQule to confirm the accuracy of any reports
delivered to ArQule in accordance with Section 7.3. The relevant Party shall
retain such records relating to a given Royalty Period for at least three (3)
years after the conclusion of that Royalty Period. Each Party (acting as the
"Auditing Party") shall have the right, at its own expense, to cause an
independent certified public accountant to inspect such records of the other
Party (the "Audited Party") during normal business hours for the sole purpose of
verifying any reports and payments delivered under this Agreement. Such
accountant shall not disclose to the Auditing Party any information other than
information relating to accuracy of reports and payments delivered under this
Agreement and shall provide the Audited Party with a copy of any report given to
the Auditing Party. The Parties shall reconcile any underpayment or overpayment
within forty-five (45) days after the accountant delivers the results of the
audit. In the event that any audit performed under this Section reveals an
underpayment in excess of five percent (5%) in any Royalty Period, the Audited
Party shall bear the full cost of such audit. Each Party may exercise its rights
under this Section only once every year and only with reasonable prior notice to
the other Party.

      7.8.  LATE PAYMENTS. Any payments by Monsanto that are not paid on or
before the date such payments are due under this Agreement shall bear interest,
to the extent permitted by law, at two percentage points above the Base Rate of
Interest calculated based on the number of days that payment is delinquent.

8.    Confidential Information.
      ------------------------

      8.1.  DEFINITION OF CONFIDENTIAL INFORMATION. Confidential Information
shall mean any technical or business information furnished by the Disclosing
Party to the Receiving Party in connection with this Agreement and specifically
designated as confidential. Such Confidential Information may include, without
limitation, the identity of a chemical compound, the use of a chemical compound,
trade secrets, know-how, inventions, technical data or specifications, testing
methods, business or financial information, research and development activities,
product and marketing plans, and customer and supplier information.

      8.2.  Obligations. The Receiving Party agrees that it shall:
            -----------



                                       17
<PAGE>   19

                  (a)   maintain all Confidential Information in strict
      confidence, except that the Receiving Party may disclose or permit the
      disclosure of any Confidential Information to its, and its Primary
      Affiliates, directors, officers, employees, consultants, and advisors who
      are obligated to maintain the confidential nature of such Confidential
      Information and who need to know such Confidential Information for the
      purposes set forth in this Agreement;

                  (b)   use all Confidential Information solely for the purposes
        set forth in, or as permitted by, this Agreement; and

                  (c)   allow its Primary Affiliates, directors, officers,
      employees, consultants, and advisors to reproduce the Confidential
      Information only to the extent necessary to effect the purposes set forth
      in this Agreement, with all such reproductions being considered
      Confidential Information.

      8.3.  EXCEPTIONS. The obligations of the Receiving Party under Section
8.2 above shall not apply to any specific Confidential Information to the extent
that the Receiving Party can demonstrate that such Confidential Information:

                  (a)   was in the public domain prior to the time of its
      disclosure under this Agreement;

                  (b)   entered the public domain after the time of its
      disclosure under this Agreement through means other than an unauthorized
      disclosure resulting from an act or omission by the Receiving Party, its
      Primary Affiliates, directors, officers, employees, consultants, advisors
      or agents;

                  (c)   was independently developed or discovered by the
      Receiving Party without use of the Confidential Information;

                  (d)   is or was disclosed to the Receiving Party at any time,
      whether prior to or after the time of its disclosure under this Agreement,
      by a third party having no fiduciary relationship with the Disclosing
      Party and having no obligation of confidentiality to the Disclosing Party
      with respect to such Confidential Information; or

                  (e)   is required to be disclosed to comply with applicable
      laws or regulations (such as disclosure to the EPA or the United States
      Patent and Trademark Office or to their foreign equivalents), or to comply
      with a court or administrative order, provided that the Disclosing Party
      receives prior written notice of such disclosure and that the Receiving
      Party takes all reasonable and lawful actions to obtain confidential
      treatment for such disclosure and, if possible, to minimize the extent of
      such disclosure.

      8.4.  PUBLICATIONS. ArQule shall not publish any information with respect
to ArQule Derivative Compounds, Monsanto Compounds, or Monsanto Derivative
Compounds without the prior written permission of Monsanto, which may be
withheld in its sole discretion.



                                       18
<PAGE>   20


      8.5.  SURVIVAL OF OBLIGATIONS. The obligations set forth in this Article
  shall remain in effect after termination of this Agreement, except that the
obligations of the Receiving Party to destroy or return Confidential Information
to the Disclosing Party shall survive until fulfilled.

9.    Representations and Warranties.
      ------------------------------

      9.1.  AUTHORIZATION. Each Party represents and warrants to the other that
it has the legal right and power to enter into this Agreement, to extend the
rights and licenses granted to the other in this Agreement, and to fully perform
its obligations hereunder, and that the performance of such obligations will not
conflict with its charter documents or any agreements, contracts, or other
arrangements to which it is a party.

      9.2.  PRIOR LICENSES IN FIELD. ArQule hereby represents and warrants that
as of the Effective Date it has granted no other license, right or interest to
ArQule Compounds to any third party for the testing, making, use, development or
sale of ArQule Compounds in the Field.

      9.3.  NON-INFRINGEMENT. ArQule represents that to its knowledge the
conduct of the business of ArQule as it is currently being conducted or as it is
proposed to be conducted pursuant to this Agreement does not conflict with or
infringe on the intellectual property of any other person, and ArQule has not
received any claim or notice from any person to such effect which is still
pending. ArQule has no knowledge of any claim or fact that would give rise to a
claim that any of the ArQule Patents is invalid or unenforceable. To ArQule's
knowledge, the ArQule Patents are not infringed by any third party.

10.   Indemnification and Insurance.
      -----------------------------

      10.1. Indemnification. Each Party (the "Indemnitor") shall indemnify,
defend, and hold harmless the other Party and its Primary Affiliates and their
directors, officers, employees, and agents and their respective successors,
heirs and assigns (the "Indemnitees"), against any liability, damage, loss, or
expense (including reasonable attorneys fees and expenses of litigation)
incurred by or imposed upon the Indemnitees or any one of them in connection
with any claims, suits, actions, demands, or judgments arising out of any theory
of product liability (including, but not limited to, actions in the form of
tort, warranty, or strict liability) concerning any product (or any process or
service) that is made, used, or sold by the Indemnitor pursuant to any right or
license granted under this Agreement; provided, however, that such
indemnification right shall not apply to any liability, damage, loss, or expense
to the extent directly attributable to the negligent activities, reckless
misconduct, or intentional misconduct of the Indemnitees.

      10.2. Procedures. Any Indemnitee that intends to claim indemnification
under Section 10.1 shall promptly notify the appropriate Indemnitor of any claim
in respect of which the Indemnitee intends to claim such indemnification, and
the Indemnitor shall assume the defense thereof with counsel mutually
satisfactory to the Parties; provided, however, that an Indemnitee shall have
the right to retain its own counsel, with the fees and expenses to be paid by
the Indemnitor, if representation of such Indemnitee by the counsel retained by
the Indemnitor would be inappropriate due to actual or potential differing
interests between such Indemnitee and any other party represented by such
counsel in such proceedings. The indemnity agreement in Section 10.1. shall not
apply to amounts paid in settlement of any loss, claim, liability or action if



                                       19
<PAGE>   21


such settlement is effected without the consent of the Indemnitor, which consent
shall not be withheld unreasonably. The failure to deliver notice to the
Indemnitor within a reasonable time after the commencement of any such action,
if prejudicial to its ability to defend such action, shall relieve the
Indemnitor of any liability to the Indemnitee under Section 10.1. Each party and
its Primary Affiliates and their employees and agents shall cooperate fully with
the other party and its legal representatives in the investigation of any
action, claim or liability covered by this indemnification.

      10.3. Insurance. Each party shall maintain at least $5,000,000 in
insurance coverage for its own potential liabilities to the Indemnitees as set
forth in this Article 10.

11.   Term and Termination.
      --------------------
 
      11.1. TERM. This Agreement shall commence on the Effective Date and shall
remain in effect until the expiration of the last to expire of the applicable
Patent Rights covering any Royalty-Bearing Product as provided in this
Article 11.

      11.2. BREACH OF PAYMENT OBLIGATIONS. In the event that Monsanto fails to
make timely payment of any amounts due to ArQule under this Agreement, ArQule
may terminate this Agreement upon ninety (90) days written notice to Monsanto,
unless Monsanto pays all past-due amounts within such ninety-day notice period.

      11.3. MATERIAL BREACH. In the event that either party commits a material
breach of any of its obligations under this Agreement (other than as provided in
Section 11.2) and such party fails (i) to remedy that breach within ninety (90)
days after receiving written notice thereof from the other party or (ii) to
commence dispute resolution pursuant to Section 12.5, within ninety (90) days
after receiving written notice of that breach from the other party, the other
party may immediately terminate this Agreement upon written notice to the
breaching party.

      11.4. EFFECT OF TERMINATION. Termination of this Agreement shall not
relieve the parties of any obligation accruing prior to such termination. The
provisions of Article 4, Article 5, Article 6 and Article 7 (with respect only
to milestone payments and royalties accrued at the time of termination but not
yet paid), Article 8, Article 9 and Article 12 shall survive the expiration or
termination of this Agreement.

12.   Miscellaneous.
      -------------
 
      12.1. RELATIONSHIP OF PARTIES. Nothing in this Agreement is intended or
shall be deemed to constitute a partnership, agency, employer-employee or joint
venture relationship between the parties. No party shall incur any debts or make
any commitments for the other, except to the extent, if at all, specifically
provided herein.

      12.2. PUBLICITY. Neither party shall use the name of the other party or
reveal the terms of this Agreement in any publicity or advertising without the
prior written approval of the other party, except that (i) either party may use
the text of a written statement approved in advance by both parties without
further approval, (ii) either party shall have the right to identify the other
party and to disclose the terms of this Agreement as required by applicable
securities laws or 


                                       20
<PAGE>   22

other applicable law or regulation, and (iii) either party may use the name of
the other party and reveal the existence of this Agreement.

      12.3. NON-SOLICITATION. During the term of this Agreement and thereafter
for a period of two (2) years, each party agrees not to seek to persuade or
induce any employee of the other party to discontinue his or her employment with
that party in order to become employed by or associated with any business,
enterprise, or effort that is associated with its own business.

      12.4. GOVERNING LAW. This Agreement shall be governed by and construed in
accordance with the laws of the State of New York.

      12.5. Dispute Resolution Procedures.
            -----------------------------

                  (a) The parties hereby agree that they will attempt in good
      faith to resolve any controversy, claim or dispute ("Dispute") arising out
      of or relating to this Agreement promptly by negotiations. Any such
      Dispute which is not settled by the parties within fifteen (15) days after
      notice of such Dispute is given by one party to the other in writing shall
      be referred to the President of ArQule and the Director of Plant
      Protection of the Ceregen division of Monsanto who are authorized to
      settle such Disputes on behalf of their respective companies ("Senior
      Executives"). The Senior Executives will meet for negotiations within
      fifteen (15) days of the end of the 15 day negotiation period referred to
      above, at a time and place mutually acceptable to both Senior Executives.
      If the Dispute has not been resolved within thirty (30) days after the end
      of the 15 day negotiation period referred to above (which period may be
      extended by mutual agreement), subject to any rights to injunctive relief
      and unless otherwise specifically provided for herein, any Dispute will be
      settled first by non-binding mediation and thereafter by arbitration as
      described in subsections (b) and (c) below.

                  (b) Any Dispute which is not resolved by the parties within
      the time period described in subsection (a) shall be submitted to an
      alternative dispute resolution process ("ADR"). Within five (5) business
      days after the expiration of the thirty (30) day period set forth in
      subsection (a), each party shall select for itself a representative with
      the authority to bind such party and shall notify the other party in
      writing of the name and title of such representative. Within ten (10)
      business days after the date of delivery of such notice, the
      representatives shall schedule a date for engaging in non-binding ADR with
      a neutral mediator or dispute resolution firm mutually acceptable to both
      representatives. Any such mediation shall be held in Boston, Massachusetts
      if brought by Monsanto and St. Louis, Missouri if brought by ArQule.
      Thereafter, the representatives of the parties shall engage in good faith
      in an ADR process under the auspices of such individual or firm. If the
      representatives of the parties have not been able to resolve the Dispute
      within thirty (30) business days after the conclusion of the ADR process,
      or if the representatives of the parties fail to schedule a date for
      engaging in non-binding ADR within the ten (10) day period set forth
      above, the Dispute shall be settled by binding arbitration as set forth in
      subsection (c) below. If the representatives of the parties resolve the
      dispute within the thirty (30) day period set forth above, then such
      resolution shall be binding upon the parties. If either party fails to
      abide by such resolution, the other party can immediately refer the matter
      to arbitration under Section 13.5(c).



                                       21

<PAGE>   23


                  (c) If the parties have not been able to resolve the Dispute
      as provided in subsections (a) and (b) above, the Dispute shall be finally
      settled by binding arbitration. Any arbitration hereunder shall be
      conducted under rules of the American Arbitration Association. The
      arbitration shall be conducted before three arbitrators chosen according
      to the following procedure: each of the parties shall appoint one
      arbitrator and the two so nominated shall choose the third, PROVIDED THAT
      in the case of a dispute as to decisions of the Research Committee each
      party shall designate one (1) neutral having the following minimum
      scientific qualifications: a Ph.D. degree in chemistry or life sciences
      and/or an M.D. degree plus at least ten (10) years of relevant business or
      scientific research experience. These two (2) neutrals shall select a 
      third neutral having the same minimum scientific qualifications within 
      fourteen (14) days of the appointment of the first two (2) neutrals. 
      None of the neutrals shall be an employee, director or shareholder of
      either party or any of their subsidiaries, Secondary Affiliates or
      otherwise have a materially conflicting interest in the outcome of such
      proceeding. If the arbitrators chosen by the parties cannot agree on the
      choice of the third arbitrator within a period of thirty (30) days after
      their appointment, then the third arbitrator with such requisite
      qualifications shall be appointed by the Court of Arbitration of the
      American Arbitration Association. Any such arbitration shall be held in
      Boston, Massachusetts if brought by Monsanto and St. Louis, Missouri if
      brought by ArQule or such other location as the arbitrators may agree. The
      arbitrators shall have the authority to grant specific performance, and to
      allocate between the parties the costs of arbitration in such equitable
      manner as they determine. The arbitral award (i) shall be final and 
      binding upon the parties; and (ii) may be entered in any court of 
      competent jurisdiction.

                  (d) Nothing contained in this Section or any other provisions
      of this Agreement shall be construed to limit or preclude a party from
      bringing any action in any court of competent jurisdiction for injunctive
      or other provisional relief to compel the other party to comply with its
      obligations hereunder before or during the pendency of mediation or
      arbitration proceedings. The parties hereby irrevocably consent to submit
      to the jurisdiction of the federal courts located within the Commonwealth
      of Massachusetts and the state of Missouri and agree that venue is proper
      in any such court and will not seek to alter or contest such venue.

      12.6. COUNTERPARTS. This Agreement may be executed in one or more
counterparts, each of which shall be deemed an original, and all of which
together shall be deemed to be one and the same instrument.

      12.7. HEADINGS. All headings in this Agreement are for convenience only
and shall not affect the meaning of any provision hereof.

      12.8. BINDING EFFECT. This Agreement shall inure to the benefit of and be
binding upon the parties, their Primary Affiliates, and their respective lawful
successors and assigns.

      12.9. ASSIGNMENT. This Agreement may not be assigned by either party
without the prior written consent of the other party, except that either party
may assign this Agreement to a successor in connection with the merger,
consolidation, spin-off or sale of all or substantially all 





                                       22

<PAGE>   24

of its assets or that portion of its business pertaining to the subject matter
of this Agreement. Monsanto has the right to extend its rights and benefits
under this Agreement to any Primary Affiliate.

      12.10. NOTICES. All notices, requests, demands and other communications
required or permitted to be given pursuant to this Agreement shall be in writing
and shall be deemed to have been duly given upon the date of receipt if
delivered by hand, recognized international overnight courier, confirmed
facsimile transmission, or registered or certified mail, return receipt
requested, postage prepaid to the following addresses or facsimile numbers:

If to Monsanto:                           If to ArQule:

Monsanto Company                          ArQule, Inc.
700 Chesterfield Parkway North            200 Boston Avenue, Suite 3600
St. Louis, Missouri 63198                 Medford, MA  02155
Attention: Grace Bonner                   Attention:  Eric B. Gordon
Tel: (314) 694-3165                       Tel: (617) 395-4100
Fax: (314) 694-9009                       Fax: (617) 395-1225

with a copy to:                           with a copy to:

Bryan Cave LLP                            Palmer & Dodge
One Metropolitan Sq., Suite 3600          One Beacon Street
St. Louis, Missouri  63102                Boston, MA  02108
Attention:  James H. Erlinger III         Attention:  Michael Lytton, Esquire
Tel: (314) 259-2723                       Tel: (617) 573-0327
Fax: (314) 259-2020                       Fax: (617) 227-4420


Either party may change its designated address and facsimile number by notice to
the other party in the manner provided in this Section.

      12.11. AMENDMENT AND WAIVER. This Agreement may be amended, supplemented,
or otherwise modified only by means of a written instrument signed by both
parties. Any waiver of any rights or failure to act in a specific instance shall
relate only to such instance and shall not be construed as an agreement to waive
any rights or fail to act in any other instance, whether or not similar.

      12.12. SEVERABILITY. In the event that any provision of this Agreement
shall, for any reason, be held to be invalid or unenforceable in any respect,
such invalidity or unenforceability shall not affect any other provision hereof,
and the parties shall negotiate in good faith to modify the Agreement to
preserve (to the extent possible) their original intent.

      12.13. ENTIRE AGREEMENT. This Agreement constitutes the entire agreement
between the parties with respect to the subject matter hereof and supersedes all
prior agreements or understandings between the parties relating to the subject
matter hereof.



                                       23
<PAGE>   25


      12.14. FORCE MAJEURE. Neither party shall be held liable or responsible
to the other party, nor be deemed to be in breach of this Agreement, for failure
or delay in fulfilling or performing any provisions of this Agreement when such
failure or delay is caused by or results from any cause whatsoever outside the
reasonable control of the party concerned including, but not limited to, fire,
explosion, breakdown of plant, strike, lock-out, labor disputes, casualty or
accident, lack or failure of transportation facilities, flood, lack or failure
of sources of supply or of labor, raw materials or energy, civil commotion,
embargo, any law, regulation, decision, demand or requirement of any national or
local government or authority. The party claiming relief shall, without delay,
notify the other party by registered airmail or by telefax of the interruption
and cessation thereof and shall use its best efforts to remedy the effects of
such hindrance with all reasonable dispatch. The onus of proving that any such
Force Majeure event exists shall rest upon the party so asserting. During the
period that one party is prevented from performing its obligations under this
Agreement due to a Force Majeure event, the other party may, in its sole
discretion, suspend any obligations that relate thereto. Upon cessation of such
Force Majeure event the parties hereto shall use their best efforts to make up
for any suspended obligations. If such Force Majeure event is anticipated to
continue, or has existed for nine (9) consecutive months or more, this Agreement
may be forthwith terminated by either party by registered airmail or by telefax.
In case of such termination the terminating party will not be required to pay to
the other party any indemnity whatsoever.








                                       24
<PAGE>   26




      IN WITNESS WHEREOF, the undersigned have duly executed and delivered this
Agreement as a sealed instrument effective as of the date first above written.


MONSANTO COMPANY                            ARQULE, INC.



By: /s/  Derek K. Rapp                      By: /s/ Eric B. Gordon
    ------------------------------------        --------------------------------
Name:  Derek K. Rapp                        Name:  Eric B. Gordon
Title: Director, Commercial Partnerships    Title: President and Chief Executive
       and Licenses











                                       25
<PAGE>   27





                                    EXHIBIT A

                                  RESEARCH PLAN

                [                                            ]*



* Confidential information omitted and filed with the Commission.



<PAGE>   28




                                    EXHIBIT B

                      FORM OF MATERIALS TRANSFER AGREEMENT

      This Agreement, dated as of __________, __, _____, is between ArQule, Inc.
("ArQule"), a Delaware corporation, and Monsanto Company ("Monsanto"), a
Delaware corporation and _________________, a ___________________ ("Recipient").

      WHEREAS, Monsanto and ArQule have entered into that certain Array Delivery
and Testing Agreement, dated as December 23, 1996, ("Array Delivery Agreement"),
pursuant to which ArQule agreed to provide Monsanto with certain compound arrays
for screening on the terms and subject to the conditions set forth in the Array
Delivery Agreement and to perform certain other compound development activities;
and

      WHEREAS, pursuant to Section 4.1 of the Array Delivery Agreement, Monsanto
is permitted to deliver such compounds to third parties such as Recipient,
provided such parties execute and deliver this Agreement to ArQule.

      NOW, THEREFORE, in consideration of the premises and the mutual covenants
and conditions contained herein and for other good and valuable consideration,
the receipt and sufficiency of which is hereby acknowledged, the parties hereto
agree as follows:

      1. SUPPLY OF MATERIALS: Within ____ days after receiving an original of
this Agreement executed by all parties, Monsanto will supply Recipient with the
compounds set forth on Exhibit 1 (the "Materials"). Upon written request,
Monsanto may provide the Recipient with additional quantities of such Materials
or with additional compounds, which compounds shall also be considered Materials
for the purposes of this Agreement.

      2. USE AND TRANSFER RESTRICTIONS: Recipient acknowledges and agrees that
the Materials may be proprietary to and owned by ArQule and are or may be
covered by claims of U.S. and international patents or patent applications of
ArQule and/or Monsanto. Recipient agrees to use the Materials solely to screen
them for potential agricultural and in planta use for Monsanto using the assay
procedure previously disclosed to Monsanto. Recipient agrees (i) not to transfer
such Materials to any third party without the prior written consent of ArQule
and Monsanto, (ii) to permit access to the Materials only to its employees and
consultants requiring such access, (iii) to inform such employees and
consultants of the proprietary nature of the Materials, (iv) to take reasonable
precautions, at least as stringent as those observed by Recipient to protect its
own proprietary materials, to ensure that such employees and consultants observe
the obligations of Recipient pursuant to this Section and (v) to execute and
deliver any documents of assignment or conveyance that may be necessary to
effectuate the ownership rights of ArQule or Monsanto in the Materials. Upon the
expiration of this Agreement, Recipient shall, at the instruction of ArQule or
Monsanto, either destroy or return any unused Materials.

      3. COMPLIANCE WITH LAW: Recipient agrees to comply with all federal,
state, and local laws and regulations applicable to the use, testing, storage,
disposal, and transfer of the Materials. Recipient assumes sole responsibility
for any violation of such laws or regulations by Recipient or any of its
affiliates or sublicensees.

<PAGE>   29


      4. TERMINATION: This Agreement shall commence on the date last written
below and continue for a period of ____ months. Sections 3, 6 and 7 shall
survive termination of this Agreement.

      5. NO WARRANTIES: Any Materials delivered pursuant to this Agreement are
understood to be experimental in nature and may have hazardous properties.
Recipient should assume that the Materials are dangerous and should use
appropriate precautions. NEITHER MONSANTO NOR ARQULE MAKES ANY REPRESENTATIONS,
OR EXTENDS ANY WARRANTIES OF ANY KIND, EITHER EXPRESS OR IMPLIED, WITH RESPECT
TO THE COMPOUNDS. THERE ARE NO EXPRESS OR IMPLIED WARRANTIES OF MERCHANTABILITY
OR FITNESS FOR A PARTICULAR PURPOSE, OR THAT THE USE OF THE MATERIALS WILL NOT
INFRINGE ANY PATENT RIGHTS OF OTHERS.

      6. ASSIGNMENT OF INVENTIONS: Recipient agrees promptly to disclose to
Monsanto any and all ideas, concepts, discoveries, inventions, developments,
improvements, trade secrets, technical data, know-how or [agricultural or in
planta] materials that are conceived, devised, invented, developed or reduced to
practice or tangible medium by Recipient, or any of its agents, employees or
contractors, or under its direction, during the term of this Agreement and which
arise out of its screening or evaluation of the Materials (hereinafter
"Inventions"). Recipient hereby assigns to Monsanto all of its right, title and
interest in and to the Inventions and any and all related patent rights,
copyrights and applications and registrations therefor. During and after the
expiration of this Agreement, Recipient shall cooperate with Monsanto, at
Monsanto's expense, in obtaining proprietary protection for the Inventions and
shall execute all documents which Monsanto shall reasonably request in order to
perfect Monsanto's rights in the Inventions.

      7. INDEMNIFICATION: Recipient assumes all liability for, and agrees to
indemnify, defend, and hold harmless ArQule and Monsanto and their respective
directors, officers, representatives, employees, and agents against, all losses,
expenses (including without limitation any legal fees and expenses), claims,
demands, damages, judgments, suits, or other actions arising from the use,
testing, storage, or disposal of the Materials by Recipient and its agents,
employees or contractors, or from any breach of its obligations under Section 2
of this Agreement.

      8. MISCELLANEOUS: This Agreement shall not be assigned or otherwise
transferred by Recipient without the prior written consent of ArQule and
Monsanto. This Agreement shall be governed by the laws of the State of New York.
This Agreement constitutes the entire understanding of the parties and
supersedes all prior agreements, written or oral, with respect to the subject
matter hereof.




<PAGE>   30


                                          Recipient

                                          --------------------------
                                          Name:
                                          Title:
                                          Date:


Tel:

Fax:

                                                ACCEPTED AND AGREED:
                                                ArQule, Inc.


                                                ------------------------
                                                Name:
                                                Title:
                                                Date:


                                                ACCEPTED AND AGREED:
                                                Monsanto Company



                                                ------------------------
                                                Name:
                                                Title:
                                                Date:










<PAGE>   1
 
   
                                                                    EXHIBIT 23.1
    
 
   
                       CONSENT OF INDEPENDENT ACCOUNTANTS
    
 
   
We hereby consent to the use in the Prospectus constituting part of this
Registration Statement on Form S-1 of our report dated February 25, 1997
relating to the financial statements of ArQule, Inc., which appears in such
Prospectus. We also consent to the application of such report to the Financial
Statement Schedule for the three years ended December 31, 1996 listed under item
16(b) of this Registration Statement when such schedule is read in conjunction
with the financial statements referred to in our report. The audits referred to
in such report also included this schedule. We also consent to the reference to
us under the heading "Experts" in such Prospectus.
    
 
   
PRICE WATERHOUSE LLP
    
 
   
Boston, Massachusetts
    
   
April 3, 1997
    


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