SCRIPTGEN PHARMACEUTICALS INC
S-1/A, 1998-02-11
PHARMACEUTICAL PREPARATIONS
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<PAGE>
   
   AS FILED WITH THE SECURITIES AND EXCHANGE COMMISSION ON FEBRUARY 11, 1998
    
 
                                                      REGISTRATION NO. 333-40687
- --------------------------------------------------------------------------------
- --------------------------------------------------------------------------------
 
                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549
 
                            ------------------------
 
   
                                AMENDMENT NO. 3
                                       TO
                                    FORM S-1
                             REGISTRATION STATEMENT
                                     UNDER
                           THE SECURITIES ACT OF 1933
    
 
                            ------------------------
 
                        SCRIPTGEN PHARMACEUTICALS, INC.
             (Exact name of registrant as specified in its charter)
 
<TABLE>
<S>                                       <C>                                       <C>
                DELAWARE                                    2834                                   22-3193172
    (State or other jurisdiction of             (Primary Standard Industrial                    (I.R.S. Employer
     incorporation or organization)             Classification Code Number)                   Identification No.)
</TABLE>
 
                            ------------------------
 
                               200 BOSTON AVENUE
                               MEDFORD, MA 02155
                                 (781) 393-8000
    (Address, including zip code, and telephone number, including area code,
                  of registrant's principal executive offices)
 
                         ------------------------------
 
                                 MARK T. WEEDON
                     PRESIDENT AND CHIEF EXECUTIVE OFFICER
                        SCRIPTGEN PHARMACEUTICALS, INC.
                               200 BOSTON AVENUE
                               MEDFORD, MA 02155
                                 (781) 393-8000
 
               (Name, address, including zip code, and telephone
               number, including area code, of agent for service)
                         ------------------------------
 
                                with copies to:
 
<TABLE>
<S>                                                 <C>
               CARL E. KAPLAN, ESQ.                             RICHARD R. PLUMRIDGE, ESQ.
           FULBRIGHT & JAWORSKI L.L.P.                          LUCI STALLER ALTMAN, ESQ.
                 666 FIFTH AVENUE                            BROBECK, PHLEGER & HARRISON LLP
             NEW YORK, NEW YORK 10103                           1633 BROADWAY, 47TH FLOOR
                  (212) 318-3000                                 NEW YORK, NEW YORK 10019
                                                                      (212) 581-1600
</TABLE>
 
                            ------------------------
 
       APPROXIMATE DATE OF COMMENCEMENT OF PROPOSED SALE OF SECURITIES TO THE
                                    PUBLIC:
  As soon as practicable after this Registration Statement becomes effective.
 
    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, as amended (the "Securities Act"), check the following box. / /
 
    If this Form is filed to register additional securities for an offering
pursuant to Rule 462(b) under the Securities Act, please check the following box
and list the Securities Act registration statement number of the earlier
effective registration statement for the same offering. / /
 
    If this Form is a post-effective amendment filed pursuant to 462(c) under
the Securities Act, check the following box and list the Securities Act
registration statement number of the earlier effective registration statement
for the same offering. / /
 
    If this Form is a post-effective amendment filed pursuant to Rule 462(d)
under the Securities Act, check the following box and list the Securities Act
registration statement number of the earlier effective registration statement
for the same offering. / /
 
    If delivery of the prospectus is expected to be made pursuant to Rule 434,
please check the following box. /X/
 
                            ------------------------
 
    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, OR UNTIL THE REGISTRATION STATEMENT SHALL BECOME EFFECTIVE
ON SUCH DATE AS THE SECURITIES AND EXCHANGE COMMISSION, ACTING PURSUANT TO SAID
SECTION 8(A), MAY DETERMINE.
 
- --------------------------------------------------------------------------------
- --------------------------------------------------------------------------------
<PAGE>
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 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.
<PAGE>
   
PROSPECTUS                        Subject to Completion, Dated February 11, 1998
    
- --------------------------------------------------------------------------------
 
                                3,000,000 Shares
 
                                      [LOGO]
                        SCRIPTGEN PHARMACEUTICALS, INC.
 
                                  Common Stock
          ------------------------------------------------------------
 
All of the 3,000,000 shares of Common Stock offered hereby (the "Offering") are
being offered by Scriptgen Pharmaceuticals, Inc. ("Scriptgen" or the "Company").
Prior to the Offering, there has been no public market for the Common Stock. It
is currently estimated that the initial public offering price will be between
$11.00 and $13.00 per share. See "Underwriting" for the factors to be considered
in determining the initial public offering price.
 
The Common Stock has been approved for quotation on the Nasdaq National Market
under the symbol "SCRP."
 
Concurrent with the Offering, Hoechst Marion Roussel has agreed to purchase
250,000 shares of Common Stock directly from the Company (assuming an initial
public offering price of $12.00), for an aggregate purchase price of $3,000,000,
pursuant to an existing agreement with the Company (the "Private Placement").
See "Business--Collaborative Arrangements."
 
FOR A DISCUSSION OF CERTAIN RISKS OF AN INVESTMENT IN THE SHARES OF COMMON STOCK
OFFERED HEREBY, SEE "RISK FACTORS" ON PAGES 7-17.
 
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 Discounts       Proceeds to
                                                     Public      and Commissions(1)        Company(2)
<S>                                  <C>                     <C>                     <C>
- -----------------------------------------------------------------------------------------------------
Per Common Share                               $                       $                    $
- -----------------------------------------------------------------------------------------------------
Total(3)                                       $                       $                    $
- -----------------------------------------------------------------------------------------------------
</TABLE>
 
(1)  THE COMPANY HAS AGREED TO INDEMNIFY THE UNDERWRITERS AGAINST CERTAIN
     LIABILITIES, INCLUDING LIABILITIES UNDER THE SECURITIES ACT OF 1933, AS
     AMENDED. SEE "UNDERWRITING."
 
(2)  BEFORE DEDUCTING EXPENSES OF THE OFFERING PAYABLE BY THE COMPANY ESTIMATED
     TO BE $1,050,000.
 
(3)  THE COMPANY HAS GRANTED THE UNDERWRITERS A 30-DAY OPTION TO PURCHASE UP TO
     450,000 ADDITIONAL SHARES OF COMMON STOCK ON THE SAME TERMS PER SHARE
     SOLELY TO COVER OVER-ALLOTMENTS, IF ANY. IF SUCH OPTION IS EXERCISED IN
     FULL, THE TOTAL PRICE TO PUBLIC WILL BE $         , THE TOTAL UNDERWRITING
     DISCOUNTS AND COMMISSIONS WILL BE $         AND THE TOTAL PROCEEDS TO
     COMPANY WILL BE $         . SEE "UNDERWRITING."
 
The Common Stock is being offered by the Underwriters as set forth under
"Underwriting" herein. It is expected that the delivery of the certificates
therefor will be made at the offices of SBC Warburg Dillon Read Inc., New York,
New York, on or about       , 1998. The Underwriters include:
 
SBC WARBURG DILLON READ INC.                        VOLPE BROWN WHELAN & COMPANY
<PAGE>
                       SCRIPTGEN'S DRUG DISCOVERY PROCESS
 
                         GATE IDENTIFIES AND VALIDATES
                                  GENE TARGETS
 
                       [GRAPHICAL DEPICTION OF TARGET RNA
                              AND TARGET PROTEIN]
 
                         ATLAS AND SCAN RAPIDLY SCREEN
                            LARGE COMPOUND LIBRARIES
 
                   [GRAPHICAL DEPICTION OF COMPOUND LIBRARY]
 
                            ATLAS AND SCAN IDENTIFY
                             COMPOUNDS THAT BIND TO
                       TARGET RNA          TARGET PROTEIN
 
                       [GRAPHICAL DEPICTIONS OF COMPOUNDS
                              BINDING TO TARGETS]
 
                        BIOLOGICAL ASSAYS IDENTIFY LEAD
                          COMPOUNDS FOR DEVELOPMENT AS
                                DRUG CANDIDATES
 
                         [GRAPHICAL DEPICTIONS OF LEAD
                                   COMPOUNDS]
 
Scriptgen's present and future drug candidates will require marketing approval
from the FDA.
 
CERTAIN PERSONS PARTICIPATING IN THE OFFERING MAY ENGAGE IN TRANSACTIONS THAT
STABILIZE, MAINTAIN OR OTHERWISE AFFECT THE PRICE OF THE COMMON STOCK, INCLUDING
OVER-ALLOTMENT, ENTERING STABILIZING BIDS, EFFECTING SYNDICATE COVERING
TRANSACTIONS AND IMPOSING PENALTY BIDS. FOR A DESCRIPTION OF THESE ACTIVITIES,
SEE "UNDERWRITING."
 
                                       2
<PAGE>
                               PROSPECTUS SUMMARY
 
    THE FOLLOWING SUMMARY IS QUALIFIED IN ITS ENTIRETY BY REFERENCE TO, AND
SHOULD BE READ IN CONJUNCTION WITH, THE MORE DETAILED INFORMATION AND THE
FINANCIAL STATEMENTS AND RELATED NOTES THERETO APPEARING ELSEWHERE IN THIS
PROSPECTUS. UNLESS INDICATED OTHERWISE, ALL INFORMATION IN THIS PROSPECTUS (I)
ASSUMES THAT THE UNDERWRITERS' OVER-ALLOTMENT OPTION IS NOT EXERCISED, (II)
GIVES RETROACTIVE EFFECT TO THE CONVERSION OF THE COMPANY'S SERIES A PREFERRED
STOCK, SERIES B PREFERRED STOCK, SERIES C PREFERRED STOCK AND SERIES D PREFERRED
STOCK TO COMMON STOCK, PAR VALUE $0.01 PER SHARE (THE "COMMON STOCK") UPON THE
CONSUMMATION OF THE OFFERING, (III) GIVES EFFECT TO THE FILING OF AN AMENDMENT
TO THE COMPANY'S RESTATED CERTIFICATE OF INCORPORATION CREATING A CLASS OF
UNDESIGNATED PREFERRED STOCK AND (IV) GIVES RETROACTIVE EFFECT TO A SUBSEQUENT
1-FOR-3.07459 REVERSE SPLIT OF THE SHARES OF COMMON STOCK, TO BE EFFECTED BEFORE
THE COMPLETION OF THE OFFERING. THIS PROSPECTUS CONTAINS CERTAIN FORWARD-LOOKING
STATEMENTS WHICH INVOLVE RISKS AND UNCERTAINTIES. THE COMPANY'S ACTUAL RESULTS
COULD DIFFER MATERIALLY FROM THE RESULTS ANTICIPATED IN THOSE FORWARD-LOOKING
STATEMENTS AS A RESULT OF CERTAIN OF THE FACTORS SET FORTH IN THIS PROSPECTUS.
PROSPECTIVE INVESTORS SHOULD CAREFULLY CONSIDER THE INFORMATION SET FORTH UNDER
THE HEADING "RISK FACTORS."
 
                                  THE COMPANY
 
    Scriptgen Pharmaceuticals, Inc. ("Scriptgen" or the "Company") utilizes its
proprietary high throughput technologies to enable and accelerate the discovery
of innovative small molecule drugs. Scriptgen's technology platform allows the
Company and its collaborators to exploit the opportunities afforded by advances
in genomics and combinatorial chemistry, and opens new avenues of drug
discovery. The Company's technology platform identifies and validates novel gene
targets for therapeutic intervention, and then uses novel assay systems to
rapidly screen compounds against those targets, even before the gene targets'
characteristics or functions are well understood. The Company believes that the
application of its technologies addresses many of the limitations associated
with traditional drug discovery and provides substantial cost savings
opportunities. The Company commercializes its technology platform through (i)
collaborations with pharmaceutical and technology companies and (ii) the
Company's internal development program.
 
    The Company's core technologies include GATE (Genetics Assisted Target
Evaluation), a family of high throughput target identification and validation
systems, and ATLAS (Any Target Ligand Affinity Screen) and SCAN (Screen for
Compounds with Affinity for Nucleic Acids), the high speed, solution based,
assay systems which identify compounds that bind to virtually any protein or
structured RNA, respectively. GATE measures the effects of transiently removing
a specific gene from a cell, and by reproducing conditions that closely resemble
drug mechanism of action, generates data more predictive of target behavior than
traditional methods. ATLAS and SCAN rapidly measure the affinity (strength) of
compounds that bind to targets even before the gene functions are well
understood, enabling the Company to work with targets that are unsuitable for
traditional high throughput screens. The Company believes ATLAS and SCAN
increase dramatically the number of targets and compounds that may be screened
in a given time period, and reduce to weeks what often requires months or years
of assay development time when using traditional high throughput functional
assays. The Company has used GATE to identify and validate novel infectious
disease targets, and has used ATLAS and SCAN to identify lead compounds, two of
which have progressed to pre-clinical development. ATLAS and SCAN are broadly
applicable to research in multiple therapeutic areas, and have demonstrated
utility in the areas of anti-infectives, oncology, cardiovascular, and
respiratory and immunologic disorders.
 
    The Company's strategy is to maximize the commercial opportunities presented
by its technology platform and pipeline of drug candidates by entering into
multiple collaborations and retaining rights to independently develop certain
products. Scriptgen has collaborative agreements with pharmaceutical and
technology companies, and routinely evaluates opportunities to enter into
collaborations with other potential partners.
 
        HOECHST MARION ROUSSEL. The Company is using its technology platform
    to seek to identify new fungal targets and antifungal drug candidates in
    a collaboration with Hoechst Marion Roussel ("HMR"). The Company expects
    to have received an aggregate of $9 million from HMR under the
    collaboration by the completion of the Offering, of which $6 million
    will be technology access fees and $3 million will be proceeds from the
    sale of Common Stock to HMR concurrent with the Offering. The Company
    will also receive research and development payments, and will
 
                                       3
<PAGE>
    receive payments when and if certain milestones are achieved and
    royalties on the sales of any new drug resulting from the collaboration.
 
        BIOCHEM PHARMA INC. Scriptgen is using its technology platform to
    identify drug candidates which are (i) active against the Hepatitis B
    virus (the "HBV Program") and (ii) which act as small molecule mimics of
    therapeutic proteins (the "Dimerescent Program"). Scriptgen will be
    responsible for all aspects of drug discovery. BioChem Pharma Inc.
    (together with its wholly owned subsidiary, BioChem Pharma Holdings
    Inc., "BioChem") will be responsible for pre-clinical and clinical
    development, and will retain worldwide commercialization rights. The
    Company will receive milestone payments when and if BioChem exercises
    options on drug candidates in the Dimerescent Program. The companies
    will share any profits generated by the HBV Program or the Dimerescent
    Program according to the terms of the agreement. In addition, BioChem
    acquired $20 million of preferred stock of Scriptgen and a warrant to
    purchase shares of Common Stock.
 
        ELI LILLY AND COMPANY. Scriptgen is using ATLAS to identify novel
    drug candidates active against two targets selected by Eli Lilly and
    Company ("Eli Lilly"). Two additional targets may be selected by Eli
    Lilly for high throughput screening in 1998, assuming certain milestones
    are met. In October 1997, Eli Lilly and the Company expanded the scope
    of the collaboration to screen additional compounds from the Company's
    compound library. Under the agreement with Eli Lilly, Scriptgen receives
    research and development payments and will receive payments when and if
    certain milestones are achieved and royalties on the sales of any new
    drug resulting from the collaboration.
 
        HOFFMANN-LA ROCHE INC. The Company is using ATLAS to identify drug
    candidates against a cancer-related target identified by Hoffmann-La
    Roche Inc. ("Roche"). Under the agreement with Roche, Scriptgen receives
    research and development payments and will receive payments when and if
    certain milestones are achieved and royalties on the sales of any new
    drug resulting from the collaboration.
 
        MONSANTO COMPANY. Scriptgen is using its technology platform in a
    collaboration with Monsanto Company ("Monsanto") to identify and
    validate novel fungal targets from plant pathogens and to identify novel
    antifungal agents. Under the agreement with Monsanto, Scriptgen receives
    research and development payments and will receive payments when and if
    certain milestones are achieved and royalties on the sales of any
    product developed by Monsanto for IN PLANTA applications.
 
    Scriptgen's internal development efforts have initially focused on
anti-infectives, where it has identified novel cidal targets and lead compounds
in the fungal, bacterial and viral areas. The Company has also completed
feasibility studies on novel targets in a number of other areas, including
oncology and immunologic disorders, and in several cases has identified drug
candidates. The Company believes that the anti-infective market is attractive as
an initial field of focus because of the large market potential, the particular
suitability of the Company's proprietary technology and the relatively low
technical and regulatory hurdles for this class of diseases. Scriptgen has
progressed rapidly in the anti-infective area and has four lead compounds in
development as well as a number of other potential drug candidates under review.
Scriptgen has identified two small molecule lead compounds which demonstrate
oral activity in animal models against a broad spectrum of fungal pathogens,
including certain strains resistant to current drugs. The Company has also
identified a small molecule lead compound which shows broad spectrum
antibacterial efficacy against drug resistant strains and is currently in animal
studies and one lead compound that has shown strong antiviral activity IN VITRO
against Hepatitis B virus. The Company is evaluating a number of other potential
development candidates.
 
    The Company has also applied its drug discovery technologies to develop
novel coalescent compounds, which are small molecules connected by a molecular
tether that bind to both active and neutral sites. Scriptgen believes such
compounds may lead to more specific and potent therapeutics and allow for the
discovery of small molecule mimics of therapeutic proteins.
 
    Scriptgen Pharmaceuticals, Inc. was incorporated in Delaware on September
17, 1992. The Company maintains its principal executive offices at 200 Boston
Avenue, Medford, Massachusetts 02155. The Company's telephone number is (781)
393-8000.
 
                                       4
<PAGE>
                                  THE OFFERING
 
<TABLE>
<S>                                                           <C>
Common Stock offered by the Company.........................  3,000,000 shares
Common Stock to be outstanding after the Offering...........  11,669,189 shares (1)(2)
Use of proceeds.............................................  To fund research and
                                                              development and for general
                                                              corporate purposes, including
                                                              working capital.
Nasdaq National Market Symbol...............................  SCRP
</TABLE>
 
- --------------
 
(1) Includes an aggregate of 250,000 shares of Common Stock (based on an assumed
    initial public offering price of $12.00 per share) to be issued to HMR in
    the Private Placement. Excludes: (i) 790,581 shares of Common Stock issuable
    upon exercise of outstanding options at a weighted average exercise price of
    $1.75 per share, (ii) 464,537 shares of Common Stock issuable at an exercise
    price of $13.47 per share upon exercise of an outstanding warrant (the
    "BioChem Warrant"), (iii) 49,763 shares of Common Stock issuable upon
    exercise of an outstanding warrant at an exercise price of $3.07 per share
    and 32,525 shares of Common Stock issuable upon exercise of an outstanding
    warrant at an exercise price of $5.53 per share and (iv) 1,950,000 shares of
    Common Stock reserved for issuance upon exercise of options or in connection
    with other awards that may be granted in the future under the Company's 1997
    Equity Incentive Plan (the "1997 Plan") and Non-Employee Directors Stock
    Plan (the "Directors' Plan"). See "Certain Transactions--BioChem Offering,"
    "Management--Employment Agreements," "--Stock Options," "--Employee Benefit
    Plans--1997 Equity Incentive Plan," "--Non-Employee Directors Stock Plan"
    and "--1994 Stock Option Plan," "Description of Capital Stock--Warrants" and
    Notes 6, 8 and 10 of Notes to Financial Statements.
 
(2) In the event that the initial public offering price is less than $10.76 per
    share, the Company will be required to issue to BioChem, for no additional
    consideration, the number of additional shares of Common Stock equal to the
    amount by which (a) 19,993,640 divided by the initial public offering price,
    exceeds (b) 1,858,145. See "Certain Transactions--BioChem Offering."
 
                            ------------------------
 
    "SCRIPTGEN" AND THE SCRIPTGEN LOGO AS IT APPEARS ON THE COVER PAGE OF THIS
PROSPECTUS ARE TRADEMARKS OF THE COMPANY FOR WHICH REGISTRATION APPLICATIONS
HAVE BEEN FILED WITH THE UNITED STATES PATENT AND TRADEMARK OFFICE. ALL OTHER
TRADEMARKS AND TRADENAMES REFERENCED IN THIS PROSPECTUS ARE THE PROPERTY OF
THEIR RESPECTIVE OWNERS.
 
                                       5
<PAGE>
                             SUMMARY FINANCIAL DATA
                     (IN THOUSANDS, EXCEPT PER SHARE DATA)
 
<TABLE>
<CAPTION>
                                              PERIOD FROM                      YEAR ENDED                     NINE MONTHS ENDED
                                          SEPTEMBER 17, 1992                  DECEMBER 31,                      SEPTEMBER 30,
                                                  TO           ------------------------------------------  ------------------------
                                           DECEMBER 31, 1992     1993       1994       1995       1996        1996         1997
                                          -------------------  ---------  ---------  ---------  ---------  -----------  -----------
                                                                                                                 (UNAUDITED)
<S>                                       <C>                  <C>        <C>        <C>        <C>        <C>          <C>
STATEMENT OF OPERATIONS DATA:
Revenue:
  Collaborative agreements..............              --              --         --         --  $     975   $     975    $     467
  SBIR grants...........................              --              --         --  $     260        232         222          138
                                                  ------       ---------  ---------  ---------  ---------  -----------  -----------
                                                      --              --         --        260      1,207       1,197          605
                                                  ------       ---------  ---------  ---------  ---------  -----------  -----------
Cost of revenue:
  Collaborative agreements..............              --              --         --         --        174         174          124
  SBIR grants...........................              --              --         --        260        232         222          138
                                                  ------       ---------  ---------  ---------  ---------  -----------  -----------
                                                      --              --         --        260        406         396          261
                                                  ------       ---------  ---------  ---------  ---------  -----------  -----------
  Gross profit..........................              --              --         --         --        801         801          344
Operating expenses:
  Research and development..............       $     455       $   1,833  $   3,157      3,152      3,958       2,757        4,273
  General and administrative............              94             652        998      1,299        906         669          831
                                                  ------       ---------  ---------  ---------  ---------  -----------  -----------
                                                     549           2,485      4,155      4,451      4,865       3,427        5,104
                                                  ------       ---------  ---------  ---------  ---------  -----------  -----------
  Loss from operations..................            (549)         (2,485)    (4,155)    (4,451)    (4,064)     (2,626)      (4,761)
Other income (expense), net                            1             (62)      (146)      (128)        19          12          (15)
                                                  ------       ---------  ---------  ---------  ---------  -----------  -----------
  Net loss..............................       $    (549)      $  (2,547) $  (4,301) $  (4,579) $  (4,044)  $  (2,614)   $  (4,775)
                                                  ------       ---------  ---------  ---------  ---------  -----------  -----------
                                                  ------       ---------  ---------  ---------  ---------  -----------  -----------
Net loss per share (1)..................       $   (0.21)      $   (0.98) $   (1.25) $   (1.28) $   (1.20)  $   (0.77)   $   (1.35)
                                                  ------       ---------  ---------  ---------  ---------  -----------  -----------
                                                  ------       ---------  ---------  ---------  ---------  -----------  -----------
Weighted average common and common
  equivalent shares outstanding (1).....           2,556           2,607      3,435      3,591      3,360       3,374        3,528
                                                  ------       ---------  ---------  ---------  ---------  -----------  -----------
                                                  ------       ---------  ---------  ---------  ---------  -----------  -----------
Pro forma net loss per share (unaudited)
  (1)...................................                                                        $   (0.49)               $   (0.53)
                                                                                                ---------               -----------
                                                                                                ---------               -----------
Pro forma weighted average common and
  common equivalent shares outstanding
  (unaudited) (1).......................                                                            8,186                    9,069
                                                                                                ---------               -----------
                                                                                                ---------               -----------
</TABLE>
 
<TABLE>
<CAPTION>
                                                                                     SEPTEMBER 30, 1997
                                                                          ----------------------------------------
<S>                                                                       <C>        <C>            <C>
                                                                                                      PRO FORMA
                                                                           ACTUAL    PRO FORMA(2)   AS ADJUSTED(3)
                                                                          ---------  -------------  --------------
BALANCE SHEET DATA:
Cash and cash equivalents...............................................  $     858   $    20,858     $   56,288
Working capital.........................................................     (1,200)       18,800         54,230
Total assets............................................................      2,478        22,478         57,908
Noncurrent portion of capital lease obligations.........................        501           501            501
Redeemable convertible preferred stock..................................     20,279       --              --
Accumulated deficit.....................................................    (21,169)      (23,436)       (23,436)
Total stockholders' equity (deficit)....................................    (20,744)       19,535         54,965
</TABLE>
 
- --------------
(1) See Note 2 of Notes to Financial Statements for information concerning the
    computation of net loss per share and shares used in computing net loss per
    share.
(2) Pro forma to give effect to the issuance of Series D Preferred Stock
    (convertible into 1,858,145 shares of Common Stock) to BioChem for
    consideration of $20 million (the "BioChem Offering") and the application of
    the proceeds therefrom, the value of the BioChem Warrant, the retirement of
    358,748 shares of treasury stock and the conversion of the Series A, B, C
    and D Preferred Stock into shares of Common Stock upon the closing of the
    Offering. See "Use of Proceeds" and "Management's Discussion and Analysis of
    Financial Condition and Results of Operations--Liquidity and Capital
    Resources."
(3) Adjusted to give effect to: (i) the sale of 3,000,000 shares of Common Stock
    offered by the Company hereby (at an assumed initial public offering price
    of $12.00 per share) and the application of the net proceeds therefrom and
    (ii) the sale of 250,000 shares of Common Stock (at an assumed offering
    price of $12.00 per share) to HMR in the Private Placement and the
    application of the net proceeds therefrom. See "Use of Proceeds."
 
                                       6
<PAGE>
                                  RISK FACTORS
 
    AN INVESTMENT IN THE SHARES OF COMMON STOCK OFFERED BY THIS PROSPECTUS
INVOLVES A HIGH DEGREE OF RISK. IN ADDITION TO THE OTHER INFORMATION IN THIS
PROSPECTUS, THE FOLLOWING RISK FACTORS SHOULD BE CONSIDERED CAREFULLY IN
EVALUATING AN INVESTMENT IN THE COMPANY. THIS PROSPECTUS CONTAINS CERTAIN
FORWARD-LOOKING STATEMENTS WHICH INVOLVE RISKS AND UNCERTAINTIES. THE COMPANY'S
ACTUAL RESULTS COULD DIFFER MATERIALLY FROM THE RESULTS ANTICIPATED IN THESE
FORWARD-LOOKING STATEMENTS AS A RESULT OF CERTAIN OF THE FACTORS SET FORTH IN
THE FOLLOWING RISK FACTORS AND ELSEWHERE IN THIS PROSPECTUS.
 
HISTORY OF LOSSES AND EXPECTATION OF FUTURE LOSSES; UNCERTAINTY OF FUTURE
  PROFITABILITY
 
    At September 30, 1997, the Company had incurred an accumulated deficit of
approximately $21.2 million. Losses have resulted principally from costs
incurred in research and development activities related to the Company's efforts
to develop and commercialize its proprietary technology and to develop drug
candidates and from the associated administrative costs. The Company expects to
incur significant additional operating losses over the next several years and
expects cumulative losses to increase substantially due to expanded research and
development efforts, pre-clinical and clinical trials and the possible
development of manufacturing, marketing and sales capabilities. For the
foreseeable future, the Company expects that its revenues will be limited to
payments received under its drug development collaborations that it has
established or will establish (net of royalties required to be paid by the
Company with respect to such payments) and small business innovation research
("SBIR") grants. There can be no assurance, however, that the Company will be
able to establish any additional collaborative relationships on terms acceptable
to the Company or maintain in effect its current collaborative agreements. The
Company's ability to achieve significant revenue or become profitable is
dependent on the success of its collaborative arrangements and its ability to
continue to commercialize its technology platform and gain industry acceptance
of its services and technologies, to enter into additional collaborations for
the development of drugs, to identify lead compounds and successfully develop
drug candidates resulting from its own internal development programs, to obtain
patent protection for its technology and drug candidates, to obtain regulatory
approvals for drug candidates and to arrange for the manufacture and
commercialization of any drugs resulting from its operations. The Company will
not receive revenues or royalties from commercial drug sales for a significant
number of years, if at all. Failure to receive significant revenues or achieve
profitable operations would impair the Company's ability to sustain operations.
There can be no assurance that the Company will ever successfully identify,
develop, commercialize, patent, manufacture or arrange for the manufacture of,
or market or arrange for the marketing of, any products, obtain required
regulatory approvals or achieve profitability. See "Management's Discussion and
Analysis of Financial Condition and Results of Operations."
 
DEPENDENCE UPON PRESENT AND FUTURE COLLABORATIVE ARRANGEMENTS
 
    The Company's strategy for the development and commercialization of its
technology platform and drug candidates requires the Company to enter into
various collaborative arrangements. To date, substantially all revenues received
by the Company have been from its drug discovery collaborations and the Company
expects that substantially all revenues for the foreseeable future will be
limited to payments received under such collaborations and any future
collaborations the Company may enter into. Because pharmaceutical and
biotechnology companies engaged in drug discovery activities have historically
conducted drug discovery activities, including target identification and
validation and compound screening, through their own internal research
departments, these companies must be convinced that the Company's technologies
justify entering into collaborative agreements with the Company. The Company's
ability to succeed will be dependent, in part, upon the willingness of potential
collaborators to incorporate the Company's technologies into their own drug
discovery programs. There can be no assurance that the Company will be able to
negotiate additional collaborative agreements in the future on acceptable terms,
if at all, that such current or future collaborative agreements will be
successful and provide the Company
 
                                       7
<PAGE>
with expected benefits, or that current or future collaborators will not pursue
or develop alternative technologies either on their own or in collaboration with
others, including the Company's competitors, as a means for identifying lead
compounds or targets. To the extent the Company chooses not to or is unable to
enter into such agreements, or to the extent the Company is unable to maintain
in effect its current collaborative agreements, it will require substantially
greater capital to undertake the research, development and commercialization of
its technologies and drug development program at its own expense. In the absence
of such collaborative agreements, the Company may be required to curtail its
research and development activities and operations to a significant extent. In
November 1996, one of the Company's collaborative partners elected not to
continue developing a program which was the subject of a collaborative agreement
with the Company, which election the Company believes was unrelated to the
Company's performance of its obligations under such arrangement.
 
    Under the Company's current collaborative agreements, the Company has the
opportunity to receive payments upon the achievement by its collaborators of
certain drug development milestones and royalties on sales of drugs covered
under such arrangements. As a result, the Company's receipt of revenues (whether
in the form of milestone payments or royalties on sales) under the collaborative
agreements is for the most part dependent upon the decisions made by, and the
manufacturing and marketing resources of, its collaborative partners. The
Company's collaborative partners are not obligated to develop or commercialize
any drug resulting from the collaborative agreements. Development and
commercialization of drug candidates will therefore depend not only on the
achievement of research objectives by the Company and its collaborators, which
cannot be assured, but also on each collaborator's own financial, competitive,
marketing and strategic considerations, all of which are outside the Company's
control. Such strategic considerations may include the relative advantages of
alternative drugs being marketed or developed by others, including relevant
patent and proprietary positions. There can be no assurance that the interests
and motivations of the Company's collaborators are, or will remain, aligned with
those of the Company, that current or future collaborators will not pursue
alternative technology in preference to that of the Company either on their own
or in collaboration with others, including the Company's competitors, or that
such collaborators will successfully perform their development, regulatory,
compliance, manufacturing or marketing functions. In addition, there can be no
assurance that any product will be developed and commercialized as a result of
such collaborations, that any such development or commercialization would be
successful or that disputes will not arise over the application of payment
provisions for drug candidates. Failure to successfully manage existing and
future collaborative relationships, maintain confidentiality among such
relationships or prevent the occurrence of such conflicts could lead to disputes
that result in, among other things, a significant strain on management
resources, legal claims involving significant time and expense and loss of
reputation, a loss of capital or a loss of collaborators, any of which could
have a material adverse effect on the Company's business, operating results and
financial condition.
 
EARLY STAGE OF DRUG DEVELOPMENT; ABSENCE OF DEVELOPED PRODUCTS
 
    Since inception, the Company has received no revenues from drug sales. The
Company's internal drug development programs and the programs on which it is
working with its collaborative partners are at an early stage, and the Company
does not expect that any drugs resulting from its internal development efforts,
or from the joint efforts of the Company and its collaborative partners, will be
commercially available for a significant number of years, if at all. The
Company's present drug candidates, and any future drug candidates developed by
the Company or developed jointly by the Company and its collaborative partners
will require significant additional research and development efforts to
establish safety and efficacy, including extensive pre-clinical (animal and IN
VITRO data) and clinical testing and regulatory approval, prior to commercial
sale. None of the Company's drug candidates have advanced to any phase of
clinical trials, and only two of the Company's drug candidates have advanced to
pre-clinical development. There can be no assurance that the approaches of the
Company or its collaborative partners to drug discovery will be effective or
will result in the development of any drug. The Company's present and potential
drug candidates or other drug candidates resulting from the joint efforts of the
Company and its
 
                                       8
<PAGE>
collaborative partners, will be subject to the risks of failure inherent in the
development of pharmaceutical products based on new technologies. These risks
include the possibilities that any or all of the Company's drug candidates or
such other drug candidates will be found to be unsafe, ineffective or toxic or
otherwise fail to meet applicable regulatory standards or receive necessary
regulatory clearances, that these drug candidates, if safe and effective, will
be difficult to develop into commercially viable drugs or to manufacture on a
large scale or will be uneconomical to market, that proprietary rights of third
parties will preclude the Company or its collaborative partners from marketing
such drugs, or that third parties will market superior or equivalent drugs. The
failure to develop safe, commercially viable drugs would have a material adverse
effect on the Company's business, operating results and financial condition.
 
NEW AND UNCERTAIN TECHNOLOGY
 
    The Company's drug discovery technology platform and ongoing research and
development programs incorporate new and rapidly evolving approaches to the
identification and validation of novel targets and the identification of lead
compounds. Elements of the Company's technology platform are utilized by the
Company in all of its collaborative arrangements as well as in its own internal
development program. As the Company's technology platform is used, it is
possible that previously unanticipated limitations or defects may emerge. There
can be no assurance that unforseen complications will not arise as the Company's
technologies are utilized in the drug discovery process that could materially
delay or limit their use in connection with the drug development programs of the
Company or its collaborative partners, result in the termination of the
collaborative agreements, or prevent the technologies from being utilized at the
quality and capacity levels required for success. In addition, there can be no
assurance that expenditures for research and development will lead to the
development of useful technologies. Development of new drugs is highly
uncertain, and no assurance can be given that the Company's drug discovery
technologies will be used successfully in the development of drug candidates or
result in any commercially successful drug.
 
COMPETITION AND THE RISK OF OBSOLESCENCE OF TECHNOLOGY
 
    Competition among drug discovery companies, and pharmaceutical and
biotechnology companies which are involved in drug discovery, is intense.
Because the Company's technology platform incorporates a number of different
technologies, the Company competes in many areas, including target
identification and validation, assay development and high throughput screening.
The Company competes directly against other drug discovery companies, the
research departments of pharmaceutical and biotechnology companies and other
commercial enterprises, government agencies, and numerous academic and research
institutions. Such companies and other entities are conducting research in
various areas which constitute portions of the Company's technology platform,
either on their own or in collaboration with others. There can be no assurance
that drug discovery companies which currently compete with the Company in
specific areas will not merge or enter into joint ventures or other alliances
with one or more other such companies and become substantial multi-point
competitors or that the Company's collaborators will not assemble their own
competing drug discovery technologies. Genomics and combinatorial chemistry
companies, among others, may also expand their business to include compound
screening or screen development, either alone or pursuant to alliances 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
drug discovery technologies, in particular GATE, ATLAS and SCAN, 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 current or
future competitors. In particular, the Company's technology faces competition
from companies engaged in gene sequencing, functional genomics and differential
gene expression technology in the area of target validation, and companies
engaged in high throughput screening. Many of the Company's competitors have
greater financial and personnel resources, and more experience in research and
development, than the Company. There can be no assurance that the Company's
competitors will not succeed in
 
                                       9
<PAGE>
developing technologies and drugs that are more effective or less costly than
any which are being developed by the Company or which would render the Company's
technology and any future drugs obsolete and noncompetitive.
 
    In addition, some of the Company's competitors have greater experience than
the Company in conducting pre-clinical and clinical trials and obtaining U.S.
Food and Drug Administration ("FDA") and other regulatory approvals.
Accordingly, the Company's competitors may succeed in obtaining FDA or other
regulatory approvals for competing drug candidates more rapidly than the
Company. Companies that complete clinical trials, obtain required regulatory
agency approvals and commence commercial sale of their drugs, before their
competitors, may achieve a significant competitive advantage, including certain
patent and FDA marketing exclusivity rights that would delay the Company's
ability to market certain products. There can be no assurance that drugs, if
any, resulting from the Company's internal development efforts or the joint
efforts of the Company and its collaborators will be able to compete
successfully with competitors' existing products or products under development
or that they will obtain regulatory approval in the United States or elsewhere.
 
ADDITIONAL FINANCING REQUIREMENTS; UNCERTAINTY OF AVAILABLE FUNDING
 
    The Company will require substantial additional funds for the further
development of its drug discovery technologies, its internal development
programs, for operating expenses, for pursuing regulatory approvals, for the
possible development of manufacturing, marketing and sales capabilities and for
prosecuting and defending its intellectual property rights before it can expect
to realize significant revenues from commercial sales, if any. The Company
believes that the net proceeds of the Offering, the Private Placement and the
BioChem Offering, together with revenues from its collaborative agreements, its
existing capital resources, SBIR grants and interest income will be sufficient
to fund its operating expenses and capital requirements as currently planned
through the end of 2000. However, there can be no assurance that such funds will
be sufficient to fund its operating expenses and capital requirements during
such period. The Company's actual cash requirements may vary materially from
those now planned and will depend upon numerous factors, including the ability
of the Company to enter into additional collaborative arrangements, the
achievement of milestones under the Company's collaborative arrangements on a
timely basis or at all, changes in the Company's existing collaborative
arrangements, the results of the Company's internal development programs, the
timing and results of pre-clinical and clinical trials, the timing and costs of
obtaining regulatory approvals, the timing and level of the expansion of the
Company's facilities, the level of resources, if any, that the Company commits
to the development of manufacturing, marketing and sales capabilities, the
technological advances and activities of competitors and other factors.
Thereafter, the Company will need to raise substantial additional capital to
fund its operations. The Company intends to seek such additional funding through
public or private financing or collaborative or other arrangements with
collaborative partners. If additional funds are raised by issuing equity
securities, further dilution to existing stockholders may result and future
investors may be granted rights superior to those of existing stockholders.
There can be no assurance, however, that additional financing will be available
from any of these sources or, if available, will be available on acceptable or
affordable terms. If adequate funds are not available, the Company may be
required to delay, reduce the scope of or eliminate one or more of its research
and development programs or to obtain funds by entering into arrangements with
collaborative partners or others that require the Company to issue additional
equity securities or to relinquish rights to certain technologies or drug
candidates that the Company would not otherwise issue or relinquish in order to
continue independent operations. See "Use of Proceeds" and "Management's
Discussion and Analysis of Financial Condition and Results of Operations."
 
RISK OF EXPANDING OPERATIONS AND MANAGEMENT OF GROWTH
 
    The Company has recently experienced, and expects to continue to experience,
significant growth in the number of its employees and the scope of its
operations. This growth has placed, and may continue to
 
                                       10
<PAGE>
place, a significant strain on the Company's management, operations and systems.
The Company's ability to manage such growth effectively will depend upon
attracting, hiring and retaining skilled employees. In addition, in order to
increase capacity to remain competitive and satisfy the needs of current and
future collaborative partners, the Company will be required in the near future
to obtain additional office and laboratory space, capital equipment and
resources. There can be no assurance that the Company will be able to manage its
growth, and the Company's inability to manage growth effectively could have a
material adverse effect on the Company's business, operating results and
financial condition. See "Business-- Employees" and "--Properties."
 
UNCERTAINTY OF PATENTS AND PROPRIETARY RIGHTS
 
    The Company's success will depend in part on its ability to obtain U.S. and
foreign patent protection for its drug candidates and the components of its
technology platform, preserve its trade secrets and operate without infringing
the proprietary rights of third parties. Because of the length of time and
expense associated with bringing new drug candidates through the development and
regulatory approval process to the marketplace, drug discovery companies have
traditionally placed considerable importance on obtaining patent and trade
secret protection for significant new technologies, products and processes. The
Company's policy is to make diligent efforts to protect its screening
technologies, targets, compounds, and certain other technology by, among other
things, filing, or causing to be filed on its behalf, patent applications in the
United States Patent and Trademark Office ("USPTO"), and elsewhere where the
Company deems appropriate and cost effective. There can be no assurance that
patents will be granted with respect to any of the Company's or its licensors'
patent applications which are pending or may be filed in the future. Further,
there can be no assurance that any rights the Company may have under issued
patents will provide the Company with significant protection against competitive
products or otherwise be commercially viable. Legal standards relating to the
validity of patents covering pharmaceutical and biotechnological inventions and
the scope of claims made under such patents are still developing, and thus there
is no consistent policy in this regard. The patent position of a drug discovery
company such as Scriptgen is highly uncertain and involves complex legal and
factual questions. There can be no assurance that any existing or future patents
issued to, or licensed by, the Company will not subsequently be challenged,
infringed upon, invalidated or circumvented by others. In addition, patents may
have been granted, or may be granted, to others covering processes or products
that are necessary or useful to the development of the Company's technologies,
targets and compounds. If any of the Company's technologies, targets or
compounds are found to infringe upon the patents or other intellectual property
of others, the Company's ability to develop and commercialize its technologies,
targets and compounds could be severely restricted or prohibited. In such event,
the Company may be required to obtain licenses from third parties to utilize
their patents or other proprietary rights. There can be no assurance that the
Company will be able to obtain such licenses on acceptable terms, or at all.
There is significant litigation in the pharmaceutical and biotechnology industry
regarding patents and other proprietary rights. If the Company becomes involved
in litigation regarding its proprietary rights or the proprietary rights of
others, the Company could incur substantial costs in defending infringement
claims, obtaining licenses, engaging in interference and opposition proceedings
or other challenges to its patent rights or proprietary rights made by third
parties, or in bringing such proceedings or enforcing any patent rights against
third parties. The Company's inability to obtain necessary licenses or its
involvement in proceedings concerning patent rights could have a material
adverse effect on the business, operating results and financial condition of the
Company.
 
    The Company has filed a provisional patent application claiming certain
aspects of its GATE technology. The Company is aware that another party has
applied for a patent for certain technologies which may overlap with or dominate
parts of the Company's GATE technology. The Company is in negotiations with such
party to acquire a license of such party's rights covered by its patent
application. If the Company determines to seek to obtain such license, there can
be no assurance that the Company will
 
                                       11
<PAGE>
be able to obtain such a license on terms favorable to the Company, if at all.
See "Business--Patents and Proprietary Technology."
 
    In addition to patent protection, the Company relies on trade secrets,
know-how and technological advances which it seeks to protect, in part, by
confidentiality agreements with its collaborative partners, employees, advisors
and consultants. There can be no assurance that these confidentiality agreements
will not be breached, that the Company would have adequate remedies for any such
breach, or that the Company's trade secrets, know-how and technological advances
will not otherwise become known or be independently discovered by others. See
"Business--Patents and Proprietary Technology."
 
DEPENDENCE UPON ACCESS TO CERTAIN MATERIALS AND INFORMATION
 
    The Company obtains compounds and other test material, related clinical and
other biological information and animal models through collaboration with
commercial organizations and academic institutions. Use of the Company's
technology platform in connection with its collaborative arrangements and
internal development programs requires access to such materials and information
and there is substantial competition for such materials and information. There
can be no assurance that the Company will continue to be able to obtain access
to such materials and information upon terms acceptable to the Company, if at
all. Any material lack of availability of such materials and information could
have a material adverse effect on the Company's ability to perform its
obligations under one or more of its collaborative agreements, which in turn
would have a material adverse effect on the Company's business, operating
results and financial condition.
 
DEPENDENCE ON KEY PERSONNEL
 
    The Company is highly dependent upon the efforts of the members of its
management team, scientific advisory board and scientific staff. The loss of the
services of one or more of these individuals might impede the Company's
development of its technology and the achievement of its business objectives.
Because of the specialized scientific nature of the Company's business, the
Company is highly dependent upon its ability to attract and retain qualified
scientific and technical personnel. There is intense competition among drug
discovery companies, pharmaceutical companies, biotechnology companies and
universities and other research institutions for qualified personnel in the
areas of the Company's activities. There can be no assurance that the Company
will be able to continue to attract and retain the qualified personnel necessary
for the development of its business. Loss of the services of, or failure to
recruit, key scientific and technical personnel could adversely affect the
Company's business, operating results and financial condition. See
"Business--Employees" and "Management--Executive Officers, Directors and Key
Employees."
 
SIGNIFICANT FLUCTUATIONS IN QUARTERLY AND ANNUAL RESULTS
 
    To date, a majority of all revenue earned by the Company has been from its
collaborative agreements, and the Company expects that substantially all revenue
for the foreseeable future will result from such collaborations and any future
collaborations the Company may enter into. The timing of any fees or milestone
or other payments under such collaborations is expected to vary greatly from
quarter to quarter, depending on numerous factors. Operating results may
therefore vary substantially from quarter to quarter and will not necessarily be
indicative of results in subsequent periods. In addition, over the next several
years, the Company expects to incur non-cash compensation charges each quarter
resulting from the amortization of approximately $2.7 million in unearned
compensation recorded on the Company's balance sheet as of September 30, 1997.
Furthermore, the Company expects to incur a non-cash charge in the fourth
quarter of 1997 resulting from the issuance of the BioChem Warrant. See
"Management's Discussion and Analysis of Financial Condition and Results of
Operations" and Notes 6 and 10 of Notes to Financial Statements.
 
                                       12
<PAGE>
LACK OF MANUFACTURING, MARKETING AND SALES CAPABILITY AND EXPERIENCE
 
    The Company has not invested in the development of manufacturing, marketing
or sales capabilities. The Company has no experience in, and currently lacks the
facilities and personnel to engage in, the manufacture of products in accordance
with Good Manufacturing Practices ("GMP") as prescribed by the FDA or to produce
an adequate supply of compounds to meet future requirements for clinical trials.
If the Company is unable to contract for or develop manufacturing capabilities
on acceptable terms, the Company's ability to conduct pre-clinical and clinical
trials with the Company's drug candidates, will be adversely affected, resulting
in delays in the submission of drug candidates for regulatory approvals and in
the initiation of new development programs, which in turn could materially
impair the Company's competitive position and the possibility of achieving
profitability.
 
    The Company has no experience in marketing drugs. The Company will likely
seek to collaborate with a third party to market any drugs the Company may
develop, although in certain cases it may seek to market and sell such drugs
directly. If the Company seeks to collaborate with a third party, there can be
no assurance that a collaborative arrangement would be reached on acceptable
terms, if at all. If the Company seeks to market and sell such drugs directly,
the Company will need to hire additional personnel skilled in marketing and
sales if it develops any drug with commercial potential. There can be no
assurance that the Company will be able to obtain candidates, or establish
third-party relationships to provide, any or all of these capabilities.
 
UNCERTAINTY ASSOCIATED WITH PRE-CLINICAL AND CLINICAL TESTING
 
    Before obtaining regulatory approvals for the commercial sale of any of the
Company's potential drugs, the drug candidates will be subject to extensive
pre-clinical and clinical trials to demonstrate their safety and efficacy in
humans. The Company will likely be dependent on third parties to conduct
clinical trials for its internally developed drug candidates. In the event that
the Company is unable or otherwise determines not to enter into collaborative
arrangements with a third party to conduct clinical trials for its drug
candidates, the Company would need to recruit and retain the proper personnel to
manage such process. The Company has limited experience in pre-clinical
development and no experience in clinical trials, and no clinical trials have
been commenced with respect to any of the Company's potential drug candidates.
Furthermore, there can be no assurance that pre-clinical or clinical trials of
any present or future drug candidates will demonstrate the safety and efficacy
of such drug candidates at all or to the extent necessary to obtain regulatory
approvals. Companies in the biotechnology industry have suffered significant
setbacks in advanced clinical trials, even after demonstrating promising results
in earlier trials. The failure to adequately demonstrate the safety and efficacy
of a drug candidate under development could delay or prevent regulatory approval
of the drug candidate and could have a material adverse effect on the Company's
business, operating results and financial condition. See "Business--Government
Regulation."
 
IMPACT OF EXTENSIVE GOVERNMENT REGULATION
 
    The FDA and comparable agencies in foreign countries impose substantial
requirements upon the introduction of pharmaceutical products through lengthy
and detailed pre-clinical, laboratory and clinical testing procedures, sampling
activities and other costly and time-consuming procedures to establish their
safety and efficacy. All of the Company's current and future drug candidates and
any drug candidates that result from the Company's collaborations will require
governmental approvals for commercialization, none of which have been obtained.
Pre-clinical and clinical trials and manufacturing of the Company's drug
candidates will be subject to the rigorous testing and approval processes of the
FDA and corresponding foreign regulatory authorities. Satisfaction of these
requirements typically takes a significant number of years and can vary
substantially based upon the type, complexity and novelty of the product. There
can be no assurance as to when the Company, independently or with its
collaborative partners, might first submit
 
                                       13
<PAGE>
an investigational new drug application for FDA or other regulatory review.
Government regulation also affects the manufacturing and marketing of
pharmaceutical products.
 
    The effect of government regulation may be to delay marketing of the
Company's potential drugs for a considerable or indefinite period of time,
impose costly procedural requirements upon the Company's activities and furnish
a competitive advantage to larger companies or companies more experienced in
regulatory affairs. Delays in obtaining governmental regulatory approval could
adversely affect the Company's marketing as well as the Company's ability to
generate significant revenues from commercial sales. There can be no assurance
that FDA or other regulatory approvals for any drug candidates developed by the
Company will be granted on a timely basis or at all. Moreover, if regulatory
approval of a drug candidate is granted, such approval will impose limitations
on the indicated use(s) for which such drug may be marketed. Even if initial
regulatory approvals for the Company's drug candidates are obtained, the
Company, its drugs and its manufacturing facilities, if any, would be subject to
continual review and periodic inspection, and later discovery of previously
unknown problems with a drug, manufacturer or facility may result in
restrictions on such drug or manufacturer, including withdrawal of the drug from
the market. In addition, the Company would be required to comply with FDA
requirements for labeling, advertising, record keeping, and reporting of adverse
experiences and other information. The regulatory standards are applied
stringently by the FDA and other regulatory authorities and failure to comply
can, among other things, result in fines, injunctions, denial or withdrawal of
regulatory approvals, product recalls or seizures, operating restrictions and
criminal prosecution.
 
    As with many biotechnology and pharmaceutical companies, the Company is
subject to numerous environmental and safety laws and regulations. Any violation
of, and the cost of compliance with, these regulations could materially
adversely affect the Company's business, operating results and financial
condition. The Company is subject to periodic inspections and has not received
notice of any material violations of any environmental or safety law or
regulation. See "Business--Government Regulation."
 
USE OF HAZARDOUS MATERIALS
 
    The research and development processes of the Company involve the controlled
use of hazardous materials, chemicals and various radioactive compounds,
including microbial organisms and other biological 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. 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.
 
REIMBURSEMENT AND DRUG PRICING UNCERTAINTY
 
    The successful commercialization of, and the interest of potential
collaborative partners to invest in, the Company's technology platform or drug
candidates will depend substantially on reimbursement of the costs of the
resulting drugs and related treatments at acceptable levels from government
authorities, private health insurers and other organizations, such as health
maintenance organizations ("HMOs"). There can be no assurance that reimbursement
in the United States or elsewhere will be available for any drugs the Company or
its collaborative partners may develop or, if available, will not be decreased
in the future, or that reimbursement amounts will not reduce the demand for, or
the price of, such drugs, thereby adversely affecting the Company's business. If
reimbursement is not available or is available only to limited levels, there can
be no assurance that the Company will be able to obtain collaborative partners
to manufacture and commercialize any future drugs, or would be able to obtain a
sufficient financial return on its own manufacture and commercialization of any
future drugs.
 
                                       14
<PAGE>
    Third-party payors are increasingly challenging the prices charged for
medical products and services. Also, the trend toward managed health care in the
United States and the concurrent growth of organizations such as HMOs, which can
control or significantly influence the purchase of health care services and
products, as well as legislative proposals to reform health care or reduce
government insurance programs, may result in lower prices for pharmaceutical
products. The cost containment measures that health care providers are
instituting, including practice protocols and guidelines and clinical pathways,
and the effect of any health care reform, could materially adversely affect the
Company's ability to sell its drugs, if any. Moreover, the Company is unable to
predict what additional legislation or regulation, if any, relating to the
health care industry or third-party coverage and reimbursement may be enacted in
the future or what effect such legislation or regulation would have on the
Company's business, operating results or financial condition.
 
POTENTIAL PRODUCT LIABILITY AND AVAILABILITY OF INSURANCE
 
    The Company's business exposes it to potential liability risks that are
inherent in the testing, manufacturing and marketing of pharmaceutical products.
The use of the Company's drug candidates in clinical trials may expose the
Company to product liability claims and possible adverse publicity. These risks
will expand with respect to the Company's drug candidates, if any, that receive
regulatory approval for commercial sale. Product liability insurance for the
biotechnology industry is generally expensive, if available at all. The Company
does not have product liability insurance but intends to obtain such coverage if
and when its drug candidates are tested in clinical trials. However, such
coverage is becoming increasingly expensive and there can be no assurance that
the Company will be able to obtain insurance coverage at acceptable costs or in
a sufficient amount, if at all, or that a product liability claim would not
adversely affect the Company's business, operating results or financial
condition.
 
BROAD DISCRETION IN APPLICATION OF NET PROCEEDS
 
    The net proceeds to the Company from the sale of the shares of Common Stock
offered hereby are estimated to be approximately $32,430,000 ($37,452,000 if the
Underwriters' over-allotment option is exercised in full) after deducting
underwriting discounts and commissions and estimated offering expenses. The
Company intends to use the net proceeds from the Offering and the Private
Placement, together with the proceeds from the BioChem Offering, principally for
research and development, working capital and general corporate purposes. The
Company's management and Board of Directors will have broad discretion with
respect to the application of such proceeds, and the amounts actually expended
by the Company for working capital purposes may vary significantly depending on
a number of factors. See "Use of Proceeds."
 
NO PRIOR PUBLIC MARKET; POSSIBLE VOLATILITY OF STOCK PRICE
 
    Prior to the Offering, there has been no public market for the Common Stock.
The initial public offering price per share of the Common Stock will be
determined by negotiations between management of the Company and the managing
underwriters of the Offering. The Common Stock has been approved for quotation
on the Nasdaq National Market; however, there can be no assurance that an active
trading market will develop and be sustained subsequent to the Offering. The
market price of the Common Stock may fluctuate substantially because of a
variety of factors, including announcements concerning existing or future
collaborative arrangements, announcements of technological innovations or new
products by the Company, its collaborators or its competitors, disclosure of
results of clinical testing or regulatory proceedings, developments in patents
or other proprietary rights, quarterly fluctuations in results of operations,
changes in earnings estimates by analysts, sales of Common Stock by existing
holders, loss of key personnel and other factors. In addition, the stock market
in general, and the market for biotechnology and pharmaceutical stocks, has
historically been subject to extreme price and volume fluctuations. This
volatility has had a significant effect on the market prices of securities
issued by many companies for
 
                                       15
<PAGE>
reasons unrelated to the operating performance of these companies. In the past,
following periods of volatility in the market price of a company's securities,
class action securities litigation has often been instituted against such a
company. Any such litigation instigated against the Company could result in
substantial costs and diversion of management's attention and resources, which
could have a material adverse effect on the Company's business, financial
condition and operating results. See "Underwriting."
 
IMMEDIATE AND SUBSTANTIAL DILUTION
 
    The initial public offering price per share of Common Stock is substantially
higher than the net tangible book value per share of the Common Stock.
Purchasers of shares of Common Stock in the Offering will experience immediate
and substantial dilution of $7.29 in the pro forma net tangible book value per
share of Common Stock. To the extent outstanding warrants and options to
purchase Common Stock are exercised, there will be further dilution. See
"Dilution."
 
CONTROL BY CERTAIN PRINCIPAL STOCKHOLDERS
 
    Following completion of the Offering, the Company's executive officers and
directors and their affiliated entities as a group (assuming that a
representative of BioChem is elected to the Board of Directors following
completion of the Offering as contemplated in a stockholders' agreement) will
beneficially own approximately 42.2% of the outstanding Common Stock. As a
result, Scriptgen's executive officers and directors as a group will have a
significant influence over the outcome of all matters submitted to a vote of the
Company's stockholders, including the election of directors and significant
corporate transactions. The shares beneficially owned by the Company's executive
officers, directors and affiliates, combined with the ability of the Board of
Directors to issue shares of preferred stock without further vote or action by
the stockholders, may have the effect of delaying, deferring or preventing a
change in control of the Company without further action by the stockholders.
BioChem has agreed with the Company that for a period of five years following
the closing of the BioChem Offering, BioChem will not own securities
representing more than 25% of the votes entitled to be cast generally for the
election of directors or to take, or to assist in taking, steps to effect a
change in control of the Company. See "Management," "Principal Stockholders" and
"Certain Transactions--BioChem Offering."
 
AVAILABILITY OF PREFERRED STOCK FOR ISSUANCE; ANTI-TAKEOVER PROVISIONS
 
    The Company's Restated Certificate of Incorporation, as it is proposed to be
amended and restated (the "Restated Certificate"), authorizes the Board of
Directors of the Company, without stockholder approval, to issue additional
shares of Common Stock and to fix the rights, preferences and privileges of and
issue up to 4,000,000 shares of preferred stock with voting, conversion,
dividend 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, rights to purchase preferred stock or additional shares of Common Stock
may have the effect of delaying or preventing a change in control of the
Company. In addition, the possible issuance of preferred stock or additional
shares of Common Stock could discourage a proxy contest, make more difficult the
acquisition of a substantial block of the Common Stock or limit the price that
investors might be willing to pay for shares of the Common Stock. Further, the
Restated Certificate provides that any action required or permitted to be taken
by stockholders of the Company must be effected at a duly called annual or
special meeting of stockholders and may not be effected by any consent in
writing. Special meetings of the stockholders of the Company may be called only
by the Chairman of the Board of Directors, the President of the Company, or by a
majority of the Board of Directors pursuant to a resolution adopted by a
majority of the total number of authorized directors. These and other provisions
contained in the Restated Certificate and the Company's By-Laws, as well as
certain provisions of the Delaware General Corporation Law, could delay or make
more difficult certain types of transactions involving an actual or potential
change in control of the Company or its management (including transactions in
which stockholders might otherwise receive a premium for their shares over then
current
 
                                       16
<PAGE>
market prices) and may limit the ability of stockholders to remove current
management of the Company or approve transactions that stockholders may deem to
be in their best interests and, therefore, could adversely affect the price of
the Common Stock. See "Description of Capital Stock--Preferred Stock" and
"--Delaware Anti-Takeover Law and Certain Charter Provisions."
 
SHARES ELIGIBLE FOR FUTURE SALE
 
    Sales of substantial amounts of Common Stock in the public market or the
availability of such shares for future sale could adversely affect the market
price of the Common Stock and the Company's ability to raise additional capital
at a price favorable to the Company. Upon completion of the Offering and the
Private Placement, the Company will have 11,669,189 shares of Common Stock
outstanding (assuming no exercise of outstanding options or warrants). Of these
shares, the 3,000,000 shares sold pursuant to the Offering will be freely
tradable without restriction or further registration under the Securities Act of
1933, as amended (the "Securities Act"), except those shares acquired by
"affiliates" of the Company within the meaning of the Securities Act which will
be subject to the resale limitations of Rule 144 promulgated thereunder. The
remaining 8,669,189 shares (the "Restricted Shares") (including the 250,000
shares of Common Stock, based on an assumed initial public offering price of
$12.00 per share, sold in the Private Placement and the 1,858,145 shares sold
pursuant to the BioChem Offering) will be restricted securities within the
meaning of Rule 144 and may be sold only if registered under the Securities Act
or sold in accordance with an applicable exemption from registration, such as
Rule 144. The Company, its executive officers and directors and holders of
substantially all of the Common Stock have agreed not to offer, sell, contract
to sell, grant any option to sell, or otherwise dispose of, directly or
indirectly, any Common Stock or securities convertible into or exchangeable for
Common Stock or warrants or other rights to purchase Common Stock owned by them,
subject to certain limited exceptions, during the 180 days after the date of
this Prospectus (the "Lock-Up Period"), without the prior consent of SBC Warburg
Dillon Read Inc. However, SBC Warburg Dillon Read Inc. may, in its sole
discretion, and at any time without notice, release all or any portion of the
securities subject to lock-up agreements. Commencing at the end of the Lock-Up
Period, approximately 6,520,950 Restricted Shares will be eligible for sale in
the public market, subject to compliance with Rule 144. Of such shares,
approximately 5,158,797 will be eligible for sale, without limitation, pursuant
to Rule 144(k) or Rule 701 promulgated under the Securities Act, including
approximately 68,544 shares of Common Stock not subject to lock-up agreements
which will be eligible for sale following the Offering. The remaining
approximately 2,148,239 Restricted Shares will become eligible for sale at
various times over a period of six months from the end of the Lock-Up Period. In
addition, any shares issued upon exercise of the Company's outstanding warrants
may be eligible for sale pursuant to Rule 144 at various times following the
expiration of the Lock-Up Period. The Company has granted to certain
securityholders demand and/or piggyback registration rights covering an
aggregate of 8,113,670 shares of Common Stock. The Company expects to file a
Registration Statement on Form S-8 registering shares of Common Stock reserved
for issuance upon exercise of options granted under the Company's 1997 Plan,
Directors' Plan and 1994 Stock Option Plan following completion of the Offering.
See "Shares Eligible for Future Sale" and "Underwriting."
 
                                       17
<PAGE>
                                USE OF PROCEEDS
 
    The net proceeds to the Company from the sale of the 3,000,000 shares of
Common Stock offered by the Company hereby, at an assumed initial public
offering price of $12.00 per share, and after deducting underwriting discounts
and commissions and other estimated offering expenses, are estimated to be
approximately $32,430,000 ($37,452,000 if the Underwriters' over-allotment
option is exercised in full). The gross proceeds to the Company from the sale of
shares of Common Stock pursuant to the Private Placement are expected to be
$3,000,000.
 
    The Company intends to use the net proceeds from the Offering, the Private
Placement and the BioChem Offering primarily to fund its research and
development activities and for general corporate purposes, including working
capital. The amounts actually expended by the Company for working capital
purposes will vary significantly depending upon a number of factors, including
the progress of the Company's collaborations and its internal development
efforts, the timing of the Company's leasing of additional laboratory and office
space, future revenue growth, if any, and the amount of cash, if any, generated
by the Company's operations. The Company's management will retain broad
discretion in the allocation of the net proceeds of the Offering, the Private
Placement and the BioChem Offering. See "Risk Factors--Broad Discretion in
Application of Net Proceeds."
 
    Pending such uses, the Company intends to invest the net proceeds in
short-term, investment grade, interest-bearing securities.
 
                                DIVIDEND POLICY
 
    The Company has never declared or paid any cash dividends on its Common
Stock. The Company currently anticipates that any future earnings will be
retained by the Company for the development and operations of its business.
Accordingly, the Company does not anticipate paying cash dividends on the Common
Stock in the foreseeable future.
 
                                       18
<PAGE>
                                 CAPITALIZATION
 
    The following table sets forth the capitalization of the Company (i) as of
September 30, 1997, (ii) pro forma to give effect to the issuance of the shares
of Series D Preferred Stock and the value of the BioChem Warrant, the retirement
of 358,748 shares of treasury stock, the conversion of the Series A Preferred
Stock, Series B Preferred Stock, Series C Preferred Stock and Series D Preferred
Stock into shares of Common Stock and the amendment of the Company's Restated
Certificate of Incorporation and (iii) pro forma as adjusted to reflect the sale
by the Company of the 3,000,000 shares of Common Stock offered hereby and the
250,000 shares of Common Stock offered pursuant to the Private Placement
(assuming an initial public offering price of $12.00 per share). See
"Description of Capital Stock." The following table should be read in
conjunction with "Management's Discussion and Analysis of Financial Condition
and Results of Operations" and the Financial Statements and Notes thereto
included elsewhere in this Prospectus.
 
<TABLE>
<CAPTION>
                                                                                 AS OF SEPTEMBER 30, 1997
                                                                         -----------------------------------------
<S>                                                                      <C>         <C>          <C>
                                                                                                     PRO FORMA
                                                                                                         AS
                                                                           ACTUAL     PRO FORMA    ADJUSTED(2)(3)
                                                                         ----------  -----------  ----------------
                                                                                      (IN THOUSANDS)
Capital lease obligations, less current portion (1)....................  $      501   $     501      $      501
Redeemable convertible preferred stock, $0.01 par value; 21,500,000
  shares authorized and 17,036,265 shares issued and outstanding,
  actual; 27,250,000 shares authorized and no shares issued and
  outstanding, pro forma and pro forma as adjusted.....................      20,279      --              --
                                                                         ----------  -----------       --------
Stockholders' equity (deficit):
  Preferred stock, $0.01 par value, no shares authorized or issued and
    outstanding, actual; 4,000,000 shares authorized and no shares
    issued and outstanding, pro forma and pro forma as adjusted........      --          --              --
  Common stock, $0.01 par value, 30,000,000 shares authorized and
    1,373,378 shares issued and 1,014,630 outstanding, actual;
    35,000,000 shares authorized and 8,413,763 shares issued and
    outstanding, pro forma; 35,000,000 shares authorized and 11,663,763
    shares issued and outstanding, pro forma as adjusted...............          14          84             117
  Additional paid-in capital...........................................       3,126      45,547          80,944
  Accumulated deficit..................................................     (21,169)    (23,436)        (23,436)
  Unearned compensation................................................      (2,660)     (2,660)         (2,660)
  Treasury stock, at cost (358,748 shares at actual, none pro forma and
    pro forma as adjusted).............................................         (55)     --              --
                                                                         ----------  -----------       --------
    Total stockholders' equity (deficit)...............................     (20,744)     19,535          54,965
                                                                         ----------  -----------       --------
      Total capitalization.............................................  $       36   $  20,036      $   55,466
                                                                         ----------  -----------       --------
                                                                         ----------  -----------       --------
</TABLE>
 
- --------------
(1) See Note 8 of Notes to Financial Statements for a description of the
    Company's capital lease obligations.
 
(2) Excludes: (i) 790,581 shares of Common Stock issuable upon exercise of
    outstanding options at a weighted average exercise price of $1.75 per share,
    (ii) 464,537 shares of Common Stock issuable at an exercise price of $13.47
    per share upon exercise of the BioChem Warrant, (iii) 49,763 shares of
    Common Stock issuable upon exercise of an outstanding warrant at an exercise
    price of $3.07 per share and 32,525 shares of Common Stock issuable upon
    exercise of an outstanding warrant at an exercise price of $5.53 per share
    and (iv) 1,950,000 shares of Common Stock reserved for issuance upon
    exercise of options or in connection with other awards that may be granted
    in the future under the 1997 Plan and the Directors' Plan. See "Certain
    Transactions-- BioChem Offering," "Management--Employment Agreements,"
    "--Stock Options," "Employee Benefit Plans--1997 Equity Incentive Plan,"
    "--Non-Employee Directors Stock Plan" and "--1994 Stock Option Plan,"
    "Description of Capital Stock-- Warrants" and Notes 6, 8 and 10 of Notes to
    Financial Statements.
 
(3) In the event that the initial public offering price is less than $10.76 per
    share, the Company will be required to issue to BioChem, for no additional
    consideration, the number of additional shares of Common Stock equal to the
    amount by which (a) 19,993,640 divided by the initial public offering price,
    exceeds (b) 1,858,145. See "Certain Transactions--BioChem Offering."
 
                                       19
<PAGE>
                                    DILUTION
 
    As of September 30, 1997, the pro forma net tangible book value of the
Company was approximately $19,535,000, or $2.32 per share. Pro forma net
tangible book value per share represents the amount of tangible net assets of
the Company, less total liabilities, divided by the pro forma number of shares
of Common Stock outstanding as of September 30, 1997 (giving effect to the
BioChem Offering). After giving effect to the sale by the Company of the shares
of Common Stock offered hereby and offered pursuant to the Private Placement
(assuming an initial public offering price of $12.00 per share) and the
application of the net proceeds therefrom, the pro forma net tangible adjusted
book value of the Company at September 30, 1997 would have been approximately
$54,965,000, or $4.71 per share. This amount represents an immediate increase in
pro forma net tangible book value of $2.39 per share to existing stockholders
and an immediate dilution in net tangible book value of $7.29 per share to
purchasers of Common Stock in the Offering. The following table illustrates this
per share dilution, without giving effect to any exercise of the Underwriters'
over-allotment option:
 
<TABLE>
<S>                                                                   <C>        <C>
Assumed initial public offering price per share.....................             $   12.00
  Pro forma net tangible book value per share as of September 30,
    1997............................................................  $    2.32
  Increase per share attributable to new investors(1)...............       2.39
                                                                      ---------
Pro forma net tangible book value per share after the Offering and
  the Private Placement.............................................                  4.71
                                                                                 ---------
Dilution per share to new investors.................................             $    7.29
                                                                                 ---------
                                                                                 ---------
</TABLE>
 
- --------------
 
    (1) Includes increase attributable to the sale of shares in the Offering and
       the Private Placement.
 
    The following table summarizes, on a pro forma basis as of September 30,
1997, the number of shares of Common Stock purchased from the Company (giving
effect to the BioChem Offering), the total consideration paid, and the average
price per share paid by existing stockholders of the Company and by new
investors purchasing shares from the Company in the Offering and the Private
Placement, at an assumed initial public offering price of $12.00 per share,
before deducting underwriting discounts and commissions and the estimated
offering expenses payable by the Company:
 
<TABLE>
<CAPTION>
                                                 SHARES PURCHASED          TOTAL CONSIDERATION        AVERAGE
                                             -------------------------  --------------------------     PRICE
                                                NUMBER     PERCENT(1)      AMOUNT        PERCENT     PER SHARE
                                             ------------  -----------  -------------  -----------  -----------
<S>                                          <C>           <C>          <C>            <C>          <C>
Existing stockholders......................     8,413,763        72.1%  $  43,416,000        52.7%   $    5.16
New investors..............................     3,250,000        27.9      39,000,000        47.3        12.00
                                             ------------       -----   -------------       -----
Total......................................    11,663,763       100.0%  $  82,416,000       100.0%
                                             ------------       -----   -------------       -----
                                             ------------       -----   -------------       -----
</TABLE>
 
- --------------
 
    (1) If exercised, the Underwriters' over-allotment option to purchase
       450,000 additional shares will further reduce the percentage held by
       existing stockholders to 69.5% and increase the percentage held by new
       investors to 30.5%.
 
    The foregoing tables exclude as of December 31, 1997: (i) 792,299 shares of
Common Stock issuable upon exercise of outstanding options at a weighted average
exercise price of $1.75 per share, (ii) 464,537 shares of Common Stock issuable
at an exercise price of $13.47 per share upon exercise of the BioChem Warrant,
(iii) 49,763 shares of Common Stock issuable upon exercise of an outstanding
warrant at an exercise price of $3.07 per share and 32,525 shares of Common
Stock issuable upon exercise of an outstanding warrant at an exercise price of
$5.53 per share and (iv) 1,950,000 shares of Common Stock reserved for issuance
upon exercise of options or in connection with other awards that may be granted
in the future and otherwise under the 1997 Plan and the Directors' Plan. In the
event that the initial public
 
                                       20
<PAGE>
offering price is less than $10.76 per share, the Company will be required to
issue to BioChem, for no additional consideration, the number of additional
shares of Common Stock equal to the amount by which (a) 19,993,640 divided by
the initial public offering price, exceeds (b) 1,858,145. See "Certain
Transactions--BioChem Offering," "Management--Employment Agreement," "--Stock
Options," "Employee Benefit Plans--1997 Equity Incentive Plan," "--Non-Employee
Directors Stock Plan" and "--1994 Stock Option Plan," "Description of Capital
Stock--Warrants" and Notes 6, 8 and 10 of Notes to Financial Statements.
 
                                       21
<PAGE>
                            SELECTED FINANCIAL DATA
                     (IN THOUSANDS, EXCEPT PER SHARE DATA)
 
    The selected financial data set forth below as of December 31, 1995 and 1996
and for the years ended December 31, 1994, 1995 and 1996 have been derived from
the Company's financial statements, which have been audited by Price Waterhouse
LLP, independent accountants, and are included elsewhere herein. The selected
financial data as set forth below as of December 31, 1992, 1993 and 1994 and for
the period from September 17, 1992 ("Inception") to December 31, 1992 and for
the year ended December 31, 1993 have been derived from the Company's audited
financial statements not included herein. The selected financial data as set
forth below as of September 30, 1997, and for the nine months ended September
30, 1996 and 1997 have been derived from the Company's unaudited financial
statements which are included elsewhere herein. The unaudited financial
statements have been prepared by the Company on a basis consistent with the
Company's audited financial statements and, in the opinion of management,
include all adjustments, consisting of only normal recurring adjustments,
necessary for a fair presentation of the Company's results of operations and
financial condition for such periods. Operating results for the nine months
ended September 30, 1997 are not necessarily indicative of results that may be
expected for the entire year ending December 31, 1997. The selected financial
data set forth below should be read in conjunction with the Financial Statements
and related Notes thereto and with "Management's Discussion and Analysis of
Financial Condition and Results of Operations," which are included elsewhere
herein.
 
<TABLE>
<CAPTION>
                                                                                                           NINE MONTHS ENDED
                                               PERIOD FROM                    YEAR ENDED
                                              INCEPTION TO                   DECEMBER 31,                    SEPTEMBER 30,
                                              DECEMBER 31,    ------------------------------------------  --------------------
                                                  1992          1993       1994       1995       1996       1996       1997
                                             ---------------  ---------  ---------  ---------  ---------  ---------  ---------
<S>                                          <C>              <C>        <C>        <C>        <C>        <C>        <C>
STATEMENT OF OPERATIONS DATA:                                                                                 (UNAUDITED)
Revenue:
  Collaborative agreements.................        --            --         --         --      $     975  $     975  $     467
  SBIR grants..............................        --            --         --      $     260        232        222        138
                                                   ------     ---------  ---------  ---------  ---------  ---------  ---------
                                                   --            --         --            260      1,207      1,197        605
                                                   ------     ---------  ---------  ---------  ---------  ---------  ---------
Cost of revenue:
  Collaborative agreements.................        --            --         --         --            174        174        124
  SBIR grants..............................        --            --         --            260        232        222        138
                                                   ------     ---------  ---------  ---------  ---------  ---------  ---------
                                                   --            --         --            260        406        396        261
                                                   ------     ---------  ---------  ---------  ---------  ---------  ---------
  Gross profit.............................        --            --         --         --            801        801        344
Operating expenses:
  Research and development.................     $     455     $   1,833  $   3,157      3,152      3,958      2,757      4,273
  General and administrative...............            94           652        998      1,299        906        669        831
                                                   ------     ---------  ---------  ---------  ---------  ---------  ---------
                                                      549         2,485      4,155      4,451      4,865      3,427      5,104
                                                   ------     ---------  ---------  ---------  ---------  ---------  ---------
  Loss from operations.....................          (549)       (2,485)    (4,155)    (4,451)    (4,064)    (2,626)    (4,761)
                                                   ------     ---------  ---------  ---------  ---------  ---------  ---------
Other income (expense), net................             1           (62)      (146)      (128)        19         12        (15)
                                                   ------     ---------  ---------  ---------  ---------  ---------  ---------
  Net loss.................................     $    (549)    $  (2,547) $  (4,301) $  (4,579) $  (4,044) $  (2,614) $  (4,775)
                                                   ------     ---------  ---------  ---------  ---------  ---------  ---------
                                                   ------     ---------  ---------  ---------  ---------  ---------  ---------
  Net loss per share(1)....................     $   (0.21)    $   (0.98) $   (1.25) $   (1.28) $   (1.20) $   (0.77) $   (1.35)
                                                   ------     ---------  ---------  ---------  ---------  ---------  ---------
                                                   ------     ---------  ---------  ---------  ---------  ---------  ---------
  Weighted average common and common
    equivalent shares outstanding(1).......         2,556         2,607      3,435      3,551      3,360      3,374      3,528
                                                   ------     ---------  ---------  ---------  ---------  ---------  ---------
                                                   ------     ---------  ---------  ---------  ---------  ---------  ---------
Pro forma net loss per share
  (unaudited)(1)...........................                                                    $   (0.49)            $   (0.53)
                                                                                               ---------             ---------
                                                                                               ---------             ---------
Pro forma weighted average common and
  common equivalent shares outstanding
  (unaudited)(1)...........................                                                        8,186                 9,069
                                                                                               ---------             ---------
                                                                                               ---------             ---------
</TABLE>
<TABLE>
<CAPTION>
                                                                                   DECEMBER 31,
                                                               -----------------------------------------------------
                                                                 1992       1993       1994       1995       1996
                                                               ---------  ---------  ---------  ---------  ---------
<S>                                                            <C>        <C>        <C>        <C>        <C>
BALANCE SHEET DATA:
Cash and cash equivalents....................................     --      $   1,418  $     922  $     241  $   1,314
Working capital..............................................  $    (573)     2,274     (1,939)        92      3,350
Total assets.................................................         25      3,726      2,760      2,689      5,747
Noncurrent portion of capital lease obligations..............     --            345        926        636        424
Redeemable convertible preferred stock.......................     --          6,203      6,403     12,982     20,279
Accumulated deficit..........................................       (549)    (3,256)    (7,685)   (12,309)   (16,394)
Total stockholders' deficit..................................       (549)    (3,230)    (7,494)   (12,123)   (16,126)
 
<CAPTION>
 
                                                                SEPTEMBER 30,
                                                                    1997
                                                               ---------------
<S>                                                            <C>
BALANCE SHEET DATA:
Cash and cash equivalents....................................     $     858
Working capital..............................................        (1,200)
Total assets.................................................         2,478
Noncurrent portion of capital lease obligations..............           501
Redeemable convertible preferred stock.......................        20,279
Accumulated deficit..........................................       (21,169)
Total stockholders' deficit..................................       (20,744)
</TABLE>
 
- --------------
(1) See Note 2 of Notes to Financial Statements for information concerning the
    computation of net loss per share and shares used in computing net loss per
    share.
 
                                       22
<PAGE>
                    MANAGEMENT'S DISCUSSION AND ANALYSIS OF
                 FINANCIAL CONDITION AND RESULTS OF OPERATIONS
 
    THE FOLLOWING DISCUSSION SHOULD BE READ IN CONJUNCTION WITH "SELECTED
FINANCIAL DATA" AND THE COMPANY'S FINANCIAL STATEMENTS AND RELATED NOTES
THERETO, APPEARING ELSEWHERE IN THIS PROSPECTUS. THIS PROSPECTUS CONTAINS
CERTAIN FORWARD-LOOKING STATEMENTS WHICH INVOLVE RISKS AND UNCERTAINTIES. THE
COMPANY'S ACTUAL RESULTS COULD DIFFER MATERIALLY FROM THE RESULTS ANTICIPATED IN
THESE FORWARD-LOOKING STATEMENTS AS A RESULT OF CERTAIN OF THE FACTORS SET FORTH
IN THIS PROSPECTUS.
 
OVERVIEW
 
    Scriptgen utilizes its proprietary high throughput technologies to enable
and accelerate the discovery of innovative small molecule drugs. Scriptgen's
technology platform allows the Company and its collaborators to exploit the
opportunities afforded by advances in genomics and combinatorial chemistry, and
opens new avenues of drug discovery. The Company's strategy is to maximize the
commercial opportunities presented by its technology platform and pipeline of
drug candidates by entering into multiple collaborations and retaining rights to
independently develop certain products.
 
    Since its incorporation and commencement of operations in September 1992,
the Company has been developing its drug discovery technologies, and has used
such technologies in its collaborations and for its internal development
programs. As of January 7, 1998, the Company has received approximately
$51,000,000 in funding through the sale of preferred stock and from payments
under the Company's collaborative agreements, and it expects to receive an
additional $3,000,000 upon the closing of the Private Placement. Additionally,
the Company has received approximately $2,100,000 in SBIR grants from the
National Institutes of Health, of which approximately $600,000 has been funded
as of September 30, 1997. The Company has a limited history of operations and
has experienced significant operating losses since Inception. The Company
expects to incur significant additional operating losses over the next several
years and expects cumulative losses to increase substantially due primarily to
expanded research and development efforts, pre-clinical and clinical trials.
 
    To date, a majority of all revenue earned by the Company has been from its
collaborative agreements, and the Company expects that substantially all revenue
for the foreseeable future will result from such collaborations and any future
collaborations the Company may enter into. The timing of any fees or milestone
or other payments under such collaborations is expected to vary greatly from
quarter to quarter, depending on numerous factors. Operating results may
therefore vary substantially from quarter to quarter and will not necessarily be
indicative of results in subsequent periods. See "Risk Factors--Dependence Upon
Present and Future Collaborative Arrangements" and "--Significant Fluctuations
in Quarterly and Annual Results."
 
    Revenue derived under the Company's collaborative agreements is recognized
as drug discovery activities are performed. Cash received in advance of
activities performed is recorded as deferred revenue. Certain agreements also
provide for payments to the Company upon the achievement of certain milestones
as well as royalties on the net sales of any products developed resulting from
the collaborations, as defined in the respective agreements. Any revenue related
to milestones will be recognized as the milestones are achieved and any revenue
related to royalties will be recognized as earned.
 
    Revenue from SBIR grants to conduct research and development is recognized
as eligible costs are incurred up to the $2,100,000 funding limit described
above. Eligible grant-related costs which have been incurred in advance of cash
receipts are recorded as receivables.
 
                                       23
<PAGE>
RESULTS OF OPERATIONS
 
NINE MONTHS ENDED SEPTEMBER 30, 1997 AND 1996
 
    REVENUE.  Total revenue in the nine months ended September 30, 1997 was
$604,784 compared to $1,196,585 in the nine months ended September 30, 1996. The
Company recognized $467,000 of revenue in the nine months ended September 30,
1997 under its collaborative agreement with Eli Lilly and $975,000 of revenue in
the nine months ended September 30, 1996 under a collaborative agreement with
Boehringer Ingelheim ("Boehringer") which was concluded in 1996 when Boehringer
elected not to continue developing the program to which such agreement related.
In addition, the Company recognized $137,784 and $221,585 of revenue related to
SBIR grants in the nine months ended September 30, 1997 and 1996, respectively.
 
    COST OF REVENUE.  Cost of revenue reflects certain direct and overhead
expenses associated with collaborations in progress in addition to eligible
expenses incurred related to SBIR grants. Cost of revenue was $261,299 in the
nine months ended September 30, 1997 compared to $395,750 in the nine months
ended September 30, 1996.
 
    RESEARCH AND DEVELOPMENT EXPENSES.  Total research and development expenses
were $4,273,149 in the nine months ended September 30, 1997 compared to
$2,757,439 in the nine months ended September 30, 1996, an increase of
$1,515,710 or 55.0%. The increase was largely due to increased costs related to
additional personnel and, to a lesser extent, increases in depreciation,
amortization and patent expenses.
 
    GENERAL AND ADMINISTRATIVE EXPENSES.  General and administrative expenses
were $830,908 in the nine months ended September 30, 1997 compared to $669,108
in the nine months ended September 30, 1996, an increase of $161,800 or 24.2%.
The increase was primarily due to amortization of unearned compensation and an
increase in costs associated with additional personnel, public relations and
other administrative expenses offset by a decrease in the use of consultants.
 
    OTHER INCOME AND EXPENSE, NET.  Other income and expense, net was $(14,884)
in the nine months ended September 30, 1997 compared to $12,204 in the nine
months ended September 30, 1996, a decrease of $27,088 or 222.0%. The decrease
was primarily due to a decrease in interest income as a result of a decrease in
the average cash balance during the nine months ended September 30, 1997. In
addition, interest expense increased due to an increase in the average balance
of outstanding capital lease obligations.
 
YEARS ENDED DECEMBER 31, 1996 AND 1995
 
    REVENUE.  Total revenue in 1996 was $1,206,620 compared to $260,415 in 1995.
The Company recognized $975,000 of revenue in 1996 under the collaborative
agreement with Boehringer. No collaborative agreements were in progress in 1995.
In addition, the Company recognized $231,620 and $260,415 of revenue under SBIR
grants in 1996 and 1995, respectively.
 
    COST OF REVENUE.  Cost of revenue was $405,785 in 1996 compared to $260,415
in 1995.
 
    RESEARCH AND DEVELOPMENT EXPENSES.  Total research and development expenses
were $3,958,201 in 1996 compared to $3,152,494 in 1995, an increase of $805,707
or 25.6%. The increase was largely due to increased costs related to additional
personnel, laboratory materials and supplies, patent costs and depreciation and
amortization expenses.
 
    GENERAL AND ADMINISTRATIVE EXPENSES.  General and administrative expenses
were $906,452 in 1996 compared to $1,298,684 in 1995, a decrease of $392,232 or
30.2%. The decrease was primarily due to expenses incurred in 1995 under a
separation agreement with a former chief executive officer of the Company.
 
                                       24
<PAGE>
    OTHER INCOME AND EXPENSE, NET.  Other income and expense, net was $19,799 in
1996 compared to $(127,749) in 1995, an increase of $147,548, or 115.5%. This
increase was due to an increase in interest income as a result of an increase in
the average cash balance in 1996. This increase was offset by a decrease in
interest expense as a result of the decrease in the average balance of
outstanding capital lease obligations and the conversion of convertible debt
during 1995.
 
YEARS ENDED DECEMBER 31, 1995 AND 1994
 
    REVENUE.  Total revenue in 1995 was $260,415, consisting only of revenue
recognized under SBIR grants. No revenue was recognized in 1994.
 
    COST OF REVENUE.  Cost of revenue related to SBIR grants was $260,415 for
1995. No such grants were in place during 1994.
 
    RESEARCH AND DEVELOPMENT EXPENSES.  Total research and development expenses
were $3,152,494 in 1995 compared to $3,156,734 in 1994.
 
    GENERAL AND ADMINISTRATIVE EXPENSES.  General and administrative expenses
were $1,298,684 in 1995 compared to $998,194 in 1994, an increase of $300,490 or
30.1%. The increase was primarily due to increased executive and administrative
staffing and consultant expenses used to support the growth of the Company's
research and development.
 
    OTHER INCOME AND EXPENSE, NET.  Other income and expense, net was $(127,749)
in 1995 compared to $(146,046) in 1994, a decrease of $18,297 or 12.5%. This
decrease was due to an increase in interest income as a result of an increase in
the average cash balance offset by an increase in interest expense as a result
of an increase in outstanding capital lease obligations and the issuance of
convertible debt.
 
INCOME TAXES
 
    The Company has generated taxable losses from operations since Inception
and, accordingly, has no taxable income available to offset the carryback of net
operating losses. Based upon the weight of all available evidence, the Company
has provided a full valuation allowance for its deferred tax assets since, in
the opinion of management, realization of these future benefits is not
sufficiently assured (defined as a likelihood of slightly more than 50 percent).
 
LIQUIDITY AND CAPITAL RESOURCES
 
    Since Inception, the Company has financed its operations through the sale of
preferred stock, payments received under the Company's collaborative
arrangements, equipment financing, SBIR grants and interest earned on invested
capital. The Company's total cash, cash equivalents and investments balance at
September 30, 1997 was $1,064,157 compared to $4,338,237 at December 31, 1996.
The Company received approximately $1,405,000 under its collaborative agreements
and $137,784 in SBIR grants during the nine months ended September 30, 1997. In
October 1997, the Company entered into a collaborative arrangement with HMR for
an initial term of three years, subject to earlier termination six months prior
to the end of such term. The Company expects that the total amounts it will have
received from HMR under its collaborative agreement from October 1997 through
February 1998 will approximate $12,000,000, of which $6,000,000 will be
technology access fees, $3,000,000 will be research and development payments and
$3,000,000 will be proceeds from the Private Placement. The Company expects to
receive additional research and development payments under its collaborative
agreements. There can be no assurance that the Company will receive any
additional payments under its present or any future collaborative agreements.
See "Risk Factors--Dependence Upon Present and Future Collaborative
Arrangements" and "Business--Collaborative Arrangements."
 
                                       25
<PAGE>
    On December 17, 1997 the Company issued to BioChem Pharma Inc. shares of its
Series D Preferred Stock (convertible into 1,858,145 shares of Common Stock) for
consideration of $20,000,000. The Company also issued to BioChem Pharma Inc. a
warrant to purchase 464,537 shares of Common Stock at an exercise price of
$13.47 per share. Subsequent to the closing of the BioChem Offering, such shares
and warrant were transferred to BioChem Pharma Holdings Inc., a wholly owned
subsidiary of Biochem Pharma Inc. The Company will record a non-cash charge of
approximately $2,200,000 associated with the value of such warrant in the fourth
quarter of 1997. See "Certain Transactions--BioChem Offering."
 
    Net cash used in operating activities for the nine months ended September
30, 1997 was $2,737,087 compared to $2,555,823 for the nine months ended
September 30, 1996. Net cash used in operating activities was $3,568,031 in 1996
compared to $3,744,478 and $3,876,939 in 1995 and 1994, respectively. The cash
used in operations was primarily to fund research and development and for
general and administrative expenses.
 
    As of September 30, 1997, the Company had invested $3,018,000 in property
and equipment, primarily in facility renovations and laboratory equipment. These
acquisitions were funded by capital lease financings which have an aggregate
outstanding principal balance of $984,627 at September 30, 1997 due at various
dates through the year 2000 with interest rates ranging between 8%-8.5% and 15%
for equipment and facility renovations, respectively. The Company expects
substantially all of its capital expenditures in 1997 to be funded through
capital lease equipment financing. In connection with these capital leases, the
Company has issued warrants for 253,000 shares of its redeemable convertible
preferred stock through November 1997.
 
    Pursuant to several license and sponsored research agreements, the Company
has paid to date an aggregate of approximately $1,200,000 in the form of license
and research and development fees. Under existing sponsored research agreements,
the Company remains obligated to pay approximately $300,000 in additional
research payments. Under such agreements and other agreements, the Company is
required to make payments upon the achievement of certain milestones, to pay
royalties on certain drug sales, if any, and to pay other amounts in connection
with sublicenses, if any (collectively, "Contingent Payments"). To date, the
Company has not become obligated to make any Contingent Payments under such
agreements and does not anticipate becoming obligated to make any such payments
in the near future.
 
    The Company believes that the net proceeds of the Offering, the Private
Placement and the BioChem Offering, together with revenue from its collaborative
agreements, its existing capital resources, SBIR grants and interest income will
be sufficient to fund its operating expenses and capital requirements as
currently planned through the end of 2000. The Company's actual cash
requirements may vary materially from those now planned and will depend upon
numerous factors, including the ability of the Company to enter into additional
collaborative arrangements, the achievement of milestones under the Company's
collaborative arrangements on a timely basis or at all, changes in the Company's
existing collaborative arrangements, the results of the Company's internal
development programs, the timing and results of pre-clinical and clinical
trials, the timing and costs of obtaining regulatory approvals, the timing and
level of the expansion of the Company's facilities, the level of resources, if
any, that the Company commits to the development of manufacturing, marketing and
sales capabilities, the technological advances and activities of competitors and
other factors. There can be no assurance that the net proceeds of the Offering,
the Private Placement and the BioChem Offering, together with the Company's
revenue from collaborative agreements, its existing capital resources, SBIR
grants and interest income will be sufficient to fund the Company's operating
expenses and capital requirements during such period. Thereafter, the Company
will need to raise substantial additional capital to fund its operations. The
Company intends to seek such additional funding through public or private
financing, collaborations or other arrangements. See "Use of Proceeds" and "Risk
Factors--Additional Financing Requirements; Uncertainty of Available Funding."
 
                                       26
<PAGE>
                                    BUSINESS
 
OVERVIEW
 
    Scriptgen utilizes its proprietary high throughput technologies to enable
and accelerate the discovery of innovative small molecule drugs. Scriptgen's
technology platform allows the Company and its collaborators to exploit the
opportunities afforded by advances in genomics and combinatorial chemistry, and
opens new avenues of drug discovery. The Company's technology platform
identifies and validates novel gene targets for therapeutic intervention, and
then uses novel assay systems to rapidly screen compounds against those targets,
even before the gene targets' characteristics or functions are well understood.
The Company believes that the application of its technologies addresses many of
the limitations associated with traditional drug discovery and provides
substantial cost savings opportunities. The Company commercializes its
technology platform through (i) collaborations with pharmaceutical and
technology companies and (ii) the Company's internal development program.
 
    The Company's core systems include GATE (Genetics Assisted Target
Evaluation), a family of high throughput target identification and validation
systems, and ATLAS (Any Target Ligand Affinity Screen) and SCAN (Screen for
Compounds with Affinity for Nucleic Acids), the high speed, solution based,
assay systems which identify compounds that bind to virtually any protein or
structured RNA, respectively. GATE measures the effects of transiently removing
a specific gene from a cell, and by reproducing conditions that closely resemble
drug mechanism of action, generates data more predictive of target behavior than
traditional methods. ATLAS and SCAN rapidly measure the affinity of compounds
that bind to targets even before the gene functions are well understood,
enabling the Company to work with targets that are unsuitable for traditional
high throughput screens. The Company believes ATLAS and SCAN increase
dramatically the number of targets and compounds that may be screened in a given
time period, and reduce to weeks what often requires months or years of assay
development time when using traditional high throughput functional assays. The
Company has used GATE to identify and validate novel infectious disease targets,
and has used ATLAS and SCAN to identify lead compounds, two of which have
progressed to pre-clinical development. ATLAS and SCAN are broadly applicable to
research in multiple therapeutic areas, and have demonstrated utility in
anti-infectives, oncology, cardiovascular, and respiratory and immunologic
disorders.
 
    The Company's strategy is to maximize the commercial opportunities presented
by its technology platform and pipeline of drug candidates by entering into
multiple collaborations and retaining rights to independently develop certain
products. Scriptgen has collaborative agreements with pharmaceutical and
technology companies, and routinely evaluates opportunities to enter into
collaborations with other potential partners. The Company currently has
collaborations with HMR, BioChem, Eli Lilly, Roche, Monsanto and ArQule, Inc.
Scriptgen's internal development efforts have initially focused on anti-
infectives, where it has identified novel cidal targets and lead compounds in
the fungal, bacterial and viral areas.
 
DRUG DISCOVERY TECHNOLOGIES
 
    Drug discovery and development is a complex process which, according to
sources cited in an article appearing in the October 1997 Pharmaceutical
Research and Manufacturing Association bulletin, averages 15 years from
inception to FDA approval at a cost of more than $500 million. The article also
states that only five in 5,000 compounds that enter pre-clinical testing advance
to clinical testing, and only one of those five is approved as a drug.
Consequently, technologies and methods which may make the drug discovery process
faster, less costly, and more effective are in great demand.
 
    The Company's technology platform is complementary to emerging drug
discovery approaches, including gene sequencing, functional genomics and
differential gene expression. The chart following outlines the drug discovery
process, and indicates the steps in that process where the Company's and these
complementary technologies apply.
 
                                       27
<PAGE>
                                    [CHART]
 
    Advances in genomics and related technologies are dramatically increasing
the number of potential drug targets available and have created a bottleneck in
the target validation phase of drug discovery. It has been estimated that there
are only approximately 400 human drug discovery targets for which drugs have
been developed. Although genomics and related technologies have the potential to
identify thousands of additional targets per year, these targets may not be
therapeutically relevant. For example, differential gene expression compares
gene transcription patterns in normal and diseased tissues, typically
identifying several hundred genes which are up or down regulated in diseased
cells relative to normal cells, but whose relevance to the cause of the
underlying disease is not apparent. Consequently, many of these targets will
require validation, a process that can consume two or more years with
conventional approaches. Further, existing gene-based technologies are limited
in screening potential because: (i) they can be used only to identify compounds
that affect transcription (the process by which DNA is transcribed into RNA),
(ii) they generally have very low throughput, (iii) they identify gene targets
which have unknown function and (iv) they do not accommodate the complexity of
gene interactions in the disease process.
 
SCRIPTGEN'S DRUG DISCOVERY APPROACH
 
    Scriptgen's drug discovery technology platform enables the Company and its
collaborators to exploit the opportunities afforded by advances in genomics and
combinatorial chemistry, and opens new avenues of drug discovery. Scriptgen's
primary drug discovery technologies are GATE, a family of high throughput target
identification and validation systems, and ATLAS and SCAN, the high speed,
solution based assay systems, which identify compounds that bind to virtually
any protein or structured RNA, respectively. The Company also possesses a
diverse 250,000 compound library consisting of defined small molecule chemical
entities, including 15,000 natural product extracts, and has access to validated
IN VIVO animal models of infectious diseases through the Company's collaboration
with Boston Medical Center.
 
                                       28
<PAGE>
    Scriptgen's drug discovery technology platform is unique because it
identifies and validates multiple gene targets, and rapidly measures the
affinity of compounds that bind to such gene targets even before the gene
functions are well understood. This approach enables the Company and its
collaborators to work with targets that are unsuitable for traditional high
throughput screens and greatly increases the number of targets and compounds
that may be screened in a given time period.
 
TARGET DISCOVERY AND VALIDATION SYSTEMS (GATE)
 
    GATE consists of a family of high throughput target identification and
validation technologies which the Company has successfully applied in fungi,
bacteria and viruses. GATE's regulated gene knockout technology measures the
effects of transient gene inactivation. It reproduces conditions that more
closely resemble drug mechanism of action than conventional gene inactivation
methods, which the Company believes makes GATE more predictive of target
behavior and hence more informative as a target validation technique. An
analogous technology for mammalian cells, CellGATE, is under development.
 
    GATE has been applied by the Company to infectious diseases where the
desired result of drug treatment is to kill the invading pathogen without severe
side effects to the patient. GATE determines whether the pathogen dies as a
result of a specific inactivation of a gene product, how quickly it dies and how
much of the target must be modified to kill the pathogen. Because GATE focuses
on cidal targets, the Company is able to focus its efforts on identifying
compounds which the Company believes may have a high probability of being
effective against the disease with low toxicity and side effects.
 
HIGH THROUGHPUT ASSAY SYSTEMS (ATLAS AND SCAN)
 
    ATLAS and SCAN are high throughput affinity assay systems that allow drug
discovery to focus rapidly on ligands, those rare compounds that bind to a
target, and therefore have the potential to become valid therapeutics. ATLAS and
SCAN are based on the thermodynamic principle that protein and RNA have
measurable stability, as well as the fact that all drugs act by binding to and
further stabilizing a specific target. Thus, ATLAS and SCAN may be applied to
virtually any identified target, even before its characteristics or functions
are well understood. These technologies are able to identify and distinguish
among ligands that bind to active and neutral sites, and measure the affinity of
binding, which indicates the potential of drug potency.
 
    In contrast, conventional high throughput drug discovery technologies
measure the effect of test compounds only on the function of a target. Before
such a functional screening approach may be initiated, the biochemical function
of the target must be well understood. This detailed characterization often
requires extensive time and effort before a target can be screened, if at all.
 
    ATLAS and SCAN have shown the ability to overcome many of the limitations of
high throughput drug screening and allow access to targets of unknown function,
thereby offering the following advantages:
 
    - TARGET FLEXIBILITY. ATLAS and SCAN require essentially no pre-existing
      biochemical understanding of the target molecule and are compatible with
      virtually any target protein or structured RNA. Using ATLAS and SCAN,
      screening can begin earlier than with conventional high throughput
      methods.
 
    - COMPOUND DIVERSITY. ATLAS and SCAN work in solution phase, and are used to
      search for drug candidates from a wide diversity of chemical sources
      including combinatorial, small molecule, peptide and natural product
      compound libraries.
 
    - RAPID ASSAY DEVELOPMENT. Many functional assays using biochemical, cell or
      animal based methods take months or years to develop. ATLAS and SCAN can
      be applied in a matter of weeks because they measure only the universal
      principle of drug binding and are independent of protein and nucleic acid
      function.
 
                                       29
<PAGE>
    - EFFICIENT, HIGH THROUGHPUT MODE. ATLAS and SCAN are compatible with modern
      robotic and automated equipment, operate in high throughput mode and can
      test thousands of compounds each week using minute compound amounts and
      very little target protein or RNA.
 
    - RAPID ELIMINATION OF NON-CANDIDATE COMPOUNDS. Used in a pre-screening
      mode, ATLAS and SCAN rapidly eliminate compounds that are not ligands and
      allow a focused and efficient development effort to be concentrated only
      on those compounds with the greatest potential for therapeutic benefit. In
      a typical high throughput assay using ATLAS, 99.9% of the screened
      compounds are eliminated as potential drug candidates.
 
    - QUANTITATIVE MEASURE OF DRUG BINDING. ATLAS and SCAN, unlike many drug
      discovery technologies, are sensitive assay systems which identify even
      weakly binding ligands, and provide a quantitative measure of how tightly
      a potential drug binds to its target.
 
    - EXPANDS DRUG DISCOVERY BEYOND REGULATION OF GENE TRANSCRIPTION. While
      traditional gene expression methods are limited to measuring initial gene
      transcripts, ATLAS and SCAN measure the binding to final gene products,
      thereby enhancing the ability to identify promising lead compounds.
 
    COALESCENT DRUG DESIGN.  For many target proteins, it is very difficult to
develop a single molecule with both inhibitory activity and sufficient
specificity for pharmaceutical applications. This difficulty is often a
consequence of the fact that proteins with similar functions have similar active
sites. In contrast, the neutral site surfaces of related proteins are
dissimilar, and thus compounds that also bind outside of the active site can
have specificity for the target protein. The Company has applied ATLAS to
develop novel coalescent compounds, which are small molecules connected by a
molecular tether that bind to both active and neutral sites. The binding
energies of the functional groups are nearly exponentially additive, allowing
for highly specific coalescent drug candidates to be forged even from weakly
binding compounds. Coalescent drug candidates have the potential to address a
broad spectrum of heretofore intractable protein targets.
 
    The Company is exploring the development of small molecule coalescent
compounds to mimic the action of protein drugs such as human growth hormone and
erythropoietin. The receptors for these proteins typically comprise two subunits
that span the cell membrane. The therapeutic protein binds to two distinct sites
on the extracellular portion of its receptor, one on each subunit, thereby
causing the subunits to pull together (dimerization). The dimerization of the
intracellular portions of the receptor subunits initiates a signaling pathway
which results in the intended therapeutic effect. Scientists have struggled to
design small molecule analogs of therapeutic proteins because small molecules
are unable to span the distance between the extracellular parts of the receptor
subunits. While the internal arms of the protein are much closer together, they
are not the active sites and thus have not been available as targets using
conventional assay technologies. ATLAS allows for the identification of ligands
that bind to the internal arms of these receptor subunits, making it possible to
construct small molecule coalescent compounds capable of causing dimerization of
the subunits and, hence, initiating a therapeutic response.
 
ADDITIONAL DRUG DISCOVERY TOOLS
 
    COMPOUND LIBRARY.  Scriptgen has a library of approximately 250,000
compounds including 15,000 mixtures of natural product extracts. These compounds
have been obtained from a variety of sources, and were selected from a larger
catalog of compounds based on their diversity and pharmacological profiles.
Through analogs of the compounds in the library, and the use of combinatorial
chemistry techniques, Scriptgen has access to more than 1,000,000 compounds. The
Company uses these compounds for high throughput screening in its internal
development program as well as in its collaborative arrangements. While the
compound library is used to identify therapeutic candidates against specific
targets, the lead compounds anticipated to be developed by Scriptgen will be
unique patented analogs, specifically designed using medicinal chemistry
techniques to optimize their efficacy.
 
                                       30
<PAGE>
    ANIMAL MODELS.  The Company's collaboration with Boston Medical Center to
test potential antibacterial and antifungal drug candidates gives the Company
access to a number of validated and predictive animal models of infectious
diseases to evaluate the efficacy and safety of the Company's lead compounds.
 
STRATEGY
 
    Scriptgen's strategy is to maximize the commercial opportunities presented
by its technology platform and pipeline of drug candidates. To implement this
strategy the Company will continue to:
 
    ESTABLISH COLLABORATIVE RELATIONSHIPS.  The Company enters into
collaborations with pharmaceutical and technology companies: (i) to perform high
throughput target identification and validation, assay development and lead
compound identification for its collaborators' drug discovery programs to
generate near-term revenue, (ii) to jointly discover and develop new drugs in
targeted areas, under agreements that provide the Company with near-term revenue
and the opportunity to receive substantial milestone payments and royalties and
(iii) to develop or commercialize selected drug candidates from the Company's
internal pipeline at such time as a collaboration is determined to represent the
best opportunity to maximize the commercial value of a particular candidate. The
Company currently has collaborations with HMR, BioChem, Eli Lilly, Roche and
Monsanto, and routinely evaluates opportunities to enter into collaborations
with other potential partners.
 
    DEVELOP INTERNALLY A PIPELINE OF DRUG DEVELOPMENT CANDIDATES.  Recognizing
that many promising drug candidates fail in subsequent stages of development,
the Company believes that it is essential to have a pipeline of new drug
candidates from which to choose. Scriptgen is developing a pipeline by using its
high throughput technologies to identify multiple lead candidates, initially
focusing in the antifungal, antibacterial and antiviral areas. The Company
develops drug candidates either alone or in conjunction with partners depending
on such factors as estimated development costs and potential regulatory approval
time and hurdles.
 
    EXPAND PROPRIETARY DRUG DISCOVERY TECHNOLOGY PLATFORM.  Scriptgen has an
ongoing research program aimed at expanding the capabilities and potential
applications for the Company's technologies, while simultaneously attempting to
increase their efficiency. In addition, the Company strives to identify, develop
and acquire other technologies, and to collaborate to obtain technologies that
can substantially enhance the drug discovery process. For example, the Company
has enhanced and expanded its core drug discovery technologies to include
technologies that allow ligands to be sorted rapidly according to the active and
neutral sites on the target. These technology enhancements have been
instrumental in the Company's obtaining SBIR funding for its coalescent drug
design program.
 
    MAINTAIN AND ENHANCE STRONG PROPRIETARY POSITION.  Scriptgen pursues an
aggressive strategy to protect its proprietary drug discovery technologies,
including certain targets, assays, lead compounds and certain other
technologies, through patents, trade secret law and confidentiality agreements.
 
COLLABORATIVE ARRANGEMENTS
 
    The Company has entered into collaborative arrangements with pharmaceutical
and technology companies.
 
    HOECHST MARION ROUSSEL.  In October 1997, the Company entered into a
collaboration with HMR pursuant to which the Company will seek to identify new
fungal targets and antifungal drug candidates. In each year of the
collaboration, Scriptgen will use GATE to identify and validate fungal targets,
some of which will be screened against compounds from Scriptgen's and HMR's
compound libraries utilizing ATLAS, SCAN and other technologies. HMR will
determine whether to proceed with the development of any lead compounds
discovered, and will receive an exclusive, worldwide license to develop and
commercialize any resulting drug candidate. The collaboration agreement with HMR
has an initial term of three
 
                                       31
<PAGE>
years, subject to HMR's right to terminate the agreement by giving six months'
written notice at any time after the second year of the agreement. Under such
agreement, Scriptgen has received initial cash payments, and HMR is required to
fund Scriptgen's research and development activities in connection with the
collaboration up to a specified amount for a period of three years. The Company
expects to have received payments which include an aggregate of $9 million from
HMR under the collaboration by the completion of the Offering, of which $6
million will be technology access fees and $3 million will be proceeds from the
sale of Common Stock (at a purchase price per share equal to the initial public
offering price) to HMR concurrently with the Offering. The Company will also
receive research and development payments and will receive payments when and if
certain milestones are achieved and royalties on the sales of any new drug
resulting from the collaboration. HMR may terminate the collaboration by giving
the Company six months' prior written notice at any time after the end of the
second year of the collaboration.
 
    BIOCHEM.  In December 1997, Scriptgen entered into a collaboration with
BioChem pursuant to which Scriptgen is using its technology to identify drug
candidates which are (i) active against the Hepatitis B virus and (ii) which act
as small molecule mimics of therapeutic proteins by activating dimerization of
certain receptors such as the erythropoietin receptor. The programs will involve
the use of SCAN, ATLAS and other technologies as well as Scriptgen's compound
library. The collaboration agreement with BioChem has an initial term of five
years. Scriptgen is responsible for all aspects of drug discovery and will
provide BioChem with small molecule drug candidates for novel molecular targets
in the HBV and Dimerescent Programs. BioChem is responsible for pre-clinical and
clinical development, and will retain worldwide commercialization rights.
BioChem has options to the Dimerescent Program, and is required to make a
milestone payment to Scriptgen when and if an option is exercised. Any profits
on any commercialized products emanating from the HBV and Dimerescent Programs
will be shared in accordance with the terms of the agreement. BioChem has
exclusive rights to these programs which continue as long as it performs certain
specified obligations under the agreement. In addition, BioChem acquired Series
D Preferred Stock for total consideration of $20 million and the BioChem
Warrant. See "Certain Transactions--BioChem Offering."
 
    ELI LILLY.  In May 1997, the Company entered into a collaboration with Eli
Lilly under which Scriptgen is using ATLAS to identify novel drug candidates
against two targets selected by Eli Lilly. Two additional targets may be
selected by Eli Lilly for high throughput screening in 1998, assuming certain
milestones are met. In October 1997, Eli Lilly and the Company expanded the
scope of the collaboration to screen additional compounds from the Company's
compound library. The collaboration agreement with Eli Lilly has an initial term
of 58 to 64 weeks. Under such agreement, Scriptgen receives research and
development payments and will receive payments when and if certain milestones
are achieved and royalties on the sales of any new drug resulting from the
collaboration.
 
    ROCHE.  In September 1995, the Company entered into a collaboration with
Roche pursuant to which the Company is using ATLAS to identify drug candidates
against a cancer-related target identified by Roche. The initial term of the
collaboration agreement with Roche runs through June 1998. Under the agreement
with Roche, Scriptgen receives research and development payments and will
receive payments when and if certain milestones are achieved and royalties on
the sales of any new drug resulting from the collaboration.
 
    MONSANTO.  In November 1997, the Company entered into a collaboration with
Monsanto under which Scriptgen is using its technology platform to identify and
validate novel fungal targets from plant and human pathogens and to identify
novel agents and drugs against such targets. The collaboration agreement with
Monsanto has an initial term of two years. The agreement provides Scriptgen with
68,000 small molecule compounds from Monsanto's library for use by the Company.
The Company will pay Monsanto royalties and milestones on any human
anti-infective drug developed and commercialized as a result of the
collaboration. Scriptgen receives research and development payments and will
receive payments when and
 
                                       32
<PAGE>
if certain milestones are achieved and royalties on the sales of any product
developed by Monsanto for IN PLANTA applications.
 
    ARQULE, INC.  The Company has entered into a collaboration with ArQule, Inc.
("ArQule") pursuant to which the Company incorporates compounds owned by ArQule
into the Company's library. The Company is screening certain of the ArQule
compounds against the Company's fungal, bacterial and viral targets. In the
event that active compounds are identified and selected for development,
Scriptgen and ArQule may enter into an agreement to share the costs of
development and the proceeds of any resulting commercial product.
 
    There can be no assurance that any drug candidates will be identified during
the Company's present collaborations or that, if identified, the Company's
collaborative partners will elect to proceed with the development of any drug
candidates. The Company's collaborative partners are not obligated to develop or
commercialize any drug candidates resulting from the collaborative agreements.
As a result, there can be no assurance that any of the milestone or royalty
payments contemplated by such collaborations will be made. See "Risk
Factors--Dependence Upon Present and Future Collaborative Arrangements."
 
SCRIPTGEN'S INTERNAL DEVELOPMENT PROGRAM
 
OVERVIEW
 
    Scriptgen's internal development efforts have initially focused on
anti-infectives, where it has identified novel cidal targets and lead compounds
in the fungal, bacterial and viral areas. Scriptgen has progressed rapidly in
the anti-infective area and has four lead compounds in development as well as a
number of other potential drug candidates under review. The Company has also
completed feasibility studies on novel targets in a number of other areas,
including oncology and immunologic disorders, and in several cases has
identified drug candidates. The Company believes that the anti-infective market
is attractive as an initial field of focus because of the following:
 
    - LARGE MARKET. Infectious diseases are the leading cause of death
      worldwide. According to 1996 sales data compiled by IMS International,
      anti-infective drugs generated approximately $30 billion in worldwide
      sales and constituted the fourth largest pharmaceutical market worldwide.
 
    - SCRIPTGEN TECHNOLOGY UNIQUELY SUITED FOR ANTI-INFECTIVES. The clinical
      efficacy of certain anti-infective drugs is being threatened by emerging
      strains of drug resistant pathogens and opportunistic infections arising
      from the growing number of immunosuppressed patients. In addition,
      scientists have recognized that newly identified pathogens are causing
      outbreaks of disease. GATE allows a determination of whether the pathogen
      dies as a result of a specific inactivation of a gene product, how quickly
      it dies and how much of the target must be modified to produce the desired
      effect. ATLAS and SCAN are used to quickly identify potential drug
      candidates for these validated targets. These technologies allow the
      Company to focus its efforts on identifying compounds with a high
      probability of being effective against the disease with low toxicity and
      side effects.
 
    - FEWER TECHNICAL AND REGULATORY HURDLES TO OVERCOME. Anti-infective drug
      development faces fewer technical hurdles in large part because invading
      pathogens are distinct organisms that can be identified and targeted
      separately from human host cells. In addition, because animal models for
      anti-infectives are considered to be fairly predictive of the therapeutic
      response in patients, and pharmacokinetic and pharmacodynamic parameters
      can be modeled in animals, there are fewer technical and regulatory
      hurdles. Initial human clinical studies to determine safety and efficacy
      of new anti-infective drugs can be conducted in short-term studies.
      Additionally, measures of drug efficacy are well established.
 
                                       33
<PAGE>
TARGET IDENTIFICATION AND VALIDATION AND HIGH THROUGHPUT SCREENING
 
    Scriptgen focuses on the identification and validation of targets essential
for the survival of the pathogen. Scriptgen uses GATE in its structured target
selection process to focus on targets which are predictive of the following
desirable therapeutic objectives: microbicidal, fast-acting, low toxicity, broad
spectrum activity and low resistance. Scriptgen has validated more than 45 cidal
fungal, bacterial and viral targets and is validating a number of others.
 
    Validated targets meeting the selection criteria are screened against the
Company's compound library in a high throughput mode. Depending upon the nature
of the individual target, functional assays may be used directly, or after
pre-screening with ATLAS or SCAN. Compounds that demonstrate specific anti-
infective activity are carefully scrutinized for their suitability as drug
candidates before being advanced into preliminary development. Criteria used for
selecting development candidates include: low molecular weight, chemical
feasibility and manufacturing cost, potential toxicity, cellular uptake,
metabolic stability and specificity. Compounds selected are then subjected to
preliminary modifications using medicinal as well as directed combinatorial
chemistry techniques, and a variety of analogs are produced for testing in
animal models.
 
DRUG CANDIDATES IN DEVELOPMENT
 
    Scriptgen's internal development program has made rapid progress in the
anti-infective area. The Company currently has four lead compounds in
development as well as a number of other compounds under review, even though it
has not yet screened all of its compounds against all of its targets.
 
    ANTIFUNGALS.  Scriptgen's program has identified three families of compounds
that show broad spectrum antifungal activity, including effectiveness against
drug resistant strains of CANDIDA ALBICANS, the most widespread cause of life
threatening fungal infections. Two low molecular weight compounds, ST61219 and
ST61769, have been chosen for further development. In animal studies, these
compounds have cured mice infected with CANDIDA ALBICANS, including a strain
resistant to a marketed antifungal, flucanazole, at oral doses that produced no
overt side effects.
 
    Initial pre-clinical data, including animal studies, on ST61219 and ST61769
indicate that these compounds may have several advantages over Diflucan
(flucanazole) and Sporanox (itraconazole), the current market leaders in the
antifungal area with worldwide sales in excess of $1.0 billion in 1996. These
advantages include:
 
    - CIDALITY. ST61219 and ST61769 kill the pathogen rather than simply inhibit
      its growth temporarily (static). Cidality eliminates the need for chronic
      application of static compounds which has the potential of adverse side
      effects and may give rise to drug resistance. Cidality is particularly
      important for that large segment of the patient population suffering from
      opportunistic infections because of impaired immune systems.
 
    - RAPID ACTIVITY. ST61219 and ST61769 act much more rapidly, which may allow
      for reduced dosing over a shorter time period. This faster cidality may
      result in a lower probability for the development of resistance.
 
    - BROAD SPECTRUM. ST61219 and ST61769 are effective against a broad range of
      pathogens, as well as specific strains that have developed resistance to
      the current drugs.
 
    ANTIBACTERIALS.  Scriptgen's program has identified a family of compounds
which shows broad spectrum antibacterial activity, and is efficacious against
drug resistant strains of STAPHYLOCOCCUS AUREUS, a major cause of bacterial
infections. From this family, one low molecular weight compound, ST41590, has
been selected for further development. ST41590 is a natural product extract and
is amenable to an efficient chemical synthesis.
 
                                       34
<PAGE>
    Initial pre-clinical data on ST41590 indicate that it may have a significant
therapeutic advantage over available antibiotics because of its broad spectrum
activity, rapid cidality and efficacy against pathogenic strains resistant to
current drugs.
 
    ANTIVIRALS.  High throughput functional screening has traditionally been
unavailable to antiviral drug discovery because the small genomes of viruses
produce few potential targets for therapeutic intervention. Furthermore, most of
the targets that have been identified are not fully characterized and are
difficult to incorporate into high throughput assays. ATLAS and SCAN overcome
these difficulties and enable Scriptgen to screen compounds against novel
targets in Hepatitis B virus and Hepatitis C virus. The Company has identified
four families of compounds that have shown antiviral activity against Hepatitis
B virus. One low molecular weight compound, ST135647, has been selected for
further development. The remaining compounds are being analyzed for their
suitability as drug candidates.
 
    Initial pre-clinical data on ST135647 indicate that it may have several
advantages over drug candidates known by the Company to be in development
("Known Drug Candidates"), including the following:
 
    - NOVEL TARGET. ST135647 acts on a novel target of the Hepatitis B virus
      that is critical for replication. The Company believes that ST135647 will
      overcome problems of resistance that have already emerged with some of the
      Known Drug Candidates that act on different viral targets.
 
    - EFFICACIOUS. ST135647 has been shown in preliminary tests to be a potent
      inhibitor of viral replication at concentrations that have shown minimal
      toxic effects to the human liver cells in which the virus replicates. Some
      of the Known Drug Candidates have shown limited efficacy or undesirable
      side effects.
 
    - POTENTIAL FOR COMBINATION THERAPY. ST135647 may act beneficially in
      combination with some of Known Drug Candidates because of its novel site
      of action. Many experts agree that multi-drug therapy represents the most
      effective approach for treatment of Hepatitis B virus.
 
PATENTS AND PROPRIETARY TECHNOLOGY
 
    Patent protection for the Company's technologies, targets and compounds is
important to its business. The Company has filed certain U.S. and foreign patent
applications and has certain issued U.S. patents and allowed U.S. patent
applications. To date, no foreign patents have been issued and no foreign patent
applications have been allowed. The Company usually employs the Patent
Cooperation Treaty ("PCT") to file foreign counterparts to its pending U.S.
patent applications. Under the PCT it is possible to defer the filing of
national patent applications in the jurisdictions in which such protection is
being sought until 30 months after the filing date of the corresponding U.S.
patent application, at which time the Company has the option of filing the
national phase patent applications that would be prosecuted according to the
procedures and practices of the respective national patent offices.
 
    Two of the Company's U.S. patents and one of its allowed U.S. patent
applications claim aspects of the Company's ATLAS screening technology. The two
issued U.S. patents and the allowed U.S. patent application in the ATLAS field
claim certain methods whereby a target protein is incubated in the presence and
absence of several test ligands, and evaluated based on the extent to which the
target protein is folded, unfolded, or intermediately folded in the absence or
presence of the test ligands. The Company also has a notice of allowance for a
patent application that claims a certain fungal target protein complex, known as
TAF, which is important in certain gene transcription events in the model yeast
S. CEREVISIAE. This fungal protein complex may be relevant to the Company's
research because it may be used as a target protein in the Company's screening
technologies in order to identify compounds that interfere with the fungal life
cycle, and to confirm the biological activity of such compounds. A notice of
allowance is issued by the USPTO after a patent application has been examined
and it has been found that the applicant is entitled to a patent. The notice
calls for payment of a specified sum constituting the government issue fee which
must be paid within three months. The patent is generally granted (issued)
several months after the issue fee has been paid. The Company's issued patents
expire between 2013 and 2015.
 
                                       35
<PAGE>
    The Company's success will depend in part on its ability to obtain U.S. and
foreign patent protection for its drug candidates and the components of its
technology platform, preserve its trade secrets and operate without infringing
the proprietary rights of third parties. Because of the length of time and
expense associated with bringing new drug candidates through the development and
regulatory approval process to the marketplace, drug discovery companies have
traditionally placed considerable importance on obtaining patent and trade
secret protection for significant new technologies, products and processes. The
Company's policy is to make diligent efforts to protect its screening
technologies, targets, compounds, and certain other technology by, among other
things, filing, or causing to be filed on its behalf, patent applications in the
USPTO, and elsewhere where the Company deems appropriate and cost effective.
There can be no assurance that patents will be granted with respect to any of
the Company's or its licensors' patent applications which are pending or may be
filed in the future. Further, there can be no assurance that any rights the
Company may have under issued patents will provide the Company with significant
protection against competitive products or otherwise be commercially viable.
Legal standards relating to the validity of patents covering pharmaceutical and
biotechnological inventions and the scope of claims made under such patents are
still developing, and thus there is no consistent policy in this regard. The
patent position of a drug discovery company such as Scriptgen is highly
uncertain and involves complex legal and factual questions. There can be no
assurance that any existing or future patents issued to, or licensed by, the
Company will not subsequently be challenged, infringed upon, invalidated or
circumvented by others. In addition, patents may have been granted, or may be
granted, to others covering processes or products that are necessary or useful
to the development of the Company's technologies, targets and compounds. If any
of the Company's technologies, targets or compounds are found to infringe upon
the patents or other intellectual property of others, the Company's ability to
develop and commercialize its technologies, targets and compounds could be
severely restricted or prohibited. In such event, the Company may be required to
obtain licenses from third parties to utilize their patents or other proprietary
rights. There can be no assurance that the Company will be able to obtain such
licenses on acceptable terms, or at all. There is significant litigation in the
pharmaceutical and biotechnology industry regarding patents and other
proprietary rights. If the Company becomes involved in litigation regarding its
proprietary rights or the rights of others, the Company could incur substantial
costs in defending infringement claims, obtaining licenses, engaging in
interference and opposition proceedings or other challenges to its patent rights
or other proprietary rights, or in bringing such proceedings or enforcing any
proprietary rights against third parties. The Company's inability to obtain
necessary licenses or its involvement in proceedings concerning proprietary
rights could have a material adverse effect on the business, operating results
and financial condition of the Company.
 
    The Company initially applies for patents on many of its inventions by
filing a provisional patent application in the USPTO. The Uruguay Round
Agreements Act (effective June 8, 1995) established a domestic priority system
and a mechanism to enable those seeking to quickly and inexpensively file
provisional applications for their inventions. Unlike regular (non-provisional)
U.S. patent applications, provisional applications do not need claims and no
oath or declaration is required. The specification of the provisional
application must describe the invention in sufficient detail to enable those
skilled in the art to practice the invention. Applicants are entitled to claim
the benefit of the priority of their provisional application in a subsequently
filed regular (non-provisional) U.S. patent application. The domestic priority
period (one year) during which the provisional patent application is pending
does not count in the measurement of the 20-year U.S. patent term. Thus, by
filing provisional applications domestic applicants are placed on an equal
footing with foreign applicants with respect to the patent term and can also
file initial patent applications for their inventions quickly and inexpensively.
Provisional applications are automatically abandoned by the USPTO 12 months
after their filing date. The Company generally converts those provisional
applications that cover subject matter of continuing commercial interest to the
Company into regular U.S. patent applications (which claim the priority of the
underlying provisional application) before the end of the 12-month priority
period.
 
                                       36
<PAGE>
    The Company has filed a provisional patent application claiming certain
aspects of its GATE technology. The Company is aware that another party has
applied for a patent for certain technologies which may overlap with or dominate
parts of the Company's GATE technology. The Company is in negotiations with such
party to acquire a license of such party's rights covered by its patent
application. If the Company determines to seek to obtain such license, there can
be no assurance that the Company will be able to obtain such a license on terms
favorable to the Company, if at all. Further, if the claims in the two
aforementioned patent applications are found to be sufficiently similar, the
USPTO may declare an interference proceeding which may result in the Company's
patent application being rejected. Even if the interference proceeding is
decided favorably to the Company, participation in the proceeding would likely
be costly to the Company. Whether or not an interference proceeding is declared,
the other party may be issued a patent which claims all or part of the Company's
GATE technology. If the Company determines to pursue such license and is
unsuccessful, the Company could be severely restricted or barred from using,
manufacturing and selling products resulting from the Company's GATE technology.
Such restriction or prohibition, or the failure to obtain such license could
have a material adverse effect on the Company's business, operating results and
financial condition.
 
    The Company has filed a provisional patent application claiming certain
antitumor drug candidates. The Company has acquired certain rights in this
invention pursuant to an assignment agreement with two of the inventors (the
"Assignors"), Michael Palfreyman, Ph.D., D.Sc., and Mark Wuonola, Ph.D. The
Company is pursuing parallel assignment agreements with the remaining four
inventors, three of whom are affiliated with academic institutions. Should it be
necessary for these inventors to assign their rights to their academic
institutions, the Company would seek to obtain exclusive licenses to these
institutions' rights in the invention; however, there can be no assurance that
the Company will be able to obtain such licenses on terms favorable to the
Company, if at all.
 
    The Company and Boston University are joint owners of two U.S. patent
applications and an international patent application covering improvements to
the synthesis of ST41590. The Company has obtained an exclusive license to
Boston University's rights under such patent applications.
 
    The Company acquired certain rights in its ATLAS screening technology
pursuant to an Assignment Agreement with the two inventors of ATLAS (the
"Assignors"), Andrew A. Pakula, Ph.D. and James Bowie, Ph.D. Dr. Pakula is the
Company's Director of Drug Discovery Technologies and Dr. Bowie is a consultant
to the Company. Pursuant to the terms of the Assignment Agreement, as amended,
the Company is obligated to pay to the Assignors certain royalties on amounts
received by the Company from (i) net sales of products developed using ATLAS,
(ii) royalties from licenses granting third parties the right to make, use or
sell products developed using ATLAS and (iii) royalties from licenses granting
third parties the right to use ATLAS.
 
    In addition to patent protection, the Company relies on trade secrets,
know-how and technological advances which it seeks to protect, in part, by
confidentiality agreements with its collaborative partners, employees, advisors
and consultants. There can be no assurance that these confidentiality agreements
will not be breached, that the Company would have adequate remedies for any such
breach, or that the Company's trade secrets, know-how and technological advances
will not otherwise become known or be independently discovered by others.
 
GOVERNMENT REGULATION
 
OVERVIEW
 
    Regulations imposed by United States federal, state and local authorities,
as well as their counterparts in other countries, are a significant factor in
the conduct of the research, development, manufacturing and marketing activities
for the Company's potential drug candidates.
 
    The development, manufacture and marketing of drugs developed by the Company
or its collaborative partners are subject to regulation by numerous governmental
agencies in the United States, principally the
 
                                       37
<PAGE>
FDA, by state and local governments, and in some instances by foreign
governments. Pursuant to the Federal Food, Drug, and Cosmetic Act and the
regulations promulgated thereunder (the "FDC Act"), the FDA regulates the
pre-clinical and clinical trials, safety, effectiveness, manufacture, labeling,
storage, distribution and promotion of drugs. Noncompliance with applicable
requirements can result in, among other things, fines, injunctions, recall or
seizure of products, total or partial suspension of production, refusals to
permit products to be imported into or exported out of the United States,
failure of the government to grant approval for new drugs or antibiotic
products, withdrawal of marketing approvals, denial or suspension of government
contracts and criminal prosecution.
 
    Product development and approval within the FDA regulatory framework usually
take a significant number of years, involve the expenditure of substantial
capital resources and are uncertain. Moreover, there is no assurance that the
current regulatory framework will not change or that additional regulatory
standards will not be promulgated at any stage of the Company's or its
collaborative partners' product development that may adversely affect approval,
delay the submission or review of an application or require additional
expenditures by the Company.
 
U.S. REGULATORY PROCESS
 
    New drugs must be found safe and effective by the FDA through the approval
of a new drug application ("NDA") pursuant to section 505 of the FDC Act prior
to marketing in interstate commerce. Prior to this, the pre-clinical data
(animal and IN VITRO laboratory data) and clinical data (human data) are
regulated by the FDA pursuant to regulations and the issuance and continuing FDA
oversight of an investigational new drug application ("IND"). Post-NDA approval,
the FDA maintains continuing regulatory control over the marketing of approved
drugs, regulating most closely manufacturing, promotional activities and the
appropriate submission of adverse reaction information. Any material changes to
the indication for use, other labeling or manufacturing, require FDA approval of
a supplement to the NDA prior to any such change being made.
 
    Before testing in the United States of any compounds with potential
therapeutic value in human test subjects may begin, stringent government
requirements for pre-clinical data must be satisfied. Pre-clinical testing
includes both IN VITRO and IN VIVO laboratory evaluation and characterization of
the safety and efficacy of a drug and its formulation. Laboratories involved in
pre-clinical testing must comply with FDA regulations regarding Good Laboratory
Practices. Pre-clinical testing results obtained from studies in several animal
species, as well as from IN VITRO studies, are submitted to the FDA as part of
the IND and are reviewed by the FDA prior to the commencement of human clinical
trials. These pre-clinical data must provide an adequate basis for evaluating
both the safety and the scientific rationale for the initial (Phase I) studies
in human volunteers. Unless the FDA objects to an IND, the IND becomes effective
30 days following its receipt by the FDA. There can be no assurance that
submission of an IND will result in the commencement of human clinical trials.
Moreover, once trials have commenced, the FDA may stop the trials by placing
them on "clinical hold" because of concerns about, for example, the safety of
the product being tested. Such clinical holds either before the clinical studies
commence or after commencement may result in either a temporary halt to the
study or abandonment of any further work whatsoever.
 
    Clinical trials, which involve the administration of the investigational
drug to healthy volunteers or to patients under the supervision of a qualified
principal investigator, are typically conducted in three sequential phases,
although the phases may overlap with one another. Clinical trials must be
conducted in accordance with the FDA's Good Clinical Practices, under protocols
that detail the objectives of the study, the parameters to be used to monitor
safety and the efficacy criteria to be evaluated. Each protocol must be
submitted to the FDA as part of the IND. Further, each clinical study must be
conducted under the auspices of an independent Institutional Review Board (the
"IRB") at the institution where the study will be conducted. The IRB will
consider, among other things, ethical factors, the safety of human subjects,
informed consent requirements and the possible liability of the institution.
Compounds must be formulated according to the FDA's current Good Manufacturing
Practice regulations ("cGMP").
 
                                       38
<PAGE>
    Phase I clinical trials represent the initial administration of the
investigational drug to a small group of healthy human subjects or to a group of
selected patients with the targeted disease or disorder. The goal of Phase I
clinical trials is typically to test for safety (adverse effects), dose
tolerance, absorption, biodistribution, metabolism, excretion and clinical
pharmacology and, if possible, to gain early evidence regarding efficacy.
 
    Phase II clinical trials involve a small sample of the actual intended
patient population and seek to assess the efficacy of the drug for specific
targeted indications, to determine dose tolerance and the optimal dose range and
to gather additional information relating to safety and potential adverse
effects.
 
    Once an investigational drug is found to have some efficacy and an
acceptable safety profile in the targeted patient population, Phase III clinical
trials are initiated to confirm the further clinical safety and efficacy of the
investigational drug in a broader sample of the general patient population at
geographically dispersed study sites in order to determine the overall
risk-benefit ratio of the drug and to provide an adequate basis for product
labeling. The Phase III clinical development program consists of expanded,
large-scale studies of patients with the target disease or disorder to obtain
definitive statistical evidence of the efficacy and safety of the proposed
product and dosage regimen. These studies may include investigation of the
effects in subpopulations of patients, such as the elderly, children, etc. All
of the phases of clinical studies must be conducted in conformance with the
FDA's investigational new drug and bioresearch monitoring regulations (such as
IRB, informed consent and sponsor monitoring requirements).
 
    All data obtained from a comprehensive development program including
research and product development, manufacturing, pre-clinical and clinical
trials and related information are submitted in an NDA to the FDA and the
corresponding agencies in other countries for review and approval. In addition
to reports of the trials conducted under the IND application, the NDA includes
information pertaining to the preparation of the new drug, analytical methods,
details of the manufacture of finished products and proposed product packaging
and labeling. Although the FDC Act requires the FDA to review NDAs within 180
days of their filing, in practice longer times are usually required. The FDA
also frequently requests that additional information be submitted, requiring
significant additional review time. As a result of the Prescription Drug User
Fee Act, the FDA has made commitments to speed the review of NDAs and NDA
Supplements. While implementation of this by the FDA has sped up certain
decision-making by the FDA, it has not, with regard to many drugs, sped up the
overall development and approval time. Any proposed product of the Company
likely would be subject to demanding and time-consuming NDA approval procedures
in virtually all countries where marketing of the products is intended. These
regulations define not only the form and content of safety and efficacy data
regarding the proposed product but also impose specific requirements regarding
manufacture of the product, quality assurance, packaging, storage, documentation
and record keeping, labeling, advertising and marketing procedures.
 
    Timetables for the various phases of clinical trials and NDA approval cannot
be predicted with any certainty. The Company, its collaborative partners or the
FDA may suspend clinical trials at any time if it is believed that individuals
participating in such trials are being exposed to unacceptable health risks.
Even assuming that clinical trials are completed and that an NDA is submitted to
the FDA, there can be no assurance that the NDA will be reviewed by the FDA in a
timely manner or that once reviewed, the NDA will be approved. The approval
process is affected by a number of factors, including the severity of the
targeted indications, the availability of alternative treatments and the risks
and benefits demonstrated in clinical trials. The Company's ability to market
its products successfully is further dependent on the patent and marketing
exclusivity rights of a competitor's products.
 
    Among the other requirements for drug product approval is the requirement
that the manufacturer conform to the FDA's cGMP regulations. Manufacturers also
must continue to expend time, money and effort in product, record keeping and
quality control to assure that the product meets applicable specifications and
other requirements. The manufacturer also has obligations to report post
marketing adverse drug experiences to the FDA. The FDA periodically inspects
manufacturing facilities in the United
 
                                       39
<PAGE>
States to assure compliance with applicable cGMP and other regulatory
requirements. Failure of the Company (or manufacturer of a Company product) to
comply with cGMP regulations or other FDA regulatory requirements could have a
material adverse effect on the Company and result in one or more regulatory
actions affecting either the product, the Company and its officials, or both.
 
    Completing the multitude of steps necessary before marketing can begin
requires the expenditure of considerable resources and can consume a long period
of time. Delay or failure in obtaining the required approvals or clearances by
the Company, its collaborative partners or its licensees would have an adverse
effect on the ability of the Company to generate sales or royalty revenue. In
addition, the impact of new or changed laws or regulations cannot be predicted.
 
    There can be no assurance that the regulatory framework described above will
not change or that additional regulations will not arise that may affect
approval of or delay an IND or an NDA. In addition, there can be no assurance
that there will not be a change in currently accepted scientific standards that
may affect the ultimate approval of such products. Moreover, because the
Company's present collaborative partners are, and it is expected that the
Company's future collaborative partners may be, primarily responsible for
pre-clinical and clinical trials, regulatory approvals, manufacturing and
commercialization of drugs, the ability to obtain and the timing of regulatory
approvals are not within the control of the Company. Should the collaborative
partners develop regulatory problems, for example, cGMP violations, such
problems may adversely impact upon the Company's resources.
 
    Prior to the commencement of marketing a product in other countries,
approval by the regulatory agencies in such countries is required, whether or
not FDA approval has been obtained for such product. The requirements governing
the conduct of clinical trials and product approvals vary widely from country to
country, and the time required for approval may be longer or shorter than the
time required for FDA approval. Although there are some procedures for unified
filings for certain European countries, in general, each country has its own
procedures and requirements.
 
    The Company is also subject to regulation under other federal laws and
regulation under state and local laws, including laws relating to occupational
safety, laboratory practices, controlled substances, the use, handling and
disposition of radioactive materials, environmental protection and hazardous
materials. Although the Company believes that its safety procedures for handling
and disposing of radioactive compounds and other hazardous materials used in its
research and development activities comply with the standards prescribed by
federal, state and local regulations, the risk of accidental contamination or
injury from these materials cannot be completely eliminated. In the event of any
such accident, the Company could be held liable for any damages that result and
any such liability could exceed the resources of the Company.
 
COMPETITION
 
    Competition among drug discovery companies and pharmaceutical and
biotechnology companies which are involved in drug discovery is intense. Because
the Company's technology platform incorporates a number of different
technologies, the Company competes in many areas, including target
identification and validation, assay development and high throughput screening.
The Company competes directly against other drug discovery companies, the
research departments of pharmaceutical and biotechnology companies, other
commercial enterprises, government agencies and numerous academic and research
institutions. Such companies and other entities are conducting research in
various areas which constitute portions of the Company's technology platform,
either on their own or in collaboration with others. There can be no assurance
that drug discovery companies which currently compete with the Company in
specific areas will not merge or enter into joint ventures or other alliances
with one or more other such companies and become substantial multi-point
competitors or that the Company's collaborators will not assemble their own
competing drug discovery technologies. Genomics and combinatorial chemistry
companies, among others, may also expand their business to include compound
screening or screen development, either alone or pursuant to alliances with
others. The Company anticipates that it will face increased competition in the
 
                                       40
<PAGE>
future as new companies enter the market and advanced technologies, including
more sophisticated information technologies, become available. The Company's
drug discovery techologies, in particular GATE, ATLAS and SCAN, 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 current or
future competitors. In particular, the Company's technology faces intense
competition from drug discovery companies engaged in gene sequencing, functional
genomics, and differential gene expression technology in the area of target
validation, and companies engaged in high throughput screening. Many of the
Company's competitors have greater financial and personnel resources, and more
experience in research and development, than the Company. There can be no
assurance that the Company's competitors will not succeed in developing
technologies and drugs that are more effective or less costly than any which are
being developed by the Company or which would render the Company's technology
and any future drugs obsolete and noncompetitive.
 
    In addition, some of the Company's competitors have greater experience than
the Company in conducting pre-clinical and clinical trials and obtaining FDA and
other regulatory approvals. Accordingly, the Company's competitors may succeed
in obtaining FDA or other regulatory approvals for competing drug candidates
more rapidly than the Company. Companies that complete clinical trials, obtain
required regulatory agency approvals and commence commercial sale of their
drugs, before their competitors may achieve a significant competitive advantage,
including certain patent and FDA marketing exclusivity rights that would delay
the Company's ability to market certain products. There can be no assurance that
drugs, if any, resulting from the Company's internal development efforts or the
joint efforts of the Company and its collaborators will be able to compete
successfully with competitors' existing products or products under development
or that they will obtain regulatory approval in the United States or elsewhere.
 
EMPLOYEES
 
    As of December 31, 1997, the Company had 51 full time employees, 43 of whom
were engaged in research and development and eight of whom were engaged in
management, administration and finance. Doctorates are held by approximately 38%
of the Company's full time employees. In addition, the Company employs
individuals on a rotating, full time basis to fill a variety of research
positions. The Company's policy is to have each of its directors, officers,
employees and advisors sign an agreement which prohibits the disclosure of
confidential information to anyone outside the Company and requires disclosure
and assignment to the Company of ideas, developments, discoveries and inventions
made by the employee.
 
    The Company's employees are not covered by a collective bargaining
agreement. The Company has never experienced an employment-related work stoppage
and considers its employee relations to be good.
 
PROPERTIES
 
    The Company's headquarters and research and development facilities are
located in a 15,440 square foot facility in Medford, Massachusetts. The Company
has leased the premises through October 30, 1998. The Company plans to lease
approximately 85,000 square feet of additional office and laboratory space
within the next twelve months to support expansion of its programs.
 
LEGAL PROCEEDINGS
 
    The Company is not a party to any material legal proceedings.
 
                                       41
<PAGE>
                                   MANAGEMENT
 
EXECUTIVE OFFICERS, DIRECTORS AND KEY EMPLOYEES
 
    The following sets forth the name, ages and positions of the executive
officers, directors and key employees of the Company:
 
<TABLE>
<CAPTION>
NAME                                                       AGE      POSITION
- -----------------------------------------------------      ---      -----------------------------------------------------
 
<S>                                                    <C>          <C>
EXECUTIVE OFFICERS AND DIRECTORS:
Mark T. Weedon.......................................          46   President, Chief Executive Officer and Director
Michael G. Palfreyman, M.R.
  Pharm. S., Ph.D., D.Sc.............................          52   Vice President of Research and Development
Michael W. Heslop....................................          38   Vice President of Business Development
Karen A. Hamlin......................................          38   Senior Director of Operations, Secretary and
                                                                      Treasurer
Barry Weinberg(1)....................................          59   Chairman of the Board
David Baltimore, Ph.D.(1)............................          59   Director
Allan R. Ferguson(2).................................          55   Director
Jason S. Fisherman, M.D.(2)..........................          41   Director
 
KEY EMPLOYEES:
Jacob J. Clement, Ph.D...............................          53   Senior Director of Technology Development
Yibin Xiang, Ph.D....................................          47   Director of Chemistry
Andrew A. Pakula, Ph.D...............................          40   Director of Drug Discovery Technologies
C. Richard Wobbe, Ph.D...............................          40   Director of Drug Discovery
</TABLE>
 
- --------------
 
(1) Member of Audit Committee
 
(2) Member of Compensation Committee
 
    MARK T. WEEDON has been President, Chief Executive Officer and director of
the Company since August 1997. From 1987 to August 1997, Mr. Weedon held various
positions with Glaxo Wellcome plc, a pharmaceutical company, including Global
General Manager of OTC Operations (1995-August 1997), Director of Group
Licensing for the Wellcome Foundation plc (1993-1995) and President of Burroughs
Wellcome Inc. (Canada) (1990-1993). Mr. Weedon received a B.A. from the
University of Toronto and an M.B.A. from the University of Western Ontario.
 
    MICHAEL G. PALFREYMAN, M.R. PHARM. S., PH.D., D.SC. joined the Company in
October 1994 as Vice President of Research and Development. From 1976 until
October 1994, Dr. Palfreyman held various positions with Marion Merrell Dow Inc.
and its predecessor, the Merrell Dow Research Institute, including Vice
President of Marion Merrell Dow Research North America (1992 to October 1994),
Vice President of Global Biological and Scientific Affairs (1991-1992) and
Director of Pharmacological Sciences (1987-1991). Dr. Palfreyman received his
undergraduate, Ph.D. and D.Sc. degrees from the University of Nottingham,
England, from which he also holds an advanced degree in Pharmacy.
 
    MICHAEL W. HESLOP joined the Company in December 1997 as Vice President of
Business Development. From 1982 to December 1997, Mr. Heslop held various
Marketing and Sales positions at Glaxo Wellcome Inc., including Director of
Marketing-Anti-Infectives (1995-December 1997) and Director of Marketing-
Central Nervous System (1994-1995), and Director of Marketing-Corporate and
National Sales Manager for Burroughs Wellcome Inc. (Canada) (1990-1994). Mr.
Heslop received a B.S. in Biology from McGill University and an M.B.A. from
Concordia University.
 
    KAREN A. HAMLIN joined the Company in December 1992 and serves as Senior
Director of Operations, Secretary and Treasurer. From December 1988 until
December 1992, Ms. Hamlin was Director of Operations at Transkaryotic Therapies,
Inc., a biotechnology company. From January 1987 to December 1988, Ms. Hamlin
was responsible for Laboratory Operations and Regulatory Compliance at Cambridge
 
                                       42
<PAGE>
Research Laboratory, a division of Ortho-Clinical Diagnostics, an affiliate of
Johnson & Johnson. Ms. Hamlin received a B.S. in Biology from St. Anselm College
and an M.S. in Biological Sciences from Rutgers University.
 
    BARRY WEINBERG has served as Chairman of the Board of Directors of the
Company since September 1993. Mr. Weinberg was also the Company's acting
President and Chief Executive Officer from December 1995 until August 1997. Mr.
Weinberg was a co-founder and is currently President of CW Group, a venture
capital firm specializing in the health-care industry. Mr. Weinberg holds a B.S.
in Electrical Engineering from the Massachusetts Institute of Technology and an
M.B.A. from New York University. Mr. Weinberg serves as a director of AutoImmune
Inc. and CareAdvantage, Inc.
 
    DAVID BALTIMORE, PH.D. has served as a director of the Company since August
1994. Since July 1994, Dr. Baltimore was the Ivan R. Cottrell Professor of
Molecular Biology at the Massachusetts Institute of Technology until October
1997 when he became President of California Institute of Technology. From 1990
until July 1994, Dr. Baltimore was a professor at Rockefeller University and
served as its president from 1990 until 1991. Dr. Baltimore founded the
Whitehead Institute at the Massachusetts Institute of Technology in 1982 and
served as its Director from 1982 until 1990. Dr. Baltimore received the Nobel
Prize in 1975 for his discovery of reverse transcriptase. Dr. Baltimore holds a
B.S. in Chemistry from Swarthmore College, and a Ph.D. from Rockefeller
University.
 
    ALLAN R. FERGUSON has served as a director of the Company since September
1993. Since 1993, Mr. Ferguson has been a general partner of Atlas Venture, a
venture capital firm, and since 1991 he has served as the Managing General
Partner of the venture capital firm of Aspen Ventures. From 1986 to 1991 he
served as President of 3i Ventures, another venture capital firm. Mr. Ferguson
currently serves as a director of ArQule, Inc. and AutoImmune Inc. He received a
B.S. in Chemical Engineering from the University of Delaware.
 
    JASON S. FISHERMAN, M.D. has served as a director of the Company since April
1995. Dr. Fisherman is a partner at Advent International Corporation, a venture
capital firm where he specializes in biotechnology and health-care companies.
From 1991 to 1994, Dr. Fisherman was Senior Director of Medical Research at
Enzon, Inc., a biopharmaceutical company. He currently serves as a director of
ILEX Oncology, Inc. and several private health-care companies. Dr. Fisherman
received a B.A. in Molecular Biophysics and Biochemistry from Yale University,
an M.D. from the University of Pennsylvania and an M.B.A. from the Wharton
School at the University of Pennsylvania.
 
    JACOB J. CLEMENT, PH.D. joined the Company in March 1997 and serves as
Senior Director of Technology Development. From 1988 until March 1997, Dr.
Clement held various positions with Abbott Laboratories, including Director, New
Lead Discovery Area (1993-March 1997), Head, Antitumor Development Venture
(1992-1993) and Senior Project Leader, Anti-infectives Area (1991-1993). Dr.
Clement received a B.A. in Biology from St. Mary's University and an M.S. in
Microbiology from Roosevelt University and a Ph.D. and an M.S.P.H. from the
University of North Carolina. Dr. Clement conducted research and taught at the
University of Minnesota.
 
    YIBIN XIANG, PH.D. joined the Company in October 1997 as Director of
Chemistry. From May 1993 until October 1997, Dr. Xiang held various positions
with Genetics Institute, including Senior Scientist and Head of Medicinal
Chemistry (October 1996-October 1997) and Principal Scientist and Head of
Medicinal Chemistry (1993-October 1996) in the Small Molecule Drug Discovery
department. From 1988 until 1993 Dr. Xiang worked in the Medicinal Chemistry
Department at Merck-Frosst in Canada as Research Fellow. Dr. Xiang received a
B.A. in Chemistry from Shanghai Medical University and a Ph.D. in Chemistry from
the Swiss Federal Polytechnic Institute. Dr. Xiang conducted postdoctoral
studies with Professor E.J. Corey at Harvard University.
 
    ANDREW A. PAKULA, PH.D. joined the Company in February 1993 and serves as
Director of Drug Discovery Technologies. Dr. Pakula received a B.S. in Biology
and Chemistry from Tufts University and a
 
                                       43
<PAGE>
Ph.D. in Biology from the Massachusetts Institute of Technology. From 1989 until
the end of 1992 Dr. Pakula conducted postdoctoral studies in the laboratory of
Dr. Melvin Simon at the California Institute of Technology, where he was a
Senior Postdoctoral Fellow.
 
    C. RICHARD WOBBE, PH.D. joined the Company in August 1994 and serves as
Director of Drug Discovery. From July 1991 until August 1994, Dr. Wobbe was with
Merck Research Laboratories, where he developed assays for analyzing the
regulation of viral gene transcription. Dr. Wobbe received a B.S. in
Biochemistry from Centre College and a Ph.D. in Biochemistry from the University
of Tennessee. Dr. Wobbe conducted postdoctoral studies at Sloan-Kettering Cancer
Center and at Harvard University.
 
    All directors hold office until the next meeting of the stockholders of the
Company and until their successors are elected and qualified. All directors were
elected to the Board of Directors pursuant to a stockholders' agreement, which
will terminate upon consummation of the Offering. Officers are appointed to
serve, at the discretion of the Board of Directors, until their successors are
appointed.
 
    Pursuant to the terms of the stockholders' agreement which became effective
upon the closing of the BioChem Offering, BioChem has the right to designate one
member of the Board of Directors. Such stockholders' agreement also requires
certain stockholders to vote their shares of Common Stock in favor of such
nominee at any meeting of stockholders for the election of directors. BioChem's
right to designate a director will terminate in the event that BioChem and its
permitted transferees own less than 10% of the Series D Preferred Stock and any
Common Stock issued upon conversion of such stock, or December 17, 2007. It is
expected that following the completion of the Offering, the Board of Directors
will be increased to six members and a designee of BioChem will be elected to
the Board of Directors. See "Certain Transactions--BioChem Offering."
 
    The Board of Directors has established an Audit Committee composed of Dr.
Baltimore and Mr. Weinberg and a Compensation Committee composed of Mr. Ferguson
and Dr. Fisherman. The Audit Committee is charged with reviewing the Company's
annual audit and meeting with the Company's independent accountants to review
the Company's internal controls and financial management practices. The
Compensation Committee recommends to the Board of Directors the compensation for
the Company's key employees.
 
SCIENTIFIC ADVISORY BOARD
 
    The Company has established a Scientific Advisory Board consisting of twelve
members with experience in fungal, bacterial and viral gene expression,
structural biology, pharmacology and drug design. Its members work closely with
the Company's management and scientists, assess the scientific and medical
direction of the Company, review research and development progress, and evaluate
new technologies that relate to the Company's development. The Scientific
Advisory Board meets as a group two times per year and members are available
individually on an ongoing basis. The co-chairmen of the Scientific Advisory
Board are the two founding scientists of the Company, Michael R. Green, M.D.,
Ph.D., and Peter S. Kim, Ph.D.
 
    All of the Company's Scientific Advisory Board members have signed
consulting agreements with the Company and have either purchased shares of
Common Stock or been granted options to purchase Common Stock.
 
    The members of Scriptgen's Scientific Advisory Board are:
 
    MICHAEL R. GREEN, M.D., PH.D. is a Professor of Biochemistry and Molecular
Biology at the University of Massachusetts Medical Center and an Investigator at
the Howard Hughes Medical Institute. Dr. Green's expertise is in the
transcriptional control of viral, fungal and human gene expression. He is a
recipient of the Presidential Young Investigator Award, the Searle Scholar Award
and the McKnight Award in Neurosciences. Dr. Green consults with the Company on
its antifungal and antiviral programs with specific emphasis on transcription
and its role in gene expression. Dr. Green received his B.S. in
 
                                       44
<PAGE>
Biochemistry from the University of Wisconsin, Madison and his M.D. and Ph.D. in
Biochemistry from Washington University in St. Louis.
 
    PETER S. KIM, PH.D. is a Member of the Whitehead Institute, a Professor of
Biology at the Massachusetts Institute of Technology and an Associate
Investigator at the Howard Hughes Medical Institute. Dr. Kim is also a member of
the National Academy of Sciences. Dr. Kim's expertise is in macromolecular
recognition, including the interaction between transcription factors, and in
protein design, protein folding and viral membrane fusion. He has received the
1994 Eli Lilly Award in Biological Chemistry from the American Chemical Society,
the 1994 DuPont Merck Award of the Protein Society and the 1993 National Academy
of Sciences Award in Molecular Biology. Dr. Kim consults with the Company on its
drug discovery programs focusing on structural biology and protein chemistry.
Dr. Kim received his A.B. in Chemistry from Cornell University and his Ph.D. in
Biochemistry from Stanford University.
 
    THOMAS C. ALBER, PH.D. is a Professor of Molecular and Cell Biology at the
University of California, Berkeley. Dr. Alber is an expert in X-ray
crystallography and protein structure. He consults with the Company on its
affinity programs utilizing his expertise in protein structure/function
relationships. Dr. Alber received his B.A. in Chemistry from the University of
California, Santa Cruz and his Ph.D. in Biology from the Massachusetts Institute
of Technology.
 
    STEPHEN K. BURLEY, M.D., D. PHIL. is an investigator at the Howard Hughes
Medical Institute. Dr. Burley is an expert in structural biology. He consults
with the Company on the biochemistry and molecular biology of fungal
transcription factors and in certain target areas. Dr. Burley received his B.S.
in Physics from the University of Western Ontario and his D. Phil. from Oxford
University and his M.D. from Harvard Medical School.
 
    FRED E. COHEN, M.D., D. PHIL. is a Professor of Medicine and Pharmaceutical
Chemistry at the University of California, San Francisco. He is an expert in the
molecular modeling of low molecular weight drugs and their interactions with
macromolecules. Dr. Cohen consults with the Company on pharmaceutical drug
design and in molecular modeling. Dr. Cohen was a Rhodes Scholar and received
his B.S. in Molecular Biochemistry and Biophysics from Yale University, his M.D.
from Stanford University and his D. Phil. in Molecular Biophysics from Oxford
University.
 
    DANIEL S. KEMP, PH.D. is a Professor of Chemistry at the Massachusetts
Institute of Technology. Dr. Kemp is an expert in the chemical synthesis of
peptides and proteins, protein structure and function and bio-organic chemistry.
He consults with the Company on organic and medicinal chemistry. Dr. Kemp
received his B.A. in Chemistry from Reed College and his Ph.D. in Organic
Chemistry from Harvard University.
 
    DAVID M. LIVINGSTON, M.D. is a staff member at the Brigham and Women's
Hospital and the Dana-Farber Cancer Institute, where he was Director and
Physician-in-Chief from 1991 to 1995. Dr. Livingston also holds the Emil Frei
Professor of Medicine chair at Harvard Medical School. Dr. Livingston, an expert
in Oncology, specializes in tumor suppressor gene function and cell cycle
control. He consults with the Company on the clinical aspects of pharmaceutical
drug development. Dr. Livingston received his B.A. from Harvard University and
his M.D. from Tufts University of Medicine.
 
    BERNARD MACH, M.D., PH.D. is a Professor of Genetics and Microbiology at the
University of Geneva Medical School in Geneva, Switzerland. Dr. Mach is a Member
of the French Academy. He is an expert in the molecular and genetic basis of
immune responses. Dr. Mach discovered and first reported cDNA cloning in 1975
and introduced and developed molecular genotyping of HLA in 1985. Dr. Mach
consults with the Company on its drug development programs with an emphasis on
gene expression and cellular immunology. Dr. Mach received his M.D. from the
University of Geneva and his Ph.D. from Rockefeller University.
 
    CAROL PRIVES, PH.D. is a Professor at Columbia University. She is an expert
on p53 and other tumor suppressor proteins and their role in the regulation of
transcription. Dr. Prives consults with the Company
 
                                       45
<PAGE>
on the selection of transcription based targets and their role in the cause of
disease. Dr. Prives received her B.Sc. and Ph.D. degrees in Biochemistry from
McGill University.
 
    ROBERT T. SAUER, PH.D. is the Edwin C. Whitehead Professor of Biology and
the Associate Head of the Department of Biology at the Massachusetts Institute
of Technology. Dr. Sauer is also a member of the National Academy of Sciences.
He is an expert in protein structure determination through genetic selection
methodology. Dr. Sauer consults with the Company on ATLAS and SCAN, as well as
bacterial transcription and its role in genetic selection. Dr. Sauer received
his B.A. in Biophysics from Amherst College and his Ph.D. in Biochemistry from
Harvard University.
 
    KEVIN STRUHL, PH.D. holds the David Wesley Gaiser Professorship in and is
the Acting Chairman of Biological Chemistry at the Harvard Medical School. Dr.
Struhl is an expert in transcriptional regulatory mechanisms in yeast and
functional relationships between yeast and human proteins. He developed early
methods for elucidating the relationships between protein structure and function
particularly as they relate to transcriptional regulation in yeast. Dr. Struhl
consults with the Company on its antifungal program with a focus on fungal
transcription and genetic selection. Dr. Struhl received his B.S. and M.S.
degrees in Biology from the Massachusetts Institute of Technology and his Ph.D.
in Biochemistry from Stanford University.
 
    ALAN M. SUGAR, M.D. is a Professor of Medicine at Boston University School
of Medicine and the Director of the Clinical Center Laboratory at Boston Medical
Center. Dr. Sugar's expertise is in pre-clinical and clinical antifungal drug
development and the pathogenesis of fungal diseases. He consults with the
Company on its antifungal program, with an emphasis on microbiology, animal
modeling systems and clinical evaluation. Dr. Sugar received his M.D. from
Jefferson Medical College.
 
DIRECTOR COMPENSATION
 
    David Baltimore receives $10,000 annually for being a director of the
Company. No other non-employee director receives any cash compensation. Barry
Weinberg, the Chairman of the Board of the Company, was granted stock options in
1996. See "--Stock Options."
 
EXECUTIVE COMPENSATION
 
    The following table sets forth information concerning all cash and non-cash
compensation awarded to, earned by or paid to the Company's Chief Executive
Officer and the next most highly compensated executive officers for services
rendered to the Company during the fiscal year ended December 31, 1997 (the
"Named Executive Officers"). No other executive officer of the Company earned in
excess of $100,000 during 1997.
 
                                       46
<PAGE>
                           SUMMARY COMPENSATION TABLE
 
<TABLE>
<CAPTION>
                                                                                             LONG-TERM
                                                               ANNUAL COMPENSATION         COMPENSATION
                                                         --------------------------------  -------------
                                                                                  OTHER     SECURITIES       ALL
                                                                                 ANNUAL     UNDERLYING      OTHER
                                                                                 COMPEN-     OPTIONS/      COMPEN-
NAME AND PRINCIPAL POSITION                                SALARY      BONUS     SATION        SARS        SATION
- -------------------------------------------------------  ----------  ---------  ---------  -------------  ---------
<S>                                                      <C>         <C>        <C>        <C>            <C>
Mark T. Weedon.........................................  $   90,673  $       0  $   6,770(2)     339,558  $       0
  President and Chief
  Executive Officer(1)
Barry Weinberg.........................................  $        0  $       0  $       0            0    $       0
  Acting President and Chief Executive
  Officer and Chairman of the Board(1)
Michael G. Palfreyman..................................  $  175,000  $       0  $  14,583(3)      16,262  $       0
  Vice President of Research
  and Development
Karen A. Hamlin........................................  $  107,906  $       0  $       0        5,041    $       0
  Senior Director of Operations,
  Secretary and Treasurer
</TABLE>
 
- --------------
 
(1) Mark T. Weedon became President and Chief Executive Officer of the Company
    in August 1997. Mr. Weinberg acted as the Company's President and Chief
    Executive Officer from December 1995 to August 1997. See "--Employment
    Agreements."
 
(2) Represents reimbursement of relocation expenses of $6,770.
 
(3) Represents a housing allowance of $14,583.
 
EMPLOYMENT AGREEMENTS
 
    In June 1997, the Company entered into an employment agreement with Mark T.
Weedon, President and Chief Executive Officer of the Company, which may be
terminated by either party upon 30 days' notice. Pursuant to such agreement, Mr.
Weedon receives an annual base salary of $230,000, subject to a review at the
end of his first year of employment. Also pursuant to such agreement, Mr. Weedon
will receive a $25,000 bonus upon the closing of the Offering and a guaranteed
$25,000 bonus no later than the first anniversary of his employment with the
Company. Pursuant to his employment agreement, Mr. Weedon was awarded options to
purchase 339,558 shares of Common Stock exercisable at $0.15 per share. Such
options vest over the first four years of his employment with the Company at the
rate of 1/48th of such shares each month, provided that all options will vest if
the Company is sold for a purchase price of at least $15.37 per share. The
options are immediately exercisable, although the shares of Common Stock issued
upon exercise are restricted, and remain subject to repurchase by the Company,
until such time as the corresponding options vest. Each vested option is
exercisable at any time after the date of vesting up until one year following
Mr. Weedon's termination of employment with the Company. Pursuant to his
employment agreement, Mr. Weedon will be reimbursed for relocation and other
expenses incurred as a result of his commencement of employment with the
Company, which are expected to total approximately $50,000. In the event that
Mr. Weedon's employment is terminated without cause during the first year of his
employment with the Company, he will continue to receive his then-current salary
and benefits for the shorter of nine months or the period during which he
remains unemployed. In the event that Mr. Weedon's employment is terminated
without cause during the second year of his employment with the Company, he will
continue to receive his then-current salary and benefits for the shorter of six
months or the period during which he remains unemployed. In the event that Mr.
Weedon's employment is terminated after his second year of employment with the
Company, he will continue to receive his then-current salary and benefits for
the shorter of four months or the period during which he remains unemployed.
 
                                       47
<PAGE>
    In September 1994, the Company entered into an employment agreement with Dr.
Michael G. Palfreyman, Vice President of Research and Development for the
Company. Dr. Palfreyman's employment agreement provides for the payment of an
annual base salary of $175,000 and an annual performance bonus of up to 20% of
his annual salary as of January of such year. Pursuant to his employment
agreement, Dr. Palfreyman was awarded options to purchase 53,666 shares of
Common Stock exercisable at $0.15 per share. Twenty-five percent of such options
vested in September 1995 and the remaining shares vest in equal monthly
installments through September 1998. Pursuant to his employment agreement, Dr.
Palfreyman was reimbursed for relocation expenses aggregating approximately
$38,000 and temporary living expenses aggregating approximately $12,000. Dr.
Palfreyman also received housing allowances of approximately $21,000, $18,000
and $15,000 in 1995, 1996 and 1997, respectively, and he will receive a $6,000
housing allowance for 1998. Dr. Palfreyman also received a one-time cash payment
of $30,000 as compensation for lost bonus from his previous employer. In the
event that Dr. Palfreyman's employment is terminated without cause, he will be
entitled to severance payments equal to three times his then-current monthly
base salary.
 
    In November 1997, the Company entered into an employment agreement with
Michael W. Heslop, Vice President of Business Development for the Company. Mr.
Heslop's employment agreement provides for the payment of an annual base salary
of $165,000 and an annual performance bonus of up to 20% of his annual salary as
of January of such year. Pursuant to his employment agreement, Mr. Heslop was
awarded options to purchase 73,181 shares of Common Stock exercisable at $8.76
per share. Twenty-five percent of such options will vest in November 1998 and
the remaining shares will thereafter vest in equal monthly installments through
November 2001. Mr. Heslop also received a one-time cash payment of $40,000 as
compensation for lost bonus from his previous employer. Pursuant to his
employment agreement, Mr. Heslop will also be reimbursed for relocation and
temporary living expenses which are expected to total approximately $22,000.
 
    In December 1992, the Company entered into an employment agreement with
Karen A. Hamlin, Senior Director of Operations, Secretary and Treasurer of the
Company. Ms. Hamlin's employment agreement provides for the payment of an annual
base salary of $75,000. Pursuant to her employment agreement, Ms. Hamlin was
awarded 11,384 shares of restricted Common Stock at a price of $0.03 per share.
Of such shares, 1,138 vested immediately, twenty-five percent of the remaining
shares vested in December 1993, and the remaining shares vested in equal monthly
installments through December 1996. In the event that Ms. Hamlin's employment is
terminated without cause at any time, she will be entitled to severance payments
equal to six times her then-current monthly base salary.
 
STOCK OPTIONS
 
    The following table sets forth certain summary information concerning
individual grants of stock options made during the year ended December 31, 1997
to each of the Named Executive Officers:
 
                                       48
<PAGE>
                 OPTION GRANTS IN YEAR ENDED DECEMBER 31, 1997
 
<TABLE>
<CAPTION>
                                                                                             POTENTIAL
                                                                                          REALIZABLE VALUE
                                          INDIVIDUAL GRANTS                                  AT ASSUMED
                          --------------------------------------------------              ANNUAL RATES OF
                           NUMBER OF   % OF TOTAL                                           STOCK PRICE
                            SHARES       OPTIONS     EXERCISE                             APPRECIATION FOR
                          UNDERLYING   GRANTED TO     OR BASE                              OPTION TERM(1)
                            OPTIONS     EMPLOYEES    PRICE PER   EXPIRATION   ----------------------------------------
NAME                        GRANTED    IN 1997(2)      SHARE        DATE           0%            5%           10%
- ------------------------  -----------  -----------  -----------  -----------  ------------  ------------  ------------
<S>                       <C>          <C>          <C>          <C>          <C>           <C>           <C>
Mark T. Weedon..........     339,558         60.9%   $    0.15      8/11/07   $  2,349,741  $  3,859,513  $  6,175,799
Barry Weinberg..........           0            0%      --           --            --            --            --
Michael G. Palfreyman...      16,262          2.9%   $    0.15      6/18/07        112,533       184,839       295,769
Karen A. Hamlin.........       2,602          0.5%   $    0.15      6/18/07         18,006        29,575        47,325
                               2,439          0.4%   $    8.76      12/5/07        --             13,437        34,051
</TABLE>
 
- --------------
 
(1) These amounts represent assumed rates of appreciation in the price of the
    Company's Common Stock during the terms of the options in accordance with
    rates specified in applicable federal securities regulations. Actual gains,
    if any, on stock option exercises will depend on the future price of the
    Common Stock and overall stock market conditions. There is no representation
    that the rates of appreciation reflected in this table will be achieved.
 
(2) Based on an aggregate of options to purchase 557,425 shares of Common Stock
    granted to employees in 1997, including options granted to the Named
    Executive Officers.
 
    The following table sets forth at December 31, 1997 the number of options
and the value of unexercised options held by each of the Named Executive
Officers:
 
                       AGGREGATED YEAR END OPTION VALUES
 
<TABLE>
<CAPTION>
                                              NUMBER OF SHARES SUBJECT
                                                         TO                 VALUE OF UNEXERCISED
                                               UNEXERCISED OPTIONS AT           IN-THE-MONEY
                                                      YEAR END             OPTIONS AT YEAR END(1)
                                             --------------------------  --------------------------
                 SHARES ACQUIRED    VALUE
NAME              OR EXERCISED    REALIZED   EXERCISABLE  UNEXERCISABLE  EXERCISABLE  UNEXERCISABLE
- ---------------  ---------------  ---------  -----------  -------------  -----------  -------------
<S>              <C>              <C>        <C>          <C>            <C>          <C>
Mark T.
  Weedon.......        33,956     $ 234,976     305,602        --         $3,621,384       --
Barry
  Weinberg.....        48,787        97,574      --            --            --            --
Michael G.
  Palfreyman...        --            --          68,793        77,568       814,939     $ 918,892
Karen A.
  Hamlin.......        --            --           1,306         6,663        15,466        57,932
</TABLE>
 
- --------------
 
(1) The dollar values have been calculated by determining the difference between
    the fair market value of the securities underlying the options at December
    31, 1997 and the exercise prices of the options. Solely for purposes of
    determining the value of options at December 31, 1997, the Company has
    assumed that the fair market value of shares of Common Stock issuable upon
    exercise of options was $12.00 per share, the assumed initial public
    offering price, since the Common Stock was not traded in an established
    market prior to the Offering.
 
                                       49
<PAGE>
COMPENSATION COMMITTEE INTERLOCKS AND INSIDER PARTICIPATION
 
    The Board of Directors established a Compensation Committee in December 1997
composed of Mr. Ferguson and Dr. Fisherman. Prior to that time, matters
concerning executive officer compensation were addressed by the Board of
Directors. Mr. Ferguson is a general partner of Atlas Venture, and Dr. Fisherman
is a partner of Advent International Corporation. See "Certain
Transactions--Private Placements of Securities" and "Principal Stockholders."
 
EMPLOYEE BENEFIT PLANS
 
1997 EQUITY INCENTIVE PLAN
 
    The Company adopted the 1997 Plan in December 1997. An aggregate of
1,700,000 shares of the Company's Common Stock have been reserved for issuance
pursuant to the exercise of stock awards granted to employees, directors,
consultants and advisers under the 1997 Plan (the "Stock Awards"). The 1997 Plan
will terminate in December 2007, unless sooner terminated by the Board of
Directors.
 
    The 1997 Plan permits the granting of options intended to qualify as
incentive stock options ("Incentive Stock Options") within the meaning of
Section 422 of the Internal Revenue Code of 1986, as amended (the "Code"), to
employees (including officers and employee directors), and options that do not
so qualify ("Nonstatutory Stock Options," and, together with Incentive Stock
Options, the "Options") to employees (including officers and employee
directors), non-employee directors, consultants and advisers. In addition, the
1997 Plan permits the granting of stock appreciation rights appurtenant to or
independently of other Stock Awards granted under the 1997 Plan, as well as the
granting of Common Stock based upon the attainment of specified performance
goals ("Performance Awards"), rights to purchase restricted stock and any form
of equity-based or equity-related awards that the Board of Directors determines
to be consistent with the 1997 Plan and in the interests of the Company. No
person is eligible to receive Stock Awards under the 1997 Plan covering more
than 200,000 shares of the Company's Common Stock in any calendar year.
 
    The 1997 Plan will be administered by the Board of Directors or a committee
appointed by the Board of Directors. Subject to the limitations set forth in the
1997 Plan, the Board of Directors has the authority to select the person to whom
grants are to be made, to designate the number of shares to be covered by each
Stock Awards, to determine whether an Option is to be an Incentive Stock Option
or a Nonstatutory Stock Option, to establish vesting schedules, to specify the
Option exercise price and the type of consideration to be paid to the Company
upon exercise and, subject to certain restrictions, to specify other terms of
Stock Awards.
 
    No Incentive Stock Option may be exercised later than ten years from the
date it was granted. The aggregate fair market value, determined at the time of
grant, of the shares of Common Stock with respect to which Incentive Stock
Options are exercisable for the first time by an optionee during any calendar
year (under all such plans of the Company and its affiliates) may not exceed
$100,000. Options granted under the 1997 Plan are generally non-transferable.
 
    Options granted under the 1997 Plan vest at the rate specified in the option
agreement. The exercise price of Options granted under the 1997 Plan is
determined by the Board of Directors in accordance with the guidelines set forth
in the 1997 Plan. The exercise price of an Incentive Stock Option cannot be less
than 100% of the fair market value of the Common Stock on the date of the grant.
The exercise price of Incentive Stock Options granted to any person who at the
time of grant owns stock representing more than 10% of the total combined voting
power of all classes of the Company's capital stock must be at least 110% of the
fair market value of such stock on the date of grant and the term of such
Incentive Stock Options cannot exceed five years.
 
    The Board of Directors shall determine the performance goals applicable to
Performance Awards, the period during which such goals are effective and all
other limitations and conditions applicable to the
 
                                       50
<PAGE>
Performance Awards. The Board of Directors shall determine the purchase price,
if any, of restricted stock awarded pursuant to the 1997 Plan, as well as the
conditions under which shares of restricted stock may be forfeited to or
repurchased by the Company and any other terms and conditions applicable to
restricted stock.
 
    Pursuant to the 1997 Plan, the Board of Directors has full authority to
determine and specify the effect, if any, that a participant's termination of
employment will have on the terms of an outstanding Stock Award. Shares subject
to Stock Awards that have expired or otherwise terminated without having been
exercised in full again become available for award under the 1997 Plan.
 
    The terms and provisions of all Stock Awards must be set forth in an award
agreement made available to the participant following the grant. The Board of
Directors may accelerate (i) the vesting or payment of any Stock Award, (ii) the
lapse of restrictions on any Stock Award and (iii) the date on which any Option
or stock appreciation right first becomes exercisable.
 
    Upon certain changes in control of the Company, all outstanding Stock Awards
under the 1997 Plan must either be made exercisable immediately prior to the
change in control or substituted by the surviving entity.
 
    The Company has not granted any Stock Awards under the 1997 Plan as of the
date of this Prospectus.
 
NON-EMPLOYEE DIRECTORS STOCK PLAN
 
    The Company adopted the Directors' Plan in December 1997 to provide for the
automatic grant of options to purchase shares of Common Stock to directors of
the Company who are not current or former employees of the Company
("Non-Employee Directors"). The Directors' Plan will become effective upon the
consummation of the Offering.
 
    The maximum number of shares of Common Stock that may be issued pursuant to
the exercise of options granted under the Directors' Plan is 250,000. Pursuant
to the terms of the Directors' Plan, each Non-Employee Director on the date of
this Prospectus will receive options to purchase 10,000 shares of Common Stock.
Thereafter, on the date of each annual meeting of the stockholders of the
Company, each Non-Employee Director continuing in office will receive options to
purchase 4,000 shares of Common Stock and each newly elected Non-Employee
Director (including each Non-Employee Director elected to office since the then
last annual meeting of stockholders) will receive options to purchase 10,000
shares of Common Stock. Additionally, each Non-Employee Director who is a member
of a committee of the Company's Board of Directors will receive options to
purchase 250 shares of Common Stock on each one-year anniversary of his or her
appointment to such committee.
 
    No options granted under the Directors' Plan may be exercised after the
expiration of ten years from the date they were granted. Options granted under
the Directors' Plan vest yearly over a three-year period. The exercise price of
options granted under the Directors' Plan on the date of this Prospectus will
equal the initial public offering price. Thereafter, the exercise price of
options granted under the Directors' Plan will equal 100% of the fair market
value of the Common Stock on the date of the grant. Options granted under the
Directors' Plan are generally non-transferable. If options granted under the
Directors' Plan terminate without having been exercised, the number of shares of
Common Stock underlying such options becomes available for future grant under
the Directors' Plan. All options outstanding under the Directors' Plan terminate
upon certain changes in control of the Company, provided that all such options
must be made immediately exercisable 20 days prior to the effective date of any
such change in control. The Compensation Committee may terminate the Directors'
Plan at any time.
 
1994 STOCK OPTION PLAN
 
    During 1994, the Company adopted the 1994 Stock Option Plan, which provides
for the issuance of incentive stock options to officers and other employees of
the Company and nonstatutory stock options,
 
                                       51
<PAGE>
awards of stock, and direct stock purchase opportunities to directors, officers,
employees and consultants of the Company. No shares remain available for
issuance under the Plan. The options are exercisable at various dates and will
expire no more than ten years from the date of grant or in the case of certain
nonstatutory options, 15 years from the date of grant. The exercise price of
each option is determined by the Board of Directors. In the case of incentive
stock options, the exercise price may not be less than 100% of the fair market
value of the share at the time the option is granted. For holders of more than
10% of the Company's total combined voting power of all classes of stock,
incentive stock options may not be granted at less than 110% of the fair market
value of the Company's Common Stock at the date of grant and may not exceed a
term of five years.
 
401(K) PLAN
 
    The Company adopted a retirement savings plan (the "401(k) Plan") effective
in January 1995. Employees who have attained age 18 and have completed six
months of service with the Company may participate in the 401(k) Plan.
Participants in the 401(k) Plan may defer compensation in an amount not in
excess of 15% of the employee's total annual compensation from the Company, up
to the annual statutory limit ($9,500 in 1997). The Company may make matching
contributions in an amount determined by the Board of Directors. All
contributions are credited to separate accounts maintained in trust for each
participant and are invested, at the participant's direction, in one or more of
the investment funds made available under the 401(k) Plan. Matching
contributions become 20% vested after a participant's second year of service
with the Company and are subject to 20% annual vesting thereafter. The 401(k)
Plan is intended to qualify under Section 401 of the Internal Revenue Code so
that contributions to the 401(k) Plan, and income earned on plan contributions,
are not taxable to employees until withdrawn, and so that the contribution will
be deductible by the Company when made.
 
STOCK RESTRICTION AGREEMENTS
 
    The Company has executed stock restriction agreements with certain common
stockholders. Each agreement gives the Company the right to repurchase a certain
number of shares, at the original issuance price, held by such stockholder if he
or she ceases to be a director, employee or consultant, as applicable, of the
Company. The purchase option rights lapse at various dates through July 1998. At
December 31, 1997, approximately 30,378 shares of the Company's outstanding
Common Stock were subject to these repurchase options.
 
                                       52
<PAGE>
                              CERTAIN TRANSACTIONS
 
PRIVATE PLACEMENTS OF SECURITIES
 
    Since the Company's inception in September 1992 through February 1998, the
Company issued, in private placement transactions (not including the BioChem
Offering), the following shares of Common Stock and Preferred Stock (including
shares of Common Stock issued upon the exercise of options and net of shares of
Common Stock repurchased by the Company): 938,713 shares of Common Stock at
prices ranging between $0.03 and $0.15 per share; 81,312 shares of Common Stock
at a price of $0.15 in cash in connection with loans in an aggregate of
$2,500,000 to the Company (the "Bridge Loan Transaction"); 6,403,325 shares of
Series A Preferred Stock (convertible into 2,082,660 shares of Common Stock) at
a price of $1.00 per share; 6,579,086 shares of Series B Preferred Stock
(convertible into 2,139,826 shares of Common Stock) at a price of $1.00 per
share; 4,053,854 shares of Series C Preferred Stock (convertible into 1,318,502
shares of Common Stock) at a price of $1.80 per share.
 
    In connection with the Bridge Loan Transaction, the Company became indebted
to the following parties in the following amounts from September 1994 through
February 1995: CW Ventures II, L.P. in the amount of $645,250; Atlas Venture
Fund II, L.P. in the amount of $524,250; New Enterprise Associates V in the
amount of $443,500; Accel IV L.P. in the amount of $371,210; Accel Investors '93
L.P. in the amount of $16,409; Accel Japan L.P. in the amount of $35,480; Accel
Keiretsu L.P. in the amount of $7,983; Ellmore C. Patterson Partners in the
amount of $9,757; Prosper Partners in the amount of $2,661 and Venrock
Associates in the amount of $443,500. All of such loans were evidenced by
promissory notes bearing an interest rate of 4.25% until December 31, 1994 and
9.50% from January 1, 1995 until April 15, 1995, when these notes, together with
accrued interest thereon, were converted into an aggregate of 2,579,086 shares
of Series B Preferred Stock (convertible into 838,839 shares of Common Stock).
Barry Weinberg and Allan R. Ferguson, directors of the Company, are affiliated
with CW Ventures II, L.P. and Atlas Venture Fund II, L.P., respectively. See
"Management."
 
    In August 1997, the Company issued to Mark T. Weedon options to purchase
339,558 shares of Common Stock at an exercise price of $0.15 per share in
connection with his acceptance of employment with the Company. Mr. Weedon
subsequently exercised options to purchase 33,956 shares of Common Stock, which
shares are subject to certain restrictions. See "Management--Employment
Agreements."
 
    In connection with certain equipment leasing agreements, the Company issued
warrants to purchase the following shares of Preferred Stock: 153,000 shares of
Series A Preferred Stock at an exercise price of $1.00 per share and 100,000
shares of Series C Preferred Stock at an exercise price of $1.80 per share. Such
warrants will be exercisable for an aggregate of 82,288 shares of Common Stock
following the Offering. See "Description of Capital Stock--Warrants."
 
    Each outstanding share of Series A Preferred Stock, Series B Preferred
Stock, Series C Preferred Stock and Series D Preferred Stock will automatically
convert into 0.32525 shares of Common Stock upon the closing of the Offering.
 
                                       53
<PAGE>
    The purchasers of the Common Stock, Series A Preferred Stock, Series B
Preferred Stock and Series C Preferred Stock described above include, among
others, the following officers, directors and beneficial owners of more than
five percent of the Company's voting securities:
 
<TABLE>
<CAPTION>
                                                                                SHARES OF PREFERRED STOCK, AS
                                                                                        CONVERTED (2)
                                                                   COMMON     ----------------------------------
PURCHASER (1)                                                       STOCK      SERIES A    SERIES B    SERIES C
- ---------------------------------------------------------------  -----------  ----------  ----------  ----------
<S>                                                              <C>          <C>         <C>         <C>
CW Ventures II, L.P. (3).......................................      61,507      520,814     342,424      75,387
Atlas Venture Fund II, L.P. (4)................................      68,789      423,136     278,211      61,249
New Enterprise Associates V....................................      27,038      357,887     235,358      51,809
Lombard Odier & Cie............................................      --           --          --         903,535
Advent International Investors II Limited Partnership (5)......      --           --           3,252         277
Advent Performance Materials Limited Partnership (5)...........      --           --          --          63,242
Golden Gate Development and Investment Limited Partnership
  (5)..........................................................      --           --          78,059       6,655
Rovent II Limited Partnership (5)..............................      --           --         406,558      34,662
Accel IV L.P. (6)..............................................      23,678      329,256     196,995      43,364
Accel Investors '93 L.P........................................         534       --           8,708       1,917
Accel Japan L.P................................................       2,163       28,631      18,829       4,145
Accel Keiretsu L.P.............................................         260       --           4,237         932
Ellmore C. Patterson Partners..................................         317       --           5,178       1,140
Prosper Partners...............................................          87       --           1,412         311
Venrock Associates (7).........................................      27,038      357,887     235,358      32,121
Venrock Associates II, L.P.....................................      --           --          --          19,687
Mark T. Weedon.................................................      33,956       --          --          --
Barry Weinberg (8).............................................      89,118       --          --          --
Andrew A. Pakula...............................................      11,384       --          --          --
Karen A. Hamlin................................................      11,384       --          --          --
</TABLE>
 
- --------------
 
(1) Certain of the purchasers are entitled to registration rights. See
    "Description of Capital Stock-- Registration Rights."
 
(2) The number of shares under each column reflects the number of shares of
    Common Stock into which the shares of Series A, Series B and Series C
    Preferred Stock are convertible, giving effect to the conversion of each
    share of Preferred Stock into 0.32525 shares of Common Stock.
 
(3) Does not include 89,118 shares of Common Stock issued to Barry Weinberg,
    Chairman of the Board of Directors of the Company. Mr. Weinberg is a general
    partner of CW Partners III, L.P., which is the general partner of CW
    Ventures II, L.P.
 
(4) Allan R. Ferguson, a director of the Company, is a general partner of Atlas
    Venture Associates II, L.P., which is the general partner of Atlas Venture
    Fund II, L.P.
 
(5) Jason S. Fisherman, a director of the Company, is Vice President of Advent
    International Corporation, which is the general partner of Advent
    International Investors II Limited Partnership and Advent International
    Limited Partnership, which is the general partner of Advent Performance
    Materials Limited Partnership, Golden Gate Development and Investment
    Limited Partnership and Rovent II Limited Partnership.
 
(6) Includes an aggregate of 1,047 shares of Common Stock and 91,330 shares of
    Series A Preferred Stock (convertible into 29,705 shares of Common Stock)
    subsequently transferred by Accel IV L.P. to Accel Keiretsu L.P., Accel
    Investors '93 L.P., Ellmore C. Patterson Partners and Prosper Partners.
 
(7) Includes 8,371 shares of Common Stock, 340,628 shares of Series A Preferred
    Stock (convertible into 110,788 shares of Common Stock) and 224,008 shares
    of Series B Preferred Stock (convertible into
 
                                       54
<PAGE>
    72,858 shares of Common Stock) subsequently transferred by Venrock
    Associates to Venrock Associates II, L.P.
 
(8) Does not include 61,508 shares of Common Stock, 1,601,289 shares of Series A
    Preferred Stock (convertible into 520,814 shares of Common Stock), 1,052,812
    shares of Series B Preferred Stock (convertible into 342,424 shares of
    Common Stock) and 231,783 shares of Series C Preferred Stock (convertible
    into 75,387 shares of Common Stock) issued to CW Ventures II, L.P. Mr.
    Weinberg is a general partner of CW Partners III, L.P., which is the general
    partner of CW Ventures II, L.P.
 
BIOCHEM OFFERING
 
    On December 17, 1997, the Company issued to BioChem 5,713,034 shares of its
newly created Series D Preferred Stock (convertible into 1,858,145 shares of
Common Stock) for consideration of $20 million. In addition, the Company issued
the BioChem Warrant. All of the outstanding shares of Series D Preferred Stock
will convert into shares of Common Stock upon the consummation of the Offering.
In the event that the initial public offering price is less than $10.76 per
share, the Company will be required to issue to BioChem, for no additional
consideration, the number of additional shares of Common Stock equal to the
amount by which (a) 19,993,640 divided by the initial public offering price,
exceeds (b) 1,858,145.
 
    In connection with the BioChem Offering, the Company entered into a research
and license agreement, a stockholders' agreement, a registration rights
agreement and a warrant agreement with BioChem. See "Description of Capital
Stock--Warrants" and "--Registration Rights." The research and license agreement
relates to the Company's HBV and Dimerescent Programs. See
"Business--Collaborative Arrangements." The stockholders' agreement, to which
substantially all of the Company's existing significant stockholders are a
party, permits BioChem to designate a member of the Board of Directors upon the
first to occur of a "Qualified Public Offering" (which would include the
Offering) or February 16, 1998, and requires the other parties thereto to vote
their shares in favor of such nominee at any meeting of stockholders. BioChem's
right to designate a director will terminate in the event that BioChem and its
permitted transferees own less than 10% of the Series D Preferred Stock and any
Common Stock issued upon conversion of such stock, or December 17, 2007. The
stockholders' agreement also provides for certain affirmative and negative
covenants and restrictions on the transferability of shares owned by the parties
thereto which will terminate upon the consummation of the Offering.
 
TRANSACTIONS WITH DIRECTORS, EXECUTIVE OFFICERS AND ADVISORS
 
    The Company has employment agreements with Mark T. Weedon, its President and
Chief Executive Officer and a director of the Company, Michael G. Palfreyman,
its Vice President of Research and Development, Michael W. Heslop, its Vice
President of Business Development and Karen A. Hamlin, its Senior Director of
Operations, Secretary and Treasurer. See "Management--Employment Agreements."
 
    David Baltimore receives $10,000 annually for being a director of the
Company and was granted non-statutory options to purchase 24,394, 40,656 and
8,132 shares of Common Stock in 1994, 1996 and 1997, respectively, at an
exercise price of $0.15 per share.
 
    Under the terms of a sponsored research agreement, the Company paid the
University of Massachusetts Medical Center a total of $1,000,000 in 1992 through
1994 for research performed in Dr. Green's laboratory. The Company is not
obligated to make any additional payments for research under such agreement.
 
                                       55
<PAGE>
                             PRINCIPAL STOCKHOLDERS
 
    The following table sets forth certain information regarding the beneficial
ownership of the Common Stock of the Company as of December 31, 1997, after
giving effect to the Offering and the Private Placement, by: (i) each person
known to beneficially own more than 5% of the outstanding shares of Common
Stock, (ii) each of the Company's directors, (iii) each of the executive
officers of the Company and (iv) all executive officers and directors as a
group. All persons listed have sole voting and investment power with respect to
their shares unless otherwise indicated.
 
<TABLE>
<CAPTION>
                                                                                                  PERCENTAGE OF SHARES
                                                                                                   BENEFICIALLY OWNED
                                                                                                ------------------------
<S>                                                                                <C>          <C>          <C>
                                                                                     SHARES
NAME AND ADDRESS                                                                   BENEFICIALLY   BEFORE        AFTER
OF BENEFICIAL OWNER (1)                                                             OWNED (2)    OFFERING     OFFERING
- ---------------------------------------------------------------------------------  -----------  -----------  -----------
BioChem Pharma Holdings Inc. (3).................................................   2,322,682        26.1%        19.1%
  275 Armond-Frappier Boulevard
  Laval, Quebec H7V4A7
  Canada
CW Ventures II, L.P. (4).........................................................   1,089,575        12.9%         9.3%
  c/o CW Group, Inc.
  1041 Third Avenue
  New York, NY 10021
Atlas Venture Fund II, L.P.......................................................     831,385         9.9%         7.1%
  c/o Atlas Venture
  222 Berkeley Street, 19th Floor
  Boston, MA 02166
New Enterprise Associates V......................................................     672,092         8.0%         5.8%
  c/o New Enterprise Associates
  1119 St. Paul Street
  Baltimore, MD 21202
Lombard Odier & Cie..............................................................     903,536        10.7%         7.7%
  11 rue de la Corraterie
  Geneva Switzerland
Entities affiliated with Advent International Corporation (5)....................     592,709         7.0%         5.1%
  101 Federal Street
  Boston, MA 02110
Entities affiliated with Accel Partners (6)......................................     672,094         8.0%         5.8%
  428 University Avenue
  Palo Alto, CA 94301
Venrock Associates and Venrock Associates II, L.P. (7)...........................     672,093         8.0%         5.8%
  30 Rockefeller Plaza
  New York, NY 10112
Mark T. Weedon (8)...............................................................     339,558         3.9%         2.8%
Michael G. Palfreyman (9)........................................................      74,258        *            *
Michael W. Heslop................................................................      --            *            *
Karen A. Hamlin (10).............................................................      12,813        *            *
Barry Weinberg (11)..............................................................   1,089,575        12.9%         9.3%
David Baltimore (12).............................................................      30,899        *            *
Allan R. Ferguson (13)...........................................................     831,385         9.9%         7.1%
Jason S. Fisherman (14)..........................................................     592,709         7.0%         5.1%
All directors and executive officers as a group (8 persons) (15).................   2,971,197        33.6%        24.6%
</TABLE>
 
- --------------
 
*Less than 1.0%
 
                                       56
<PAGE>
    (1) Unless indicated otherwise, the address of the beneficial owners is: c/o
Scriptgen Pharmaceuticals, Inc., 200 Boston Avenue, Medford, Massachusetts
02155.
 
    (2) Beneficial ownership is determined in accordance with the rules of the
Securities and Exchange Commission and generally includes voting or investment
power with respect to securities. Shares of Common Stock issuable pursuant to
options, to the extent such options are currently exercisable or convertible
within 60 days of December 31, 1997, are treated as outstanding for computing
the percentage of the person holding such securities but are not treated as
outstanding for computing the percentage of any other person. Unless otherwise
noted, each person or group identified possesses sole voting and investment
power with respect to shares, subject to community property laws where
applicable. Percentage of beneficial ownership is based on 8,417,795 shares of
Common Stock outstanding as of December 31, 1997 and 11,667,795 shares of Common
Stock outstanding after completion of the Offering and the Private Placement
(assuming an initial public offering price of $12.00 per share and in each case
after giving effect to the 1-for-3.07459 reverse split of the Common Stock to be
effected before the completion of the Offering and the conversion of all
outstanding shares of Series A Preferred Stock, Series B Preferred Stock, Series
C Preferred Stock and Series D Preferred Stock into Common Stock upon the
closing of the Offering).
 
    (3) Includes warrants to purchase 464,537 shares of Common Stock at an
exercise price of $13.47.
 
    (4) Includes 89,443 shares held by Barry Weinberg, Chairman of the Board of
Directors.
 
    (5) Includes the ownership by the following venture capital funds of which
Advent International Corporation is the general partner, or the general partner
of the general partner, of: 3,530 shares held by Advent International Investors
II Limited Partnership, 63,243 shares held by Advent Performance Materials
Limited Partnership, 84,715 shares held by Golden Gate Development and
Investment Limited Partnership and 441,221 shares held by Rovent II Limited
Partnership. In its capacity as general partner, Advent International
Corporation exercises sole voting and investment power with respect to all
shares held by these funds. Advent International Corporation exercises its
voting and investment power through a group of three persons: Douglas R. Brown,
President and Chief Executive Officer, Jason S. Fisherman, Vice President, and
Janet L. Hennessy, Vice President responsible for monitoring public securities,
none of whom may act independently and a majority of whom must act in concert to
exercise voting or investment power over the beneficial holdings of such entity.
Therefore, no individual in this group other than Advent International
Corporation is deemed to have sole voting or investment power. Advent
International Corporation may be deemed to beneficially own all 592,709 shares.
 
    (6) Includes 562,541 shares held by Accel IV L.P., 53,767 shares held by
Accel Japan L.P., 12,098 shares held by Accel Keiretsu L.P., 24,868 shares held
by Accel Investors '93 L.P., 14,787 shares held by Ellmore C. Patterson Partners
and 4,033 shares held by Prosper Partners.
 
    (7) Includes 460,389 shares held by Venrock Associates and 211,704 shares
held by Venrock Associates II, L.P.
 
    (8) Includes 305,602 shares issuable upon the exercise of options.
 
    (9) Includes 74,258 shares issuable upon the exercise of options.
 
   (10) Includes 1,429 shares issuable upon the exercise of options.
 
   (11) Includes 1,000,132 shares held by CW Ventures II, L.P.
 
   (12) Includes 30,899 shares issuable upon the exercise of options.
 
   (13) Includes 831,385 shares held by Atlas Venture Fund II, L.P. Mr. Ferguson
is a general partner of Atlas Venture Associates II, L.P., the general partner
of Atlas Venture Fund II, L.P. Mr. Ferguson disclaims beneficial ownership of
such shares except to the extent of his pecuniary interest therein.
 
   (14) Includes 3,530 shares held by Advent International Investors II Limited
Partnership, 63,243 shares held by Advent Performance Materials Limited
Partnership, 84,715 shares held by Golden Gate
 
                                       57
<PAGE>
Development and Investment Limited Partnership and 441,221 shares held by Rovent
II Limited Partnership. Dr. Fisherman is the Vice President of Advent
International Corporation, which is the general partner of Advent International
Investors II Limited Partnership and Advent International Limited Partnership,
which is the general partner of Advent Performance Materials Limited
Partnership, Golden Gate Development and Investment Limited Partnership and
Rovent II Limited Partnership. Dr. Fisherman disclaims beneficial ownership of
all such shares.
 
   (15) See notes 8 through 14 above. The number of shares shown does not
reflect any shares beneficially owned by BioChem. It is expected that following
the Offering, a designee of BioChem will be elected to the Board of Directors.
See "Certain Transactions--BioChem Offering."
 
                                       58
<PAGE>
                          DESCRIPTION OF CAPITAL STOCK
 
    Upon the closing of the Offering and the filing of the amendment to the
Company's Restated Certificate of Incorporation referred to below, the
authorized capital stock of the Company will consist of 35,000,000 shares of
Common Stock, $0.01 par value, and 4,000,000 shares of Preferred Stock, $0.01
par value.
 
    As of December 31, 1997, there were 1,018,638 shares of Common Stock
outstanding, which were held of record by 59 stockholders, 6,403,325 shares of
Series A Preferred Stock outstanding, which were held of record by 12
stockholders, 6,579,086 shares of Series B Preferred Stock outstanding, which
were held of record by 15 stockholders, 4,053,854 shares of Series C Preferred
Stock outstanding, which were held of record by 17 stockholders and 5,713,034
shares of Series D Preferred Stock outstanding, which were held of record by one
stockholder. Upon the closing of the Offering, and after giving effect to the
issuance of 3,000,000 shares of Common Stock offered by the Company hereby, the
issuance of 250,000 shares of Common Stock pursuant to the Private Placement
(assuming an initial public offering price of $12.00 per share) and the
conversion of each share of the Series A Preferred Stock, Series B Preferred
Stock, Series C Preferred Stock and Series D Preferred Stock into 0.32525 shares
of Common Stock, there will be 11,669,189 shares of Common Stock and no shares
of Preferred Stock issued and outstanding. See "--Preferred Stock."
 
COMMON STOCK
 
    Holders of Common Stock are entitled to one vote for each share held on all
matters submitted to a vote of stockholders. The vote required for election to
the Board of Directors is a plurality of votes properly cast at any meeting of
the stockholders at which a quorum is present. For any other action by the
stockholders, the vote required is a majority of votes properly cast at any such
meeting, unless otherwise expressly provided by law or by the Company's Restated
Certificate of Incorporation or By-Laws. Subject to the rights and preferences
of any Preferred Stock which may be outstanding, the holders of Common Stock are
entitled to receive ratably such dividends, if any, as may be declared by the
Board of Directors out of funds legally available therefor and, subject to the
rights and preferences of any Preferred Stock which may be outstanding, the
holders of Common Stock are entitled to receive ratably the net assets of the
Company upon the liquidation, dissolution or winding up of the Company after the
payment of all debts and other liabilities. Holders of Common Stock have no
preemptive, subscription, redemption or conversion rights. The outstanding
shares of Common Stock are, and the shares offered by the Company in the
Offering will be, when issued and paid for, fully paid and nonassessable. The
rights, privileges and preferences of holders of Common Stock will be subject
to, and may be adversely affected by, the rights of the holders of any shares of
Preferred Stock that are currently outstanding or that the Company may designate
and issue in the future.
 
    At present, there is no active trading market for the Common Stock. The
Common Stock has been approved for quotation on the Nasdaq National Market under
the symbol "SCRP." See "Risk Factors--No Prior Public Market; Possible
Volatility of Stock Price."
 
PREFERRED STOCK
 
    The Series A Preferred Stock, Series B Preferred Stock, Series C Preferred
Stock and Series D Preferred Stock are entitled to various preferences and
rights in the event of a liquidation, dissolution or winding-up of the Company
and upon a declaration by the Board of Directors of the payment of dividends.
Each share of Series A Preferred Stock, Series B Preferred Stock, Series C
Preferred Stock and Series D Preferred Stock is convertible into 0.32525 shares
of Common Stock, and upon the closing of the Offering, all of the outstanding
shares of Series A Preferred Stock, Series B Preferred Stock, Series C Preferred
Stock and Series D Preferred Stock will be converted automatically into an
aggregate of 7,399,133 shares of Common Stock. The holders of Common Stock,
Series A Preferred Stock, Series B Preferred Stock, Series C Preferred Stock and
Series D Preferred Stock have approved an amendment to the Company's Restated
Certificate, which will be filed with the Secretary of State of Delaware
immediately following the
 
                                       59
<PAGE>
closing of the Offering. The Restated Certificate will, among other things,
increase the number of authorized shares of Preferred Stock to 4,000,000, and
will eliminate all references to Series A Preferred Stock, Series B Preferred
Stock, Series C Preferred Stock and Series D Preferred Stock.
 
    The Restated Certificate will give the Board of Directors the authority to
issue 4,000,000 shares of Preferred Stock in one or more series and to fix the
rights, preferences, privileges and restrictions, including dividend,
conversion, voting, redemption (including sinking fund provisions), and other
rights, liquidation preferences, and the number of shares constituting any
series and the designations of such series, without any further vote or action
by the stockholders of the Company. Following the closing of the Offering and
the filing of the Restated Certificate, Preferred Stock could be issued by the
Board of Directors with voting and conversion rights that could adversely affect
the voting power of the holders of the Common Stock. In addition, because the
terms of the Preferred Stock may be fixed by the Board of Directors of the
Company without stockholder action, the Preferred Stock could be issued quickly
with terms calculated to defeat or delay a proposed takeover of the Company, or
to make the removal of the management of the Company more difficult. Under
certain circumstances, this would have the effect of decreasing the market price
of the Common Stock. The Company has no present plans to issue any Preferred
Stock. See "Risk Factors--Availability of Preferred Stock for Issuance;
Anti-Takeover Provisions."
 
WARRANTS
 
    As of December 31, 1997, there were outstanding warrants to purchase an
aggregate of 253,000 shares of Preferred Stock, which will be exercisable for an
aggregate of 82,288 shares of Common Stock following the Offering.
 
    In connection with a Master Leasing Agreement dated as of November 22, 1993
between the Company and Comdisco, Inc. ("Comdisco"), the Company issued to
Comdisco warrants to purchase up to 153,000 shares of Series A Preferred Stock
(to purchase up to 49,763 shares of Common Stock following the Offering) at an
exercise price of $1.00 per share, which warrants will expire in January 2004.
In February 1996, the Company executed an amendment to the Master Leasing
Agreement with Comdisco under which Comdisco will provide additional equipment
financing to the Company. In connection with this agreement, as of November 1,
1997 the Company had issued to Comdisco warrants to purchase 100,000 shares of
Series C Preferred Stock (to purchase up to 32,525 shares of Common Stock
following the Offering) at an exercise price of $1.80 per share. The warrants to
purchase Series C Preferred Stock will expire in May 2006.
 
    The exercise price of the warrants issued to Comdisco may be paid in cash or
by the surrender of warrants pursuant to a cashless exercise provision. The
warrants issued to Comdisco contain certain anti-dilution provisions providing
for adjustments of the exercise price and number of shares of underlying
securities which may be purchased upon exercise in the event of any
reclassification, subdivision or combination of, or dividend on, the Company's
capital stock.
 
    In connection with the BioChem Offering, the Company issued to BioChem a
warrant to purchase 464,537 shares of Common Stock at an exercise price of
$13.47 per share. The warrant is exercisable for a period of five years from the
date of issuance. The BioChem Warrant contains certain anti-dilution provisions
providing for adjustments of the exercise price and number of underlying warrant
shares in the event of any subdivision or combination of, or dividend on, the
Company's capital stock, any other dividend payable otherwise than out of
retained earnings or, prior to the Offering, upon certain issuances of the
Company's capital stock at a per share price less than the exercise price.
Pursuant to the terms of the warrant, prior to any recapitalization,
reorganization, reclassification, consolidation, merger, sale of all or
substantially all of the Company's assets or other transaction in which the
holders of Common Stock are entitled to receive stock, securities or assets, the
Company must insure that the warrant will thereafter be exercisable for the
amount of stock, securities or assets that the holder of the warrant would have
been
 
                                       60
<PAGE>
entitled to receive had such holder exercised the warrant immediately prior to
such transaction. A similar provision is contained in the Comdisco warrants.
 
REGISTRATION RIGHTS
 
    Pursuant to an agreement between the Company and certain of its securities
holders, 5,540,988 shares of Common Stock (the "Registrable Securities") will be
entitled to certain rights with respect to the registration of the Registrable
Securities under the Securities Act. If the Company receives from the holders of
at least 50% of the Registrable Securities a written request to effect a
registration with respect to all or a part of the Registrable Securities, the
Company must, as soon as practicable, use its best efforts to effect such
registration, for a maximum of two such registrations. Pursuant to this
provision, the holders of the Registrable Securities may choose to distribute
their securities by means of an underwriting, subject to the authority of the
underwriters to limit the number of shares to be underwritten due to marketing
factors. If such an underwriting is undertaken, a securityholder's right to
registration is conditioned upon such securityholder's participation in the
underwriting.
 
    If the Company registers any of its securities for its own account or
pursuant to the demand of its security holders (other than certain types of
exempted registrations), the Company must include in such registration and any
underwriting relating thereto all the Registrable Securities specified by the
holders thereof for inclusion, subject to the authority of the underwriters to
limit the number of shares to be underwritten due to marketing factors. If an
underwriting is undertaken, a securityholder's right to registration is
conditioned upon such securityholder's participation in the underwriting.
 
    Pursuant to an agreement between the Company, BioChem and certain of the
Company's securityholders, BioChem will be entitled to certain rights with
respect to the registration of its 1,858,145 shares of Common Stock, and 464,537
shares of Common Stock issuable upon exercise of the BioChem Warrant, under the
Securities Act. If, at any time after the first anniversary of the Offering, the
Company receives from BioChem a written request to effect a registration with
respect to all or a part of its Common Stock, the Company must, as soon as
practicable, use its best efforts to effect such registration, for a maximum of
two such registrations. Pursuant to this provision, BioChem may choose to
distribute securities by means of an underwriting. The agreement also provides
BioChem and other securityholders with piggyback registration rights.
 
    The Company has granted certain piggyback registration rights to HMR in
connection with the shares of Common Stock being purchased by HMR in the Private
Placement.
 
DELAWARE ANTI-TAKEOVER LAW AND CERTAIN CHARTER PROVISIONS
 
    Under Section 203 of the Delaware General Corporation Law (the "Delaware
anti-takeover law"), certain "business combinations" between a Delaware
corporation, whose stock generally is publicly traded or held of record by more
than 2,000 stockholders, and an "interested stockholder" are prohibited for a
three-year period following the date that such stockholder became an interested
stockholder, unless (i) the corporation has elected in its certificate of
incorporation or bylaws not to be governed by the Delaware anti-takeover law
(the Company has not made such an election), (ii) the business combination was
approved by the board of directors of the corporation before the other party to
the business combination became an interested stockholder, (iii) upon
consummation of the transaction that made it an interested stockholder, the
interested stockholder owned at least 85% of the voting stock of the corporation
outstanding at the commencement of the transaction (excluding voting stock owned
by directors who are also officers or held in employee stock plans in which the
employees do not have a right to determine confidentially whether to tender or
vote stock held by the plan) or (iv) the business combination was approved by
the board of directors of the corporation and ratified by two-thirds of the
voting stock which the interested stockholder did not own. The three-year
prohibition does not apply to certain business combinations proposed by an
interested stockholder following the announcement or notification of certain
extraordinary transactions involving the corporation and a person who had not
been an interested stockholder during the previous three years or who became an
interested stockholder with the approval of
 
                                       61
<PAGE>
a majority of the corporation's directors. The term "business combination" is
defined generally to include mergers or consolidations between a Delaware
corporation and an interested stockholder, transactions with an interested
stockholder involving the assets or stock of the corporation or its
majority-owned subsidiaries and transactions which increase an interested
stockholder's percentage ownership of stock. The term "interested stockholder"
is defined generally as a stockholder who becomes beneficial owner of 15% or
more of a Delaware corporation's voting stock. Section 203 could have the effect
of delaying, deferring or preventing a change in control of the Company.
 
    The Company's Restated Certificate provides that any action required or
permitted to be taken by stockholders of the Company must be effected at a duly
called annual or special meeting of stockholders and may not be effected by any
consent in writing. In addition, special meetings of the stockholders of the
Company may be called only by the Chairman of the Board, the President of the
Company, by the Board of Directors pursuant to a resolution adopted by a
majority of the total number of authorized directors. These and other provisions
contained in the Restated Certificate and the Company's By-Laws could delay or
make more difficult certain types of transactions involving an actual or
potential change in control of the Company or its management (including
transactions in which stockholders might otherwise receive a premium for their
shares over then current prices) and may limit the ability of stockholders to
remove current management of the Company or approve transactions that
stockholders may deem to be in their best interests and, therefore, could
adversely affect the price of the Common Stock.
 
LIMITATION OF LIABILITY AND INDEMNIFICATION MATTERS
 
    The Company's Restated Certificate provides that directors of the Company
shall not be personally liable to the Company or its stockholders for monetary
damages for breach of fiduciary duty as a director, except for liability (i) for
any breach of the director's duty of loyalty to the Company or its stockholders,
(ii) for acts or omissions not in good faith or which involve intentional
misconduct or a knowing violation of law, (iii) under Section 174 of the
Delaware General Corporation Law (the "DGCL"), relating to prohibited dividends
or distribution or the repurchase or redemption of stock or (iv) for any
transaction from which the director derives an improper personal benefit. The
provision does not apply to claims against a director for violations of certain
laws, including federal securities laws. If the DGCL is amended to authorize the
further elimination or limitation of directors' liability, then the liability of
directors of the Company shall automatically be limited to the fullest extent
provided by law. The Company's Restated Certificate and By-Laws also contain
provisions requiring the Company to indemnify the directors, officers, employees
or other agents to the fullest extent permitted by the DGCL. In addition, the
Company will enter into indemnification agreements with its current directors
and executive officers. These provisions and agreements may have the practical
effect in certain cases of eliminating the ability of stockholders to collect
monetary damages from directors. The Company believes that these contractual
agreements and the provisions in its Restated Certificate and By-Laws are
necessary to attract and retain qualified persons as directors and officers.
 
TRANSFER AGENT AND REGISTRAR
 
    The Transfer Agent and Registrar for the Common Stock is American Securities
Transfer & Trust, Inc., Denver, Colorado.
 
                        SHARES ELIGIBLE FOR FUTURE SALE
 
    Prior to the Offering, there has been no public market for the Common Stock
of the Company, and no prediction can be made as to the effect, if any, that
market sales of shares or the availability of such shares for sale will have on
the market price of the Common Stock prevailing from time to time. Sales of
substantial amounts of Common Stock, or the perception that such sales could
occur, could adversely affect the prevailing market price of the Common Stock
and the ability of the Company to raise capital through a sale of its
securities.
 
                                       62
<PAGE>
    Upon completion of the Offering and the Private Placement, the Company will
have 11,669,189 shares of Common Stock outstanding (assuming no exercise of
outstanding options or warrants). Of these shares, the 3,000,000 shares sold
pursuant to the Offering will be freely tradable without restriction or further
registration under the Securities Act, except those shares acquired by
"affiliates" of the Company within the meaning of the Securities Act which will
be subject to the resale limitations of Rule 144 promulgated thereunder. The
remaining 8,669,189 Restricted Shares (including the 250,000 shares of Common
Stock, based on an assumed initial public offering price of $12.00 per share,
sold in the Private Placement and the 1,858,145 shares sold pursuant to the
BioChem Offering) will be restricted securities within the meaning of Rule 144
and may be sold only if registered under the Securities Act or sold in
accordance with an applicable exemption from registration, such as Rule 144. The
Company, its executive officers and directors and holders of substantially all
of the Common Stock have agreed not to offer, sell, contract to sell, grant any
option to sell, or otherwise dispose of, directly or indirectly, any Common
Stock or securities convertible into or exchangeable for Common Stock or
warrants or other rights to purchase Common Stock, subject to certain limited
exceptions, during the 180 days after the effective date of this Prospectus (the
"Lock-Up Period"), without the prior consent of SBC Warburg Dillon Read Inc.
Commencing at the end of the Lock-Up Period, approximately 6,520,950 Restricted
Shares will be eligible for sale in the public market, subject to compliance
with Rule 144. Of such shares, approximately 5,158,797 will be eligible for sale
without limitation, pursuant to Rule 144(k) or Rule 701, including approximately
68,544 shares of Common Stock not subject to lock-up agreements which will be
eligible for sale following the Offering. The remaining approximately 2,148,239
Restricted Shares will become eligible for sale at various times over a period
of six months from the end of the Lock-Up Period. In addition, any shares issued
upon exercise of the Company's outstanding warrants may be eligible for sale
pursuant to Rule 144 at various times following the expiration of the Lock-Up
Period. The Company has granted to certain security holders demand and piggyback
registration rights covering an aggregate of 8,113,670 shares of Common Stock.
The Company expects to file a Registration Statement on Form S-8 registering
shares of Common Stock reserved for issuance upon exercise of options granted
under the Company's 1997 Plan, Directors' Plan and 1994 Stock Option Plan
following completion of the Offering.
 
    In general, under Rule 144 under the Securities Act as currently in effect,
a person (or persons whose shares are aggregated) who has beneficially owned
restricted securities within the meaning of Rule 144 ("Restricted Securities")
for at least one year, and including the holding period of any prior owner
except an affiliate, would be entitled to sell within any three-month period a
number of shares that does not exceed the greater of one percent of the then
outstanding shares of Common Stock or the average weekly trading volume of the
Common Stock on the National Association of Securities Dealers Automated
Quotation System during the four calendar weeks preceding such sale. Sales under
Rule 144 are also subject to certain manner of sale provisions, notice
requirements and the availability of current public information about the
Company. Any person (or persons whose shares are aggregated) who is not deemed
to have been an affiliate of the Company at any time during the three months
preceding a sale, and who has beneficially owned shares for at least two years
(including any period of ownership of preceding non-affiliated holders), would
be entitled to sell such shares under Rule 144(k) without regard to the volume
limitations, manner of sale provisions, public information requirements or
notice requirements. An "affiliate" is a person that directly, or indirectly
through one or more intermediaries, controls, or is controlled by, or under
common control with, such issuer.
 
    Rule 144A under the Securities Act as currently in effect generally permits
unlimited resales of certain Restricted Securities of any issuer provided that
the purchaser is a qualified institution that owns and invests on a
discretionary basis at least $100 million in securities (and in the case of a
bank or savings and loan association, has a net worth of at least $25 million)
or is a registered broker-dealer that owns and invests on a discretionary basis
at least $10 million in securities. Rule 144A allows certain existing
stockholders of the Company to sell their shares of Common Stock to such
institutions and registered broker-dealers without regard to any volume or other
restrictions. There can be no assurance that the availability of such resale
exemption will not have an adverse effect on the trading price of the Common
Stock.
 
                                       63
<PAGE>
                                  UNDERWRITING
 
    The underwriters named below (the "Underwriters") have severally agreed,
subject to the terms and conditions set forth in the Underwriting Agreement, to
purchase from the Company the number of shares of Common Stock set forth
opposite their names below:
 
<TABLE>
<CAPTION>
UNDERWRITERS                                                                 NUMBER OF SHARES
- ---------------------------------------------------------------------------  -----------------
<S>                                                                          <C>
SBC Warburg Dillon Read Inc................................................
Volpe Brown Whelan & Company, LLC..........................................
 
                                                                             -----------------
       Total...............................................................       3,000,000
                                                                             -----------------
                                                                             -----------------
</TABLE>
 
    The Managing Underwriters are SBC Warburg Dillon Read Inc. and Volpe Brown
Whelan & Company, LLC.
 
    Subject to the terms and conditions of the Underwriting Agreement, the
Underwriters have agreed to purchase all of the shares of Common Stock being
sold pursuant to the Underwriting Agreement if any are purchased (excluding
shares covered by the over-allotment option).
 
    The Underwriters propose to offer the Common Stock to the public initially
at the public offering price set forth on the cover page of this Prospectus and
to selected dealers (who may include Underwriters) at such price less a
concession of not more than $         per share. Additionally, the Underwriters
may allow, and such dealers may reallow, a concession of not more than
$         per share to certain other dealers. After the Offering, the public
offering price and other selling terms may be changed by the Managing
Underwriters.
 
    The Company has granted to the Underwriters an option for 30 days from the
date of this Prospectus to purchase up to 450,000 additional shares of Common
Stock. The Underwriters may exercise such option only to cover over-allotments
of the Common Stock offered hereby, if any. To the extent that the Underwriters
exercise this option, each Underwriter will be obligated, subject to certain
conditions, to purchase the number of additional shares of Common Stock
proportionate to such Underwriter's initial commitment.
 
    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 has 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.
 
    The executive officers and directors of the Company and certain other
stockholders, who in the aggregate own substantially all of the shares of Common
Stock, have agreed that they will not, without the prior written consent of SBC
Warburg Dillon Read Inc., offer, sell, contract to sell, grant any option to
sell
 
                                       64
<PAGE>
or otherwise dispose of, directly or indirectly, any Common Stock or securities
convertible into or exchangeable for Common Stock or warrants or other rights to
purchase Common Stock owned by them during the 180 day period following the date
of this Prospectus. The Company has agreed that it will not, without the prior
written consent of SBC Warburg Dillon Read Inc., offer, sell, contract to sell,
grant any option to sell or otherwise dispose of, directly or indirectly, any
Common Stock or securities convertible into or exchangeable for Common Stock or
warrants or other rights to purchase Common Stock during the 180 days following
the date of this Prospectus, except that the Company may issue shares of Common
Stock and options to purchase Common Stock under its 1997 Plan and Directors'
Plan and upon exercise of outstanding options and warrants.
 
    Prior to the Offering, there has been no public market for the Common Stock.
Consequently, the initial public offering price for the Common Stock has been
determined by negotiation between the Managing Underwriters and the Company.
Factors considered in determining such price were prevailing market conditions,
the state of the Company's development, the future prospects of the Company and
its industry, market valuations of securities of companies engaged in activities
deemed by the Managing Underwriters to be similar to those of the Company, and
other factors deemed relevant.
 
    The Underwriters may engage in over-allotment, stabilizing transactions,
syndicate-covering transactions and penalty bids in accordance with Regulation M
under the Exchange Act. Over-allotment involves syndicate sales in excess of the
offering size, which creates a syndicate short position. Stabilizing
transactions permit bids to purchase the underlying security so long as the
stabilizing bids do not exceed a specified maximum. Syndicate-covering
transactions involve purchases of the Common Stock in the open market after
distribution has been completed in order to cover syndicate short positions.
Penalty bids permit the Underwriters to reclaim a selling concession from a
syndicate member when the Common Stock originally sold by such syndicate member
is purchased in a syndicate-covering transaction to cover syndicate short
positions. Such stabilizing transactions, syndicate-covering transactions and
penalty bids may cause the price of the Common Stock to be higher than it would
otherwise be in the absence of such transactions.
 
    The Underwriters do not intend to confirm sales to accounts over which they
exercise discretionary authority.
 
                                 LEGAL MATTERS
 
    The validity of the shares of Common Stock offered hereby will be passed
upon for the Company by Fulbright & Jaworski L.L.P., New York, New York. Certain
legal matters in connection with the Offering will be passed upon for the
Underwriters by Brobeck, Phleger & Harrison LLP, New York, New York.
 
                                    EXPERTS
 
    The financial statements of Scriptgen Pharmaceuticals, Inc. 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.
 
    Certain legal matters with respect to information contained in this
Prospectus under the captions "Risk Factors--Uncertainty of Patents and
Proprietary Rights" and "Business--Patents and Proprietary Technology" have been
reviewed and approved by Darby & Darby P.C., New York, New York, patent counsel
for the Company, as experts in such matters and are included herein in reliance
upon that review and approval.
 
                                       65
<PAGE>
                             ADDITIONAL INFORMATION
 
    The Company has filed with the Commission in Washington, D.C. a Registration
Statement, of which this Prospectus constitutes a part, on Form S-1 under the
Securities Act (herein, together with all amendments and exhibits referred to
herein as the "Registration Statement") with respect to the Common Stock offered
hereby. This Prospectus does not contain all of the information set forth in the
Registration Statement and the exhibits and schedules to the Registration
Statement, as certain parts have been omitted in accordance with rules and
regulations of the Commission. For further information with respect to the
Company and the Common Stock offered hereby, reference is made to the
Registration Statement and the exhibits and schedules filed as a part of the
Registration Statement. Statements contained in this Prospectus as to the
contents of any contract, agreement or any other document referred to are not
necessarily complete; reference is made in each instance to the copy of such
contract or document filed as an exhibit to the Registration Statement. Each
such statement is qualified in all respects by such reference to such exhibit. A
copy of the Registration Statement, including exhibits and schedules thereto,
may be inspected without charge and obtained at prescribed rates at the Public
Reference Section of the Commission at its principal offices, located at 450
Fifth Street, N.W., Washington, D.C. 20549, and may be inspected without charge
at the regional offices of the Commission located at Seven World Trade Center,
13th Floor, New York, New York 10048, and Citicorp Center, 500 West Madison
Street, Suite 1400, Chicago, Illinois 60661. The Registration Statement,
including the exhibits and schedules thereto, is also available at the
Commission's site on the World Wide Web at http://www.sec.gov.
 
    The Company intends to furnish its stockholders annual reports containing
financial statements audited by its independent auditors and quarterly reports
containing unaudited financial information.
 
                                       66
<PAGE>
                         INDEX TO FINANCIAL STATEMENTS
 
<TABLE>
<CAPTION>
<S>                                                                                     <C>
 
Report of Independent Accountants.....................................................        F-2
 
Balance Sheet as of December 31, 1995 and 1996, September 30, 1997 (unaudited) and pro
  forma September 30, 1997 (unaudited)................................................        F-3
 
Statement of Operations for the three years ended December 31, 1996 and for the nine
  months ended September 30, 1996 (unaudited) and 1997 (unaudited)....................        F-4
 
Statement of Redeemable Preferred Stock and Stockholders' Equity (Deficit) for the
  three years ended December 31, 1996 and for the nine months ended September 30, 1997
  (unaudited) and pro forma September 30, 1997 (unaudited)............................        F-5
 
Statement of Cash Flows for the three years ended December 31, 1996 and for the nine
  months ended September 30, 1996 (unaudited) and 1997 (unaudited)....................        F-7
 
Notes to Financial Statements.........................................................        F-8
</TABLE>
 
                                      F-1
<PAGE>
                       REPORT OF INDEPENDENT ACCOUNTANTS
 
To the Board of Directors and Stockholders of
Scriptgen Pharmaceuticals, 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 Scriptgen Pharmaceuticals, Inc. at December 31, 1995 and 1996, 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.
 
   
PRICE WATERHOUSE LLP
Boston, Massachusetts
February 10, 1998
    
 
                                      F-2
<PAGE>
                        SCRIPTGEN PHARMACEUTICALS, INC.
 
                                 BALANCE SHEET
 
<TABLE>
<CAPTION>
                                                                DECEMBER 31,                         PRO FORMA
                                                          ------------------------  SEPTEMBER 30,  SEPTEMBER 30,
                                                             1995         1996          1997           1997
                                                          -----------  -----------  -------------  -------------
<S>                                                       <C>          <C>          <C>            <C>
                                                                                                     (NOTE 2)
                                                                                     (UNAUDITED)    (UNAUDITED)
ASSETS
Current assets:
  Cash and cash equivalents.............................  $   241,352  $ 1,314,305   $   858,176    $20,858,176
  Short-term investments................................      938,002    3,023,932       205,981        205,981
  Accounts and other receivables........................       74,559      136,715       144,547        144,547
  Prepaid expenses and other current assets.............       33,064       45,203        34,209         34,209
                                                          -----------  -----------  -------------  -------------
      Total current assets..............................    1,286,977    4,520,155     1,242,913     21,242,913
 
Property and equipment, net.............................    1,262,842    1,117,714     1,132,338      1,132,338
Other assets, net.......................................      139,348      108,842       102,835        102,835
                                                          -----------  -----------  -------------  -------------
                                                          $ 2,689,167  $ 5,746,711   $ 2,478,086    $22,478,086
                                                          -----------  -----------  -------------  -------------
                                                          -----------  -----------  -------------  -------------
LIABILITIES, REDEEMABLE PREFERRED STOCK AND
  STOCKHOLDERS' EQUITY (DEFICIT)
Current liabilities:
  Current portion of capital lease obligations..........  $   442,034  $   559,173   $   483,891    $   483,891
  Accounts payable......................................      142,774      252,393       518,347        518,347
  Accrued expenses......................................      409,753      158,256       210,253        210,253
  Deferred revenue......................................      200,000      200,000     1,230,000      1,230,000
                                                          -----------  -----------  -------------  -------------
    Total current liabilities...........................    1,194,561    1,169,822     2,442,491      2,442,491
                                                          -----------  -----------  -------------  -------------
Capital lease obligations...............................      635,539      423,895       500,736        500,736
                                                          -----------  -----------  -------------  -------------
Redeemable convertible preferred stock, $.01 par value,
  21,500,000 shares authorized; 12,982,411 shares issued
  and outstanding at December 31, 1995 and 17,036,265
  shares issued and outstanding at December 31, 1996 and
  September 30, 1997 (unaudited); none issued and
  outstanding on a pro forma basis at September 30, 1997
  (unaudited) (liquidating preference of $20,279,348)...   12,982,411   20,279,348    20,279,348        --
                                                          -----------  -----------  -------------  -------------
Stockholders' equity (deficit):
  Common stock, $.01 par value, 6,504,932 shares
    authorized at December 31, 1995, 30,000,000 shares
    authorized at December 31, 1996 and September 30,
    1997 (unaudited) and 35,000,000 shares authorized at
    September 30, 1997 on a pro forma basis (unaudited);
    1,112,330, 1,286,394, 1,373,378 and 8,413,763 issued
    at December 31, 1995 and 1996, September 30, 1997
    (unaudited) and September 30, 1997 on a pro forma
    basis (unaudited), respectively; 814,485, 927,646,
    1,014,630 and 8,413,763 shares outstanding at
    December 31, 1995 and 1996, September 30, 1997
    (unaudited) and September 30, 1997 on a pro forma
    basis (unaudited), respectively.....................       11,124       12,865        13,735         84,139
  Additional paid-in capital............................      219,852      403,208     3,126,457     45,547,042
  Unearned compensation.................................      --           (93,744)   (2,660,542)    (2,660,542)
  Accumulated deficit...................................  (12,308,533) (16,393,533)  (21,168,989)   (23,435,780)
                                                          -----------  -----------  -------------  -------------
                                                          (12,077,557) (16,071,204)  (20,689,339)    19,534,859
Treasury stock, at cost, 297,845 shares at December 31,
  1995 and 358,748 shares at December 31, 1996,
  September 30, 1997 (unaudited) and none at September
  30, 1997 on a pro forma basis (unaudited).............      (45,787)     (55,150)      (55,150)       --
                                                          -----------  -----------  -------------  -------------
    Total stockholders' equity (deficit)................  (12,123,344) (16,126,354)  (20,744,489)    19,534,859
                                                          -----------  -----------  -------------  -------------
Commitments and contingencies (Note 8)
                                                          $ 2,689,167  $ 5,746,711   $ 2,478,086    $22,478,086
                                                          -----------  -----------  -------------  -------------
                                                          -----------  -----------  -------------  -------------
</TABLE>
 
   The accompanying notes are an integral part of these financial statements.
 
                                      F-3
<PAGE>
                        SCRIPTGEN PHARMACEUTICALS, INC.
 
                            STATEMENT OF OPERATIONS
 
<TABLE>
<CAPTION>
                                                                                          NINE MONTHS ENDED
                                                  YEAR ENDED DECEMBER 31,                   SEPTEMBER 30,
                                        -------------------------------------------  ----------------------------
                                            1994           1995           1996           1996           1997
                                        -------------  -------------  -------------  -------------  -------------
<S>                                     <C>            <C>            <C>            <C>            <C>
                                                                                             (UNAUDITED)
Revenue:
  Collaborative agreements............  $    --        $    --        $     975,000  $     975,000  $     467,000
  SBIR grants.........................       --              260,415        231,620        221,585        137,784
                                        -------------  -------------  -------------  -------------  -------------
                                             --              260,415      1,206,620      1,196,585        604,784
                                        -------------  -------------  -------------  -------------  -------------
 
Cost of revenue:
  Collaborative agreements............       --             --              174,165        174,165        123,515
  SBIR grants.........................       --              260,415        231,620        221,585        137,784
                                        -------------  -------------  -------------  -------------  -------------
                                             --              260,415        405,785        395,750        261,299
                                        -------------  -------------  -------------  -------------  -------------
  Gross profit........................       --             --              800,835        800,835        343,485
                                        -------------  -------------  -------------  -------------  -------------
 
Operating expenses:
  Research and development............      3,156,734      3,152,494      3,958,201      2,757,439      4,273,149
  General and administrative..........        998,194      1,298,684        906,452        669,108        830,908
                                        -------------  -------------  -------------  -------------  -------------
                                            4,154,928      4,451,178      4,864,653      3,426,547      5,104,057
                                        -------------  -------------  -------------  -------------  -------------
  Loss from operations................     (4,154,928)    (4,451,178)    (4,063,818)    (2,625,712)    (4,760,572)
                                        -------------  -------------  -------------  -------------  -------------
 
Other income (expense):
  Interest income.....................         30,662         88,673        160,364        104,215         91,391
  Interest expense....................       (174,434)      (215,447)      (138,878)       (90,624)      (103,514)
  Other, net..........................         (2,274)          (975)        (1,687)        (1,387)        (2,761)
                                        -------------  -------------  -------------  -------------  -------------
                                             (146,046)      (127,749)        19,799         12,204        (14,884)
                                        -------------  -------------  -------------  -------------  -------------
  Net loss............................  $  (4,300,974) $  (4,578,927) $  (4,044,019) $  (2,613,508) $  (4,775,456)
                                        -------------  -------------  -------------  -------------  -------------
                                        -------------  -------------  -------------  -------------  -------------
 
Net loss per share....................  $       (1.25) $       (1.28) $       (1.20) $       (0.77) $       (1.35)
                                        -------------  -------------  -------------  -------------  -------------
                                        -------------  -------------  -------------  -------------  -------------
 
Weighted average common and common
  equivalent shares outstanding.......      3,435,084      3,590,895      3,360,458      3,374,007      3,528,007
                                        -------------  -------------  -------------  -------------  -------------
                                        -------------  -------------  -------------  -------------  -------------
 
Pro forma net loss per share
  (unaudited).........................                                $       (0.49)                $       (0.53)
                                                                      -------------                 -------------
                                                                      -------------                 -------------
Pro forma weighted average common and
  common equivalent shares outstanding
  (unaudited).........................                                    8,186,013                     9,068,995
                                                                      -------------                 -------------
                                                                      -------------                 -------------
</TABLE>
 
   The accompanying notes are an integral part of these financial statements.
 
                                      F-4
<PAGE>
                        SCRIPTGEN PHARMACEUTICALS, INC.
 
   STATEMENT OF REDEEMABLE PREFERRED STOCK AND STOCKHOLDERS' EQUITY (DEFICIT)
<TABLE>
<CAPTION>
                                            REDEEMABLE PREFERRED
                                                    STOCK
                                           -----------------------
                                                                                    STOCKHOLDERS' EQUITY (DEFICIT)
                                                 REDEEMABLE         --------------------------------------------------------------
                                                 CONVERTIBLE
                                               PREFERRED STOCK           COMMON STOCK       ADDITIONAL
                                           -----------------------  ----------------------   PAID-IN      UNEARNED    ACCUMULATED
                                             SHARES      AMOUNT      SHARES      AMOUNT      CAPITAL    COMPENSATION    DEFICIT
                                           ----------  -----------  ---------  -----------  ----------  ------------  ------------
Balance at December 31, 1993.............   6,203,325  $ 6,203,325    170,755   $   1,708   $   24,542   $   --        $(3,376,234)
<S>                                        <C>         <C>          <C>        <C>          <C>         <C>           <C>
Issuance of warrant to purchase Series A
 redeemable convertible prefererred
 stock...................................                                                      100,000
Issuance of common stock.................                             928,310       9,283       93,426
Issuance of Series A redeemable
 convertible preferred stock, issuance
 costs of $7,764.........................     200,000      200,000                                                         (7,764)
Net loss.................................                                                                              (4,300,974)
                                           ----------  -----------  ---------  -----------  ----------  ------------  ------------
Balance at December 31, 1994.............   6,403,325    6,403,325  1,099,065      10,991      217,968       --        (7,684,972)
Issuance of Series B redeemable
 convertible preferred stock, issuance
 costs of $44,634........................   6,579,086    6,579,086                                                        (44,634)
Issuance of common stock.................                              13,265         133        1,884
Payment on note receivable from
 stockholder.............................
Acquisition of treasury stock............
Net loss.................................                                                                              (4,578,927)
                                           ----------  -----------  ---------  -----------  ----------  ------------  ------------
Balance at December 31, 1995.............  12,982,411  $12,982,411  1,112,330   $  11,124   $  219,852   $   --       ($12,308,533)
 
<CAPTION>
                                              NOTE                      TOTAL
                                           RECEIVABLE                STOCKHOLDERS'
                                              FROM       TREASURY       EQUITY
                                           STOCKHOLDER     STOCK      (DEFICIT)
                                           -----------  -----------  ------------
Balance at December 31, 1993.............   $  --        $  --        $(3,349,984)
<S>                                        <C>          <C>          <C>
Issuance of warrant to purchase Series A
 redeemable convertible prefererred
 stock...................................                                100,000
Issuance of common stock.................     (37,500)                    65,209
Issuance of Series A redeemable
 convertible preferred stock, issuance
 costs of $7,764.........................                                 (7,764)
Net loss.................................                             (4,300,974)
                                           -----------  -----------  ------------
Balance at December 31, 1994.............     (37,500)      --        (7,493,513)
Issuance of Series B redeemable
 convertible preferred stock, issuance
 costs of $44,634........................                                (44,634)
Issuance of common stock.................                                  2,017
Payment on note receivable from
 stockholder.............................       9,375                      9,375
Acquisition of treasury stock............      28,125      (45,787)      (17,662)
Net loss.................................                             (4,578,927)
                                           -----------  -----------  ------------
Balance at December 31, 1995.............   $  --        $ (45,787)  ($12,123,344)
</TABLE>
 
   The accompanying notes are an integral part of these financial statements.
 
                                      F-5
<PAGE>
                        SCRIPTGEN PHARMACEUTICALS, INC.
 
        STATEMENT OF REDEEMABLE PREFERRED STOCK AND STOCKHOLDERS' EQUITY
                              (DEFICIT)(CONTINUED)
   
<TABLE>
<CAPTION>
                                            REDEEMABLE PREFERRED
                                                    STOCK
                                           -----------------------
                                                                                    STOCKHOLDERS' EQUITY (DEFICIT)
                                                 REDEEMABLE         --------------------------------------------------------------
                                                 CONVERTIBLE
                                               PREFERRED STOCK           COMMON STOCK       ADDITIONAL
                                           -----------------------  ----------------------   PAID-IN      UNEARNED    ACCUMULATED
                                             SHARES      AMOUNT      SHARES      AMOUNT      CAPITAL    COMPENSATION    DEFICIT
                                           ----------  -----------  ---------  -----------  ----------  ------------  ------------
Issuance of Series C redeemable
 convertible preferred stock, issuance
 costs of $40,981........................   4,053,854  $ 7,296,937                                                     $  (40,981)
<S>                                        <C>         <C>          <C>        <C>          <C>         <C>           <C>
Issuance of common stock pursuant to
 exercise of stock options...............                             174,064   $   1,741   $    5,018
Acquisition of treasury stock............
Unearned compensation related to common
 stock options granted...................                                                      178,338   $ (178,338)
Amortization of unearned compensation....                                                                    84,594
Net loss.................................                                                                              (4,044,019)
                                           ----------  -----------  ---------  -----------  ----------  ------------  ------------
Balance at December 31, 1996.............  17,036,265   20,279,348  1,286,394      12,865      403,208      (93,744)  (16,393,533)
Issuance of common stock pursuant to
 exercise of stock options (unaudited)...                              86,984         870        8,499
Unearned compensation related to common
 stock options granted (unaudited).......                                                    2,714,750   (2,714,750)
Amortization of unearned compensation
 (unaudited).............................                                                                   147,952
Net loss (unaudited).....................                                                                              (4,775,456)
                                           ----------  -----------  ---------  -----------  ----------  ------------  ------------
Balance at September 30, 1997
 (unaudited).............................  17,036,265   20,279,348  1,373,378      13,735    3,126,457   (2,660,542)  (21,168,989)
Pro forma effect of issuance of Series D
 redeemable convertible preferred stock
 (unaudited).............................   5,713,034   20,000,000
Pro forma effect of the value associated
 with the issuance of warrants
 (unaudited).............................                                                    2,215,228                 (2,215,228)
Pro forma effect of retirement of
 treasury stock (unaudited)..............                            (358,748)     (3,587)                                (51,563)
Pro forma effect of conversion of
 redeemable preferred stock
 (unaudited).............................  (22,749,299) (40,279,348) 7,399,133     73,991   40,205,357
                                           ----------  -----------  ---------  -----------  ----------  ------------  ------------
                                               --      $   --       8,413,763   $  84,139   $45,547,042  $(2,660,542) ($23,435,780)
                                           ----------  -----------  ---------  -----------  ----------  ------------  ------------
                                           ----------  -----------  ---------  -----------  ----------  ------------  ------------
 
<CAPTION>
                                              NOTE                      TOTAL
                                           RECEIVABLE                STOCKHOLDERS'
                                              FROM       TREASURY       EQUITY
                                           STOCKHOLDER     STOCK      (DEFICIT)
                                           -----------  -----------  ------------
Issuance of Series C redeemable
 convertible preferred stock, issuance
 costs of $40,981........................                             $  (40,981)
<S>                                        <C>          <C>          <C>
Issuance of common stock pursuant to
 exercise of stock options...............                                  6,759
Acquisition of treasury stock............                $  (9,363)       (9,363)
Unearned compensation related to common
 stock options granted...................                                 --
Amortization of unearned compensation....                                 84,594
Net loss.................................                             (4,044,019)
                                           -----------  -----------  ------------
Balance at December 31, 1996.............      --          (55,150)  (16,126,354)
Issuance of common stock pursuant to
 exercise of stock options (unaudited)...                                  9,369
Unearned compensation related to common
 stock options granted (unaudited).......                                 --
Amortization of unearned compensation
 (unaudited).............................                                147,952
Net loss (unaudited).....................                             (4,775,456)
                                           -----------  -----------  ------------
Balance at September 30, 1997
 (unaudited).............................      --          (55,150)  (20,744,489)
Pro forma effect of issuance of Series D
 redeemable convertible preferred stock
 (unaudited).............................                                 --
Pro forma effect of the value associated
 with the issuance of warrants
 (unaudited).............................                                 --
Pro forma effect of retirement of
 treasury stock (unaudited)..............                   55,150        --
Pro forma effect of conversion of
 redeemable preferred stock
 (unaudited).............................                             40,279,348
                                           -----------  -----------  ------------
                                            $  --        $  --        $19,534,859
                                           -----------  -----------  ------------
                                           -----------  -----------  ------------
</TABLE>
    
 
   The accompanying notes are an integral part of these financial statements.
 
                                      F-6
<PAGE>
                        SCRIPTGEN PHARMACEUTICALS, INC.
 
                            STATEMENT OF CASH FLOWS
 
                INCREASE (DECREASE) IN CASH AND CASH EQUIVALENTS
 
<TABLE>
<CAPTION>
                                                                                           NINE MONTHS ENDED
                                                          YEAR ENDED DECEMBER 31,            SEPTEMBER 30,
                                                     ----------------------------------  ----------------------
                                                        1994        1995        1996        1996        1997
                                                     ----------  ----------  ----------  ----------  ----------
<S>                                                  <C>         <C>         <C>         <C>         <C>
                                                                                              (UNAUDITED)
CASH FLOWS FROM OPERATING ACTIVITIES
Net loss...........................................  $(4,300,974) $(4,578,927) $(4,044,019) $(2,613,508) $(4,775,456)
Adjustments to reconcile net loss to net cash used
  for operating activities:
  Depreciation and amortization....................     319,045     509,214     586,049     423,910     547,877
  Amortization of unearned compensation............      --          --          84,594      --         147,952
  Accrued interest converted to preferred stock....      --          60,112      --          --          --
  Changes in operating assets and liabilities:
    Accounts receivable............................      --         (74,559)    (62,156)   (227,126)     (7,832)
    Prepaid expenses and other current assets......      70,563      40,072     (12,139)     40,683      10,994
    Other assets...................................     (93,789)     20,000      21,518      (7,239)     (8,573)
    Accounts payable...............................     127,898     (64,191)    109,619      33,991     265,954
    Accrued expenses...............................         318     143,801    (251,497)   (206,534)     51,997
    Deferred revenue...............................      --         200,000      --          --       1,030,000
                                                     ----------  ----------  ----------  ----------  ----------
    Net cash used for operating activities.........  (3,876,939) (3,744,478) (3,568,031) (2,555,823) (2,737,087)
                                                     ----------  ----------  ----------  ----------  ----------
CASH FLOWS FROM INVESTING ACTIVITIES
Purchase of short-term investments.................  (7,794,213) (1,512,583) (9,300,265) (6,199,133) (2,637,489)
Sale of short-term investments.....................   9,043,301     574,581   7,214,335   3,830,952   5,455,440
Purchase of property and equipment.................    (132,657)    (29,973)    (56,369)   (200,910)    (65,053)
                                                     ----------  ----------  ----------  ----------  ----------
    Net cash provided by (used for) investing
      activities...................................   1,116,431    (967,975) (2,142,299) (2,569,091)  2,752,898
                                                     ----------  ----------  ----------  ----------  ----------
CASH FLOWS FROM FINANCING ACTIVITIES
Proceeds from issuance of convertible debt.........   2,100,000     400,000      --          --          --
Sale of common stock...............................      65,209       2,017       6,759      --           9,369
Repurchase of common stock.........................      --          --          (9,363)     (9,363)     --
Sale of preferred stock, net of issuance costs.....     192,236   3,955,366   7,255,956   5,270,096      --
Sale of fixed assets...............................     129,528      38,078      --          --          --
Principal payments on capital lease obligations....    (222,650)   (373,143)   (470,069)   (184,932)   (481,309)
Payments from stockholder..........................      --           9,375      --          --          --
                                                     ----------  ----------  ----------  ----------  ----------
  Net cash provided by (used for) financing
    activities.....................................   2,264,323   4,031,693   6,783,283   5,075,801    (471,940)
                                                     ----------  ----------  ----------  ----------  ----------
Net increase (decrease) in cash and cash
  equivalents......................................    (496,185)   (680,760)  1,072,953     (49,113)   (456,129)
Cash and cash equivalents at beginning of period...   1,418,297     922,112     241,352     241,352   1,314,305
                                                     ----------  ----------  ----------  ----------  ----------
Cash and cash equivalents at end of period.........  $  922,112  $  241,352  $1,314,305  $  192,239  $  858,176
                                                     ----------  ----------  ----------  ----------  ----------
                                                     ----------  ----------  ----------  ----------  ----------
SUPPLEMENTAL DISCLOSURE OF CASH FLOW INFORMATION
Cash paid during the period for interest...........  $  135,460  $  135,334  $   98,599  $   90,624  $  103,514
SCHEDULE OF NON-CASH FINANCING ACTIVITIES
Assets recorded under capital lease................     971,455     164,919     375,564     169,304     482,868
Purchase of treasury stock in exchange for accounts
  payable..........................................      --          26,400      --          --          --
Issuance of warrants to lessor.....................     100,000      --          --          --          --
Issuance of common stock in exchange for note
  receivable.......................................      37,500      --          --          --          --
Issuance of preferred stock to cancel notes payable
  and accrued interest.............................      --       2,579,086      --          --          --
</TABLE>
 
    During 1995, the Company cancelled a note receivable from a stockholder of
$28,125 in exchange for treasury stock of $19,387 and a receivable from a
stockholder of $8,738 (Note 5).
 
   The accompanying notes are an integral part of these financial statements.
 
                                      F-7
<PAGE>
                        SCRIPTGEN PHARMACEUTICALS, INC.
 
                         NOTES TO FINANCIAL STATEMENTS
 
1. NATURE OF BUSINESS AND ORGANIZATION
 
    Scriptgen Pharmaceuticals, Inc. (the "Company") was incorporated in
September 1992. The Company utilizes its proprietary high throughput
technologies to enable and accelerate the discovery of innovative small molecule
drugs. The Company's technology platform identifies and validates novel gene
targets for therapeutic intervention, and then uses novel assay systems to
rapidly screen compounds against those targets. The Company commercializes its
technology through collaborations with pharmaceutical and technology companies
and the Company's internal development program.
 
    Through 1995, the Company devoted substantially all of its efforts to
research and development, business planning and financings and was considered to
be in the development stage as defined in Statement of Financial Accounting
Standards No. 7, "Accounting and Reporting by Development Stage Enterprises."
The Company is no longer considered to be a development stage enterprise as
planned operations commenced in 1996.
 
2. SIGNIFICANT ACCOUNTING POLICIES
 
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 revenue and expenses during the reporting
period. Actual amounts could differ from those estimates.
 
CASH EQUIVALENTS AND SHORT-TERM INVESTMENTS
 
    The Company considers all highly liquid instruments with an original
maturity of three months or less to be cash equivalents. The Company invests its
excess cash primarily in short-term marketable securities. Accordingly, these
investments are subject to minimal credit and market risk.
 
    The Company's cash equivalents at December 31, 1995 consisted of
approximately $82,000 in money market funds. The Company's cash equivalents at
December 31, 1996 consisted of approximately $16,000 in money market funds,
$260,000 in time deposits and $720,000 in commercial paper.
 
    Short-term investments at December 31, 1995 consisted of approximately
$938,000 in U.S. Treasury Bills. Short-term investments at December 31, 1996
consisted of approximately $2,286,000 in U.S. Treasury Bills and $738,000 in
U.S. Agency Bonds. These securities are classified as available-for-sale and are
recorded at cost which approximates fair value. Any unrealized gains or losses
are recorded as a separate component of stockholders' equity. Gross unrealized
and realized gains and losses on sales of securities at December 31, 1995 and
1996 and for the years ended December 31, 1994, 1995 and 1996 were not
significant.
 
REVENUE RECOGNITION AND ACCOUNTS RECEIVABLE
 
   
    The Company has entered into various collaborative agreements with
pharmaceutical and technology companies. Revenue derived from such collaborative
agreements is recognized as drug discovery activities are performed. Cash
received in advance of activities performed is recorded as deferred revenue.
Certain agreements also provide for payments to the Company upon the achievement
of certain milestones as well as royalties on the net sales of any products
developed resulting from the collaborations, as defined in the respective
agreements. Any revenue related to milestones will be recognized as the
milestones are achieved and revenue related to royalties will be recognized as
earned.
    
 
                                      F-8
<PAGE>
                        SCRIPTGEN PHARMACEUTICALS, INC.
 
                   NOTES TO FINANCIAL STATEMENTS (CONTINUED)
 
2. SIGNIFICANT ACCOUNTING POLICIES (CONTINUED)
    Revenue from Small Business Innovation Research ("SBIR") government grants
to conduct research and development is recognized as eligible costs are incurred
up to the funding limit. Eligible grant-related costs which have been incurred
in advance of cash receipts are recorded as receivables.
 
CONCENTRATION OF CREDIT RISK AND SIGNIFICANT CUSTOMERS
 
    Financial instruments which potentially expose the Company to concentrations
of credit risk consist primarily of trade accounts receivable. Management
believes its credit policies are prudent and reflect normal industry terms and
business risk. The Company does not anticipate non-performance by the
counterparties and, accordingly, does not require collateral.
 
    For the years ended December 31, 1995 and 1996, certain customers accounted
for more than 10% of the Company's revenue. One customer accounted for 100% of
revenue in 1995. Two customers accounted for 81% and 19% of revenue,
respectively, in 1996. Two customers accounted for 77% and 23% of revenue,
respectively, in the nine months ended September 30, 1997.
 
PROPERTY AND EQUIPMENT
 
    Equipment, furniture and fixtures are recorded at cost and are being
depreciated using the straight-line method over estimated useful lives of five
years. Leasehold improvements are stated at cost and are being amortized using
the straight-line method over the term of the lease, which is less than the
estimated useful life of the properties.
 
PATENT COSTS
 
    Costs associated with patent applications have been expensed as incurred to
date primarily because recovery of these costs is uncertain. However, certain
costs associated with patent applications for products and processes where
recovery is probable will be capitalized and amortized over their estimated
economic life. Through December 31, 1996, capitalizable patent costs have not
been significant and no patent costs have been capitalized.
 
IMPAIRMENT OF LONG-LIVED ASSETS
 
    The Company periodically assesses whether any events or changes in
circumstances have occurred that would indicate that the carrying amount of a
long-lived asset may not be recoverable. When such an event or change in
circumstance occurs, the Company evaluates whether the carrying amount of such
asset is recoverable by comparing the net book value of the asset to estimated
future undiscounted cash flows, excluding interest charges, attributable to such
asset. If it is determined that the carrying amount is not recoverable, the
Company recognizes an impairment loss equal to the excess of the carrying amount
of the asset over the estimated fair value of such asset.
 
ACCOUNTING FOR STOCK-BASED COMPENSATION
 
    In October 1995, the Financial Accounting Standards Board ("FASB") issued
Statement of Financial Accounting Standards ("SFAS") No. 123, "Accounting for
Stock-Based Compensation." SFAS 123, which is effective for the Company's 1996
financial statements, defines a fair value based method of accounting for
stock-based awards to employees. The Company has elected to account for
stock-based awards to its employees using the intrinsic value based method as
prescribed by APB Opinion No. 25, "Accounting for Stock Issued to Employees,"
and related Interpretations and has adopted the provisions of SFAS 123 through
disclosure only (Note 6).
 
                                      F-9
<PAGE>
                        SCRIPTGEN PHARMACEUTICALS, INC.
 
                   NOTES TO FINANCIAL STATEMENTS (CONTINUED)
 
2. SIGNIFICANT ACCOUNTING POLICIES (CONTINUED)
NET LOSS PER SHARE, UNAUDITED PRO FORMA NET LOSS PER SHARE AND UNAUDITED PRO
  FORMA INFORMATION
 
    Net loss per share and unaudited pro forma net loss per share are determined
by dividing net loss by the weighted average number of common shares and common
share equivalents outstanding during the period. Common share equivalents,
comprised of common stock options and warrants and convertible preferred stock,
have been excluded from the calculation as their effect is anti-dilutive, except
that, pursuant to Securities and Exchange Commission Staff Accounting Bulletin
No. 83, common share equivalents issued and common stock sold at prices below
the initial public offering price in the twelve months preceding the initial
filing of the Company's Registration Statement and through the effective date of
the initial public offering have been included in the calculation as if
outstanding for all periods presented.
 
    As described in Note 5, conversion of all redeemable convertible preferred
stock will occur upon the closing of a qualified public offering of the
Company's common stock. The unaudited pro forma net loss per share information
included in the accompanying statement of operations for the year ended December
31, 1996 and for the nine months ended September 30, 1997 reflects the impact on
unaudited pro forma net loss per share of such conversion as of the beginning of
each period or date of issuance, if later, using the if-converted method.
 
    The unaudited pro forma information at September 30, 1997 included in the
balance sheet and the statement of redeemable preferred stock and stockholders'
equity (deficit) reflects the issuance of 5,713,034 shares of Series D
redeemable convertible preferred stock for $20,000,000, the value associated
with the issuance of a warrant to purchase 464,537 shares of common stock, the
retirement of 358,758 shares of treasury stock, all as discussed in Note 10, and
the automatic conversion of each share of the redeemable convertible preferred
stock into 0.32525 shares of common stock upon the closing of the Company's
anticipated initial public offering.
 
UNAUDITED INTERIM FINANCIAL DATA
 
    The interim financial data as of September 30, 1997 and for the nine months
ended September 30, 1996 and 1997 are unaudited; however, in the opinion of
management, the interim financial data include all adjustments, consisting only
of normal recurring adjustments, necessary for a fair presentation of the
results of operations for these interim periods. The interim financial data are
not necessarily indicative of the results of operations for a full year.
 
RECENTLY ENACTED ACCOUNTING PRONOUNCEMENTS
 
   
    In February 1997, the FASB issued SFAS No. 128, "Earnings per Share", which
changes the method of calculating earnings per share. This standard becomes
effective in the Company's fourth quarter of 1997 and requires retroactive
restatement for all periods presented. SFAS No. 128 requires the presentation of
"basic" earnings per share and "diluted" earnings per share. Basic earnings per
share is computed by dividing net income by weighted average shares of
outstanding common stock. For purposes of calculating diluted earnings per
share, the denominator includes both weighted average shares of common stock
outstanding and dilutive potential common stock. In addition, on February 3,
1998, the Securities and Exchange Commission issued Staff Accounting Bulletin
("SAB") No. 98, which supersedes SAB No. 83 upon a company's adoption of SFAS
No. 128 and includes new guidance with respect to earnings per share
computations in an initial public offering. The Company will adopt SFAS No. 128
and SAB No. 98 in the fourth quarter of 1997. For periods subsequent to the
quarter in which the initial public offering is completed, the adoption of SFAS
No. 128 is not expected to have a material effect on net loss per share. For
each of the three years ended December 31, 1996 and the nine months ended
September 30, 1996
    
 
                                      F-10
<PAGE>
                        SCRIPTGEN PHARMACEUTICALS, INC.
 
                   NOTES TO FINANCIAL STATEMENTS (CONTINUED)
 
2. SIGNIFICANT ACCOUNTING POLICIES (CONTINUED)
   
(unaudited) and 1997 (unaudited), the Company is currently evaluating, and has
not yet determined, the effect that SAB No. 98 will have on net loss per share
and unaudited pro forma net loss per share for such periods. The Company does
expect, however, that basic and diluted net loss per share and unaudited basic
and diluted pro forma net loss per share calculated pursuant to SFAS No. 128 and
SAB No. 98 will exceed reported amounts for such periods.
    
 
   
    In September 1997, the FASB issued SFAS No. 130, "Reporting Comprehensive
Income" and SFAS No. 131, "Disclosures about Segments of an Enterprise and
Related Information." The Company will implement SFAS No. 130 and SFAS No. 131,
which require the Company to report and display certain information related to
comprehensive income and operating segments, respectively, as required in fiscal
1998. Adoption of SFAS No. 130 and SFAS No. 131 will not impact the Company's
financial position or results of operations.
    
 
3. PROPERTY AND EQUIPMENT
 
    Property and equipment consist of the following:
 
<TABLE>
<CAPTION>
                                                                           DECEMBER 31,
                                                                    --------------------------
<S>                                                                 <C>           <C>
                                                                        1995          1996
                                                                    ------------  ------------
Furniture and fixtures............................................  $      8,947  $      8,947
Equipment.........................................................     1,350,895     1,782,828
Leasehold improvements............................................       677,950       677,950
                                                                    ------------  ------------
                                                                       2,037,792     2,469,725
Less: Accumulated depreciation and amortization...................       774,950     1,352,011
                                                                    ------------  ------------
                                                                    $  1,262,842  $  1,117,714
                                                                    ------------  ------------
                                                                    ------------  ------------
</TABLE>
 
    Depreciation and amortization expense for the years ended December 31, 1994,
1995 and 1996 was $289,557, $498,175 and $577,061, respectively.
 
    At December 31, 1995 and 1996, the costs of equipment and leasehold
improvements held under capital leases amounted to $1,943,932 and $2,319,496,
respectively, and accumulated depreciation relating to such equipment and
leasehold improvements amounted to $485,780 and $1,028,328, respectively.
 
4. CONVERTIBLE DEBT
 
    In July 1994, the Company entered into a Loan and Stock Purchase Agreement
with certain preferred stockholders to provide bridge financing for the Company.
The agreement made available to the Company up to $2,500,000 in financing.
During 1994 and 1995, the Company issued notes in the aggregate amount of
$2,100,000 and $400,000, respectively, to these investors. The notes were
interest bearing at a rate of 4.25% until December 31, 1994 and 9.50% from
January 1, 1995 until April 19, 1995, when these notes, together with accrued
interest thereon, were converted into shares of Series B Preferred Stock at
$1.00 per share.
 
5. CAPITALIZATION
 
REDEEMABLE CONVERTIBLE PREFERRED STOCK
 
    The Company has authorized 21,500,000 shares of redeemable convertible
preferred stock designated as follows: 5,100,000 shares of Series A redeemable
convertible preferred stock ("Series A Preferred Stock"); 9,700,000 shares of
Series B redeemable convertible preferred stock ("Series B Preferred Stock");
and 6,700,000 shares of Series C redeemable convertible preferred stock ("Series
C Preferred Stock")
 
                                      F-11
<PAGE>
                        SCRIPTGEN PHARMACEUTICALS, INC.
 
                   NOTES TO FINANCIAL STATEMENTS (CONTINUED)
 
5. CAPITALIZATION (CONTINUED)
(collectively as the "Preferred Stock"). The Series A, B and C Preferred Stock
have the following characteristics:
 
    CONVERSION
 
    Each share of Preferred Stock is convertible at any time at the option of
the holder into shares of common stock at a ratio of one share of common stock
for 3.07459 shares of Preferred Stock, subject to certain stock split, stock
dividend and other adjustments. All Preferred Stock will automatically convert
to common stock upon the earlier of i) the closing of a public offering of the
Company's common stock involving aggregate proceeds of at least $10,000,000 and
a per share price of not less than $7.00 or ii) the consent of the holders of at
least 85% of the then outstanding shares of Preferred Stock.
 
    The Company has reserved 2,082,660, 2,139,826 and 1,318,502 shares of common
stock for issuance upon the conversion of the Series A Preferred Stock, Series B
Preferred Stock and Series C Preferred Stock, respectively.
 
    DIVIDENDS
 
    Holders of Series C Preferred Stock are entitled to receive dividends when,
as and if declared by the Board of Directors.
 
    Holders of Series B Preferred Stock are entitled to receive dividends when,
as and if declared by the Board of Directors, provided however that no dividends
shall be declared or paid on the Series B Preferred Stock unless the Company
shall simultaneously declare and pay an equal dividend on each outstanding share
of Series C Preferred Stock.
 
    Holders of Series A Preferred Stock are entitled to receive dividends when,
as and if declared by the Board of Directors, provided however that no dividend
shall be declared or paid on the Series A Preferred Stock unless the Company
shall simultaneously declare and pay an equal dividend on each outstanding share
of Series B and Series C Preferred Stock. Through December 31, 1996, no
dividends have been declared or paid by the Company.
 
    REDEMPTION
 
    On January 15, 2004 and 2005, the Company shall redeem 50% of the then
outstanding shares of Preferred Stock at a per share price of $1.80 for each
share of Series C Preferred Stock and $1.00 for each share of Series A Preferred
Stock and Series B Preferred Stock, plus all declared but unpaid dividends,
unless such redemption is waived by holders of 75% of the then outstanding
shares of Preferred Stock.
 
    At December 31, 1996, there are issued and outstanding 6,403,325 shares of
Series A Preferred Stock, 6,579,086 shares of Series B Preferred Stock and
4,053,854 shares of Series C Preferred Stock, which are recorded at redemption
values of $6,403,325, $6,579,086 and $7,296,937, respectively.
 
    LIQUIDATION, DISSOLUTION OR WINDING-UP OF COMPANY
 
    In the event of any liquidation, dissolution, or winding up of the Company,
the holders of Series A Preferred Stock, Series B Preferred Stock and Series C
Preferred Stock will be entitled to receive, in preference to the holders of the
common stock, an amount per share equal to $1.00, $1.00 and $1.80, respectively,
plus any declared but unpaid dividends. If the remaining assets of the Company
are insufficient to pay the preferred stockholders the full amount to which they
are entitled, any distribution of the remaining assets will be in proportion to
the respective amounts which would otherwise be payable if
 
                                      F-12
<PAGE>
                        SCRIPTGEN PHARMACEUTICALS, INC.
 
                   NOTES TO FINANCIAL STATEMENTS (CONTINUED)
 
5. CAPITALIZATION (CONTINUED)
all amounts payable were paid in full. Any assets remaining after the initial
distribution to the holders of the Preferred Stock shall be available for
distribution ratably among the Company's common stockholders.
 
    VOTING RIGHTS
 
    Each holder of the Preferred Stock is entitled to vote the number of shares
of common stock into which such holder's shares are convertible at the date such
vote is taken.
 
    RIGHTS OF FIRST REFUSAL
 
    The holders of the Preferred Stock have the right of first refusal on all
future issuances by the Company of any of its equity securities.
 
STOCK RESTRICTION AGREEMENTS
 
    The Company has executed stock restriction agreements with certain common
stockholders. Each agreement gives the Company the right to repurchase a certain
number of shares, at the original issuance price, held by such stockholder if he
or she ceases to be a director, employee or consultant, as applicable, of the
Company. The purchase option rights lapse at various dates through July 1998. At
December 31, 1996 and September 30, 1997 (unaudited), 15,395 and 28,963,
respectively, shares of the Company's outstanding common stock were subject to
these repurchase options.
 
REVERSE COMMON STOCK SPLIT
 
    On December 12, 1997, the Board of Directors authorized a 1-for-3.07459
reverse stock split of the Company's common stock which became effective on
February 2, 1998. All shares of common stock, common stock options and warrants,
preferred stock conversion ratios and per share amounts included in the
accompanying financial statements have been adjusted to give retroactive effect
to the reverse stock split for all periods presented.
 
RELATED PARTY TRANSACTIONS
 
    The Company entered into a stock agreement with an officer of the Company in
February 1994 whereby the Company issued 464,452 shares of common stock and
200,000 shares of Series A Preferred Stock to this individual in exchange for
cash and a promissory note totaling $271,400. Such promissory note was paid in
four quarterly equal installments commencing February 1, 1995.
 
    The underlying stock agreement gave the Company repurchase rights to the
stock in certain increments at a price equal to the price per share paid by this
individual. Such repurchase rights lapsed at certain dates or upon the
occurrence of certain events, as defined in the agreement.
 
    The Company entered into a separation agreement with this officer in
December 1995. Under the separation agreement, the Company was obligated to
extend the officer's salary, for a period of one year from the resignation date
or until the officer accepts full-time employment, whichever occurred first, as
well as other related costs. For the year ended December 31, 1995, the Company
recorded total compensation expense of approximately $275,000 in connection with
this agreement. The unpaid portion of the compensation expense of approximately
$265,000 was reflected in accrued expenses at December 31, 1995 and was paid in
full in 1996.
 
                                      F-13
<PAGE>
                        SCRIPTGEN PHARMACEUTICALS, INC.
 
                   NOTES TO FINANCIAL STATEMENTS (CONTINUED)
 
5. CAPITALIZATION (CONTINUED)
 
    Pursuant to the terms of the separation agreement, in 1995 the Company
exercised its repurchase rights to 297,845 shares of the Company's common stock
issued under the February 1994 stock agreement. The promissory note received in
conjunction with the stock agreement was cancelled. In 1996, the Company
exercised its repurchase rights to the remaining unvested 48,787 shares of the
Company's common stock issued under the February 1994 stock agreement.
 
6. STOCK PLAN
 
    During 1994, the Company adopted its 1994 Stock Option Plan (the "Plan").
The Plan provides for the issuance of incentive stock options to officers and
other employees of the Company and non-qualified stock options, awards of stock
and direct stock purchase opportunities to directors, officers, employees and
consultants of the Company. The total number of shares which may be issued under
the Plan is 613,090. The options are exercisable at various dates and will
expire no more than ten years from their date of grant, or in the case of
certain non-qualified options, fifteen years from the date of grant. The
exercise price of each option shall be determined by the Board of Directors. In
the case of incentive stock options, the exercise price may not be less than
100% of the fair market value of the share at the time the option is granted.
For holders of more than 10% of the Company's total combined voting power of all
classes of stock, incentive stock options may not be granted at less than 110%
of the fair market value of the Company's common stock at the date of grant and
may not exceed a term of five years.
 
    At December 31, 1996, the Company had one stock option plan, which is
described above. The Company applies APB Opinion No. 25 in accounting for awards
made under the Plan.
 
    Had compensation cost for these awards been determined based on the fair
value of these options at their date of grant consistent with the method
prescribed by SFAS No. 123, the Company's net loss would have been as follows:
 
<TABLE>
<CAPTION>
                                                                           YEAR ENDED
                                                                          DECEMBER 31,
                                                                  ----------------------------
<S>                                                               <C>            <C>
                                                                      1995           1996
                                                                  -------------  -------------
Net loss:
  As reported...................................................  $  (4,578,927) $  (4,044,019)
  Pro forma.....................................................     (4,578,933)    (4,046,130)
</TABLE>
 
    Because the determination of the fair value of all options granted after the
Company becomes a public entity will include an expected volatility factor,
additional option grants are expected to be made subsequent to December 31, 1996
and options vest over several years, the pro forma effects of applying the fair
value method may be material to reported net income or loss in future years.
 
    The fair value of each option grant is estimated on the date of grant using
the Black-Scholes option-pricing model to apply the minimum value method with
the following weighted average assumptions:
 
<TABLE>
<CAPTION>
                                                                                 1995       1996
                                                                               ---------  ---------
<S>                                                                            <C>        <C>
Expected options term (years)................................................       5          5
Risk-free interest rate......................................................       7.02%      6.14%
Dividend yield...............................................................       0.00%      0.00%
</TABLE>
 
                                      F-14
<PAGE>
                        SCRIPTGEN PHARMACEUTICALS, INC.
 
                   NOTES TO FINANCIAL STATEMENTS (CONTINUED)
 
6. STOCK PLAN (CONTINUED)
    A summary of the status of the Company's fixed stock option plan as of
December 31, 1996 and changes during the three year period ended on that date is
presented below:
 
<TABLE>
<CAPTION>
                                                                     YEAR ENDED DECEMBER 31,
                                            --------------------------------------------------------------------------
                                                     1994                     1995                      1996
                                            -----------------------  -----------------------  ------------------------
                                                         WEIGHTED-                WEIGHTED-                 WEIGHTED-
                                                          AVERAGE                  AVERAGE                   AVERAGE
                                                         EXERCISE                 EXERCISE                  EXERCISE
                                              SHARES       PRICE       SHARES       PRICE       SHARES        PRICE
                                            ----------  -----------  ----------  -----------  -----------  -----------
<S>                                         <C>         <C>          <C>         <C>          <C>          <C>
Outstanding at beginning of year..........      --       $  --          299,015   $     .15       308,155   $     .15
Granted...................................     299,503         .15        9,953         .15       210,207         .15
Exercised.................................        (335)        .15         (558)        .15      (174,064)        .15
Forfeited.................................        (153)        .15         (255)        .15       (11,717)        .15
                                            ----------               ----------               -----------
Outstanding at end of year................     299,015   $     .15      308,155   $     .15       332,581   $     .15
                                            ----------               ----------               -----------
Options available for future grant........     313,740                  304,042                   105,552
                                            ----------               ----------               -----------
Weighted-average fair value of options
  granted whose exercise price of $.15
  equals the market price.................  $      .03               $      .03               $       .03
                                            ----------               ----------               -----------
                                            ----------               ----------               -----------
Weighted-average fair value of options
  granted whose exercise price of $.15 is
  less than the market price..............  $   --                   $   --                   $      1.72
                                            ----------               ----------               -----------
                                            ----------               ----------               -----------
</TABLE>
 
    The following table summarizes information about fixed stock options
outstanding at December 31, 1996.
 
<TABLE>
<CAPTION>
                                                                   OPTIONS
                                                                 OUTSTANDING
                                                            ----------------------
                                                                        WEIGHTED-
                                                                         AVERAGE      OPTIONS
                                                                        REMAINING   EXERCISABLE
                                                                       CONTRACTUAL  -----------
EXERCISE PRICE                                               NUMBER       LIFE        NUMBER
- ----------------------------------------------------------  ---------  -----------  -----------
<S>                                                         <C>        <C>          <C>
$.15......................................................    332,581   8.8 years       59,890
</TABLE>
 
UNEARNED COMPENSATION
 
    During October 1996 through December 1996, the Company granted stock options
to purchase 105,461 shares of its common stock at an exercise price of $.15 per
share. The Company recorded unearned compensation totaling $178,338,
representing the difference between the estimated fair market value of the
common stock on the date of grant and the exercise price. Unearned compensation
related to these options is recorded as an increase to stockholders' deficit and
is being amortized over the option vesting period.
 
                                      F-15
<PAGE>
                        SCRIPTGEN PHARMACEUTICALS, INC.
 
                   NOTES TO FINANCIAL STATEMENTS (CONTINUED)
 
6. STOCK PLAN (CONTINUED)
(Unaudited)
 
    During the nine months ended September 30, 1997, the Company granted options
to purchase 407,859 shares of its common stock at exercise prices of $.15 and
$6.15 per share. The Company recorded unearned compensation totaling $2,714,750
for such options.
 
7. INCOME TAXES
 
    Deferred tax assets and (liabilities) are comprised of the following:
 
<TABLE>
<CAPTION>
                                                                           DECEMBER 31,
                                                                    --------------------------
<S>                                                                 <C>           <C>
                                                                        1995          1996
                                                                    ------------  ------------
Net operating loss carryforwards..................................  $  4,582,000  $  6,210,000
Research and development credit carryforwards.....................       426,000       604,000
Property and equipment............................................       194,000       268,000
Accrued expenses..................................................       123,000        18,000
Deferred start-up expenses........................................        34,000        17,000
                                                                    ------------  ------------
Deferred tax assets, net..........................................     5,359,000     7,117,000
Valuation allowance...............................................    (5,359,000)   (7,117,000)
                                                                    ------------  ------------
                                                                    $    --       $    --
                                                                    ------------  ------------
                                                                    ------------  ------------
</TABLE>
 
    The Company has generated taxable losses from operations since inception
and, accordingly, has no taxable income available to offset the carryback of net
operating losses. In addition, although management's operating plans anticipate
taxable income in future periods, such plans provide for taxable losses over the
near term and make significant assumptions which cannot be reasonably assured,
including approval of the Company's products by the U.S. Food and Drug
Administration and market acceptance of the Company's products by customers.
Based upon the weight of all available evidence, the Company has provided a full
valuation allowance for its deferred tax assets since, in the opinion of
management, realization of these future benefits is not sufficiently assured
(defined as a likelihood of slightly more than 50 percent).
 
    As of December 31, 1996, the Company has net operating loss carryforwards
and research and development credit carryforwards which may be used to offset
future federal and state taxable income and tax liabilities as follows:
 
<TABLE>
<CAPTION>
                                                                            RESEARCH AND
                                                                          DEVELOPMENT TAX
                                                                               CREDIT
                                                        NET OPERATING  ----------------------
YEAR OF EXPIRATION                                          LOSS        FEDERAL      STATE
- ------------------------------------------------------  -------------  ----------  ----------
<S>                                                     <C>            <C>         <C>
2007..................................................  $     338,000  $   22,000  $   12,000
2008..................................................      2,708,000      74,000      37,000
2009..................................................      4,076,000     124,000      62,000
2010..................................................      4,250,000      66,000     101,000
2011..................................................      4,085,000     121,000      87,000
                                                        -------------  ----------  ----------
                                                        $  15,457,000  $  407,000  $  299,000
                                                        -------------  ----------  ----------
                                                        -------------  ----------  ----------
</TABLE>
 
                                      F-16
<PAGE>
                        SCRIPTGEN PHARMACEUTICALS, INC.
 
                   NOTES TO FINANCIAL STATEMENTS (CONTINUED)
 
7. INCOME TAXES (CONTINUED)
    As a result of the issuance of redeemable convertible preferred stock (Note
5), a change in ownership has occurred as defined by the Internal Revenue code
which may significantly restrict future annual utilization of the Company's
federal NOL carryforwards. Under the provisions of the Internal Revenue Code,
certain substantial changes in the Company's ownership may limit the amount of
the net operating loss and tax credit carryforwards which could be utilized
annually to offset future taxable income and taxes payable. The amount of the
annual limitation is determined based upon the Company's value prior to an
ownership change. Subsequent significant ownership changes could further affect
the limitation in future years.
 
8. COMMITMENTS AND CONTINGENCIES
 
    In November 1993, the Company entered into a five-year operating lease for
office and research space. The lease requires the Company to pay a share of real
estate taxes and building operating expenses if such expenses exceed a base
level stipulated in the lease.
 
    In January 1994, the Company entered into a leasing arrangement whereby a
third party will provide up to $1,700,000 in equipment financing. In connection
with this agreement, the Company granted to the lessor warrants to purchase
153,000 shares of Series A Preferred Stock at a price of $1.00 per share. The
warrants expire in January 2004 or five years from the closing of the sale and
issuance of shares of the Company's common stock in an initial public offering,
whichever is later. The Company ascribed a value of $100,000 to such warrants,
which is included in other assets and is being amortized over the life of the
lease financing.
 
    In February 1996, the Company entered into a leasing arrangement with this
same third party who will provide up to $1,436,775 in additional equipment
financing. In connection with this agreement, the Company initially granted to
the lessor warrants to purchase 32,500 shares of Series C Preferred Stock at a
price of $1.80 per share. As of December 31, 1996, the Company is committed to
grant an additional 67,500 warrants upon commencement of certain phases of the
financing. The warrants expire in May 2006 or five years from the closing of the
sale and issuance of the Company's common stock in an initial public offering,
whichever is later. The value ascribed to the warrants granted was not
significant.
 
    Future minimum lease payments required under operating and capital leases as
of December 31, 1996 are as follows:
 
<TABLE>
<CAPTION>
                                                                      OPERATING     CAPITAL
                                                                        LEASES       LEASES
                                                                      ----------  ------------
<S>                                                                   <C>         <C>
1997................................................................  $  105,308  $    628,319
1998................................................................      87,757       301,656
1999................................................................      --           129,500
2000................................................................      --            26,095
                                                                      ----------  ------------
Total minimum lease payments........................................  $  193,065     1,085,570
                                                                      ----------
                                                                      ----------
Amount representing interest........................................                  (102,502)
                                                                                  ------------
Present value of minimum lease payments.............................              $    983,068
                                                                                  ------------
                                                                                  ------------
</TABLE>
 
    Rent expense for the years ended December 31, 1994, 1995 and 1996 was
approximately $185,000, $108,000 and $128,000, respectively.
 
                                      F-17
<PAGE>
                        SCRIPTGEN PHARMACEUTICALS, INC.
 
                   NOTES TO FINANCIAL STATEMENTS (CONTINUED)
 
8. COMMITMENTS AND CONTINGENCIES (CONTINUED)
    Obligations under capital lease have interest rates which range from 8% to
15% at December 31, 1996.
 
    Under certain licensing and other agreements, the Company is required to
make payments upon the achievement of certain milestones, to pay royalties on
certain drug sales, if any, and to pay other amounts in connection with
sublicenses, if any (collectively "Contingent Payments"). To date, the Company
has not become obligated to make any Contingent Payments under such agreements.
In addition, pursuant to several license and sponsored research agreements, the
Company is obligated to make certain payments through 1998 of up to
approximately $400,000.
 
9. SAVINGS PLAN
 
    The Company has a retirement savings plan for all employees pursuant to
Section 401(k) of the Internal Revenue Code. Employees become eligible to
participate upon completion of six months of service to the Company. Employees
may contribute any whole percentage of their salary, up to a maximum annual
statutory limit. The Company is not required to contribute to this plan and has
made no contributions to date.
 
10. SUBSEQUENT EVENTS
 
    In October 1997, the Company entered into a collaboration agreement with
Hoechst Marion Roussel ("HMR") to identify new fungal targets and antifungal
drug candidates. The agreement requires HMR to pay initial technology access
fees in the amount of $6 million, certain payments for research and development
and additional payments upon the attainment of certain milestones, plus
royalties on sales of any new drug resulting from the collaboration. As part of
this agreement, HMR has agreed to purchase shares of common stock having a value
of $3,000,000 (based on the initial public offering price) in a private
placement concurrently with the Company's initial public offering. The Company
has granted certain piggyback registration rights to HMR relating to such
shares.
 
    In December 1997, the Company authorized and issued 5,713,034 shares of
Series D redeemable convertible preferred stock for $20,000,000 to BioChem
Pharma Inc. ("BioChem") which have similar terms to those of the Series A, B and
C redeemable convertible preferred stock, except that the Series D stock is
redeemable at the option of the holder at a price per share of $3.50. In the
event that the initial public offering price is less than $10.76 per share, then
the Company will be required to issue to BioChem, for no additional
consideration, the number of additional shares of common stock equal to the
amount by which (a) 19,993,640 divided by the initial public offering price,
exceeds (b) 1,858,145. The Company also entered into a collaboration agreement
with BioChem pursuant to which the Company is using its technologies to identify
drug candidates. The Company is responsible for all aspects of drug discovery
and BioChem is responsible for pre-clinical and clinical development, and will
retain worldwide commercialization rights. Any profits on any commercialized
products emanating from these programs will be shared in accordance with the
terms of the agreement. In addition, the Company issued to BioChem a warrant to
purchase 464,537 shares of common stock at an initial exercise price of $13.47
per share, which expire in December 2002. The initial exercise price may be
adjusted downward in the event the Company sells any shares of common stock at a
price below the current exercise price (with the exception of excluded stock, as
defined by the agreement, including shares being sold in the Offering). The
adjustment provisions will terminate upon the closing of an initial public
offering of the Company's common stock having an aggregate offering value of at
least $25 million. The Company has ascribed an initial value to the warrant
 
                                      F-18
<PAGE>
                        SCRIPTGEN PHARMACEUTICALS, INC.
 
                   NOTES TO FINANCIAL STATEMENTS (CONTINUED)
 
10. SUBSEQUENT EVENTS (CONTINUED)
of approximately $2,200,000 which will be charged to research and development
expense in the fourth quarter of 1997.
 
    In December 1997, the Company adopted the 1997 Equity Incentive Plan (the
"1997 Plan"). The 1997 Plan provides for the issuance of up to 1,700,000 shares
of the Company's common stock to eligible employees, directors, consultants and
advisors of the Company. Under the 1997 Plan, the Board of Directors may award
incentive and non-qualified stock options, stock appreciation rights,
performance shares and restricted and unrestricted stock. Incentive stock
options may not be granted at less than the fair market value of the Company's
common stock at the date of grant and for a term not to exceed ten years. For
holders of more than 10% of the Company's total combined voting power of all
classes of stock, incentive stock options may not be granted at less than 110%
of the fair market value of the Company's common stock at the date of grant and
for a term not to exceed five years. The exercise price under each non-qualified
stock option shall be specified by the Board of Directors, or a committee
appointed by the Board of Directors, in accordance with the guidelines set forth
in the 1997 Plan. Grants of stock appreciation rights, performance shares,
restricted stock and unrestricted stock may be made at the discretion of the
Board of Directors with terms to be defined therein.
 
    In December 1997, the Company adopted the Non-Employee Directors Stock Plan
(the "Directors' Plan") which provides for the issuance of up to 250,000 shares
of the Company's common stock to directors of the Company who are not current or
former employees of the Company ("Non-Employee Directors"). Under the Directors'
Plan, each Non-Employee Director will receive options to purchase 10,000 shares
of common stock on the date of the final prospectus used in connection with the
Company's initial public offering. Thereafter, on the date of each annual
meeting of the stockholders of the Company, each Non-Employee Director
continuing in office will receive options to purchase 4,000 shares of common
stock and each newly elected Non-Employee Director will receive options to
purchase 10,000 shares of common stock. In addition, each Non-Employee Director
who is a member of a committee of the Company's Board of Directors will receive
options to purchase 250 shares of common stock on each one year anniversary of
his or her appointment to such committee. Options granted under the Directors'
Plan will have exercise prices equal to the fair market value of the Company's
common stock on the date of the grant. The exercise price of options granted
under the Director's Plan on the date of the final prospectus used in connection
with the Company's initial public offering will equal the offering price to the
public. All options granted under the Directors' Plan vest in three annual
installments and expire ten years from the date of grant. All options
outstanding under the Directors' Plan will become immediately exercisable upon
the occurrence of a change in control as defined in the Directors' Plan.
 
    In December 1997, the Company cancelled all of its treasury stock and such
shares resumed the status of authorized and unissued shares of common stock. In
addition, the Company increased the number of shares of common stock authorized
for issuance to 35,000,000. In December 1997, the Board of Directors approved
the authorization of 4,000,000 shares of preferred stock available for issuance,
which will become effective after the closing of the Company's initial public
offering.
 
                                      F-19
<PAGE>
No dealer, salesperson or other person has been authorized to give any
information or to make any representation other than those contained in this
Prospectus in connection with the offer contained herein, and, if given or made,
such information or representation must not be relied upon as having been
authorized by the Company or any Underwriter. This Prospectus does not
constitute an offer to sell, or a solicitation of an offer to buy, shares of
Common Stock in any jurisdiction to any person to whom it is not lawful to make
any such offer or solicitation in such jurisdiction or in which the person
making such offer or solicitation is not qualified to do so. Neither the
delivery of this Prospectus nor any sale made hereunder shall, under any
circumstances, create an implication that there has been no change in the
affairs of the Company since the date hereof or that the information contained
herein is correct as of any time subsequent to its date.
 
                               TABLE OF CONTENTS
                ------------------------------------------------
 
<TABLE>
<S>                                                                     <C>
Prospectus Summary....................................................     3
Risk Factors..........................................................     7
Use of Proceeds.......................................................    18
Dividend Policy.......................................................    18
Capitalization........................................................    19
Dilution..............................................................    20
Selected Financial Data...............................................    22
Management's Discussion and Analysis of Financial Condition and
  Results of Operations...............................................    23
Business..............................................................    27
Management............................................................    42
Certain Transactions..................................................    53
Principal Stockholders................................................    56
Description of Capital Stock..........................................    59
Shares Eligible for Future Sale.......................................    62
Underwriting..........................................................    64
Legal Matters.........................................................    65
Experts...............................................................    65
Additional Information................................................    66
Index to Financial Statements.........................................   F-1
</TABLE>
 
Until            , 1998 (25 days after the date of this Prospectus), all dealers
effecting transactions in the registered securities, whether or not
participating in the distribution, may be required to deliver a Prospectus. This
requirement is in addition to the obligation of dealers to deliver a Prospectus
when acting as Underwriters and with respect to their unsold allotments or
subscriptions.
 
  PROSPECTUS                                                              , 1998
 
                                     [LOGO]
 
                                3,000,000 Shares
 
                                   SCRIPTGEN
                             PHARMACEUTICALS, INC.
 
                                  Common Stock
 
                     S B C  W A R B U R G DILLON READ INC.
 
                          VOLPE BROWN WHELAN & COMPANY
<PAGE>
                                    PART II
 
                     INFORMATION NOT REQUIRED IN PROSPECTUS
 
ITEM 13. OTHER EXPENSES OF ISSUANCE AND DISTRIBUTION
 
    The following table sets forth the costs and expenses, other than
underwriting discounts and commissions, payable by the Company in connection
with the sale of the Common Stock being registered hereby. All the amounts shown
are estimated, except the SEC registration fee, the NASD filing fee and the
Nasdaq National Market listing fee.
 
<TABLE>
<S>                                                               <C>
SEC Registration Fee............................................  $  13,591
NASD Filing Fee.................................................      4,985
Nasdaq National Market Listing Fee..............................     46,660
Printing Expenses...............................................    150,000
Legal Fees and Expenses.........................................    390,000
Accounting Fees and Expenses....................................    270,000
Blue Sky Expenses and Counsel Fees..............................     10,000
Transfer Agent and Registrar Fees...............................      1,000
Directors' and Officers' Insurance..............................     95,000
Miscellaneous...................................................     68,764
                                                                  ---------
    Total.......................................................  $1,050,000
                                                                  ---------
                                                                  ---------
</TABLE>
 
ITEM 14. INDEMNIFICATION OF DIRECTORS AND OFFICERS
 
    Section 145(a) of the General Corporation Law of the State of Delaware
("DGCL") provides that a Delaware corporation may indemnify any 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 (other than an action by or in the right of the corporation), by
reason of the fact that he is or was a director, officer, employee or agent of
the corporation or is or was serving at the request of the corporation as a
director, officer, employee or agent of another corporation or enterprise,
against expenses (including attorneys' fees), judgments, 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
corporation, and, with respect to any criminal action or proceeding, had no
cause to believe his conduct was unlawful.
 
    Section 145(b) of the DGCL provides that a Delaware corporation may
indemnify any person who was or is a party or is threatened to be made a party
to any threatened, pending or completed action or suit by or in the right of the
corporation to procure a judgment in its favor by reason of the fact that he
acted in any of the capacities set forth above, against expenses (including
attorneys' fees) actually and reasonably incurred by him in connection with the
defense or settlement of such action or suit if he acted under similar
standards, except that no indemnification may be made in respect of any claim,
issue or matter as to which such person shall have been adjudged to be liable to
the corporation unless and only to the extent that the court in which such
action or suit was brought shall determine that despite the adjudication of
liability, such person is fairly and reasonably entitled to be indemnified for
such expenses which the court shall deem proper.
 
    Section 145 of the DGCL further provides that to the extent a director or
officer of a corporation has been successful in the defense of any action, suit
or proceeding referred to in subsections (a) and (b) or in the defense of any
claim, issue or matter therein, he shall be indemnified against expenses
actually and reasonably incurred by him in connection therewith; that
indemnification provided for by Section 145 shall not be deemed exclusive of any
other rights to which the indemnified party may be entitled; and that the
corporation may purchase and maintain insurance on behalf of any person who is
or was a director, officer, employee or agent of the corporation, or is or was
serving at the request of the corporation as a director,
 
                                      II-1
<PAGE>
officer, employee or agent of another corporation or enterprise, against any
liability asserted against him or incurred by him in any such capacity or
arising out of his status as such whether or not the corporation would have the
power to indemnify him against such liabilities under such Section 145.
 
    Section 102(b)(7) of the DGCL provides that a certificate of incorporation
may contain a provision eliminating or limiting the personal liability of a
director to the corporation or its stockholders for monetary damages for breach
of fiduciary duty as a director provided that such provision shall not eliminate
or limit the liability of a director: (i) for any breach of the director's duty
of loyalty to the corporation or its stockholders; (ii) for acts or omissions
not in good faith or which involve intentional misconduct or a knowing violation
of law; (iii) under Section 174 of the DGCL; or (iv) for any transaction from
which the director derived an improper personal benefit.
 
    The Company's Restated Certificate provides that directors of the Company
shall not be personally liable to the Company or its stockholders for monetary
damages for breach of fiduciary duty as a director, except for liability (i) for
any breach of the director's duty of loyalty to the Company or its stockholders,
(ii) for acts or omissions not in good faith or which involve intentional
misconduct or a knowing violation of law, (iii) under Section 174 of the DGCL),
relating to prohibited dividends or distribution or the repurchase or redemption
of stock, or (iv) for any transaction from which the director derives an
improper personal benefit. The provision does not apply to claims against a
director for violations of certain laws, including federal securities laws. If
the DGCL is amended to authorize the further elimination or limitation of
directors' liability, then the liability of directors of the Company shall
automatically be limited to the fullest extent provided by law. The Company's
Restated Certificate and By-Laws also contain provisions requiring the Company
to indemnify the directors, officers, employees or other agents to the fullest
extent permitted by the DGCL.
 
    The Company intends to enter into indemnification agreements with its
current directors and executive officers. The Company intends to insure its
directors and officers against losses arising from any claim against them as
such for wrongful acts or omission, subject to certain limitations.
 
    Under Section 9 of the Underwriting Agreement, the underwriters are
obligated, under certain circumstances, to indemnify officers, directors and
controlling persons of the Company against certain liabilities, including
liabilities under the Securities Act of 1933. Reference is made to the form of
Underwriting Agreement filed as Exhibit 1.1 hereto.
 
ITEM 15. RECENT SALES OF UNREGISTERED SECURITIES
 
    Since January 1995, the Company has sold unregistered securities in the
amounts, at the times, and for the aggregate amounts of consideration listed as
follows:
 
    In February 1995, the Company issued a total of 13,010 shares of Common
Stock to certain stockholders of the Company in connection with the Bridge Loan
Transaction at a price of $0.15 per share for total consideration of $2,000 in
cash.
 
    In April 1995, the Company issued a total of 6,579,086 shares of Series B
Preferred Stock (convertible into 2,139,826 shares of Common Stock) to certain
investors pursuant to a Series B Stock Purchase Agreement. For 2,579,086 of such
shares, the consideration paid per share was $1.00 of cancelled indebtedness of
the Company for total consideration of $2,579,086 of cancelled indebtedness. For
the remaining 4,000,000 shares, the consideration paid per share was $1.00 in
cash for total consideration of $4,000,000.
 
    In April 1995, the Company issued 82 shares of Common Stock to a former
employee upon the exercise of options at the exercise price of $0.15 per share
for total consideration of $12.50.
 
    In June 1995, the Company issued 175 shares of Common Stock to a former
employee upon the exercise of options at the exercise price of $0.15 per share
for total consideration of $26.75.
 
    In March 1996, the Company issued 517 shares of Common Stock to a former
employee upon the exercise of options at the exercise price of $0.15 per share
for total consideration of $79.40.
 
                                      II-2
<PAGE>
    In April 1996, the Company issued 320 shares of Common Stock to a former
employee upon the exercise of options at the exercise price of $0.15 per share
for total consideration of $49.15.
 
    In May 1996, the Company issued a total of 2,942,521 shares of Series C
Preferred Stock (convertible into 957,045 shares of Common Stock) to certain
investors pursuant to a Series C Preferred Stock Purchase Agreement. The
consideration paid per share of was $1.80 in cash for total consideration of
$5,296,537.
 
    In May 1996, the Company issued warrants to purchase up to 32,500 shares of
Series C Preferred Stock at an exercise price of $1.80 per share (to purchase up
to 10,571 shares of Common Stock at an exercise price of $5.53 per share
following the Offering) to Comdisco, Inc. ("Comdisco"), in consideration for
Comdisco (i) executing and delivering certain lease agreements and schedules
thereto and (ii) making available $686,775 of lease financing.
 
    In June 1996, the Company issued 310 shares of Common Stock to a former
employee upon the exercise of options at the exercise price of $0.15 per share
for total consideration of $47.55.
 
    In June 1996, the Company issued 216 shares of Common Stock to a former
employee upon the exercise of options at the exercise price of $0.15 per share
for total consideration of $33.20.
 
    In June 1996, the Company issued 7,478 shares of Common Stock to a former
employee upon the exercise of options at the exercise price of $0.15 per share
for total consideration of $1,149.50.
 
    In October 1996, the Company issued 2,602 shares of Common Stock to a
consultant upon the exercise of options at the exercise price of $0.15 per share
for total consideration of $400.
 
    In November 1996, the Company issued 1,111,333 shares of Series C Preferred
Stock (convertible into 361,457 shares of Common Stock) to Lombard, Odier & Cie
at $1.80 per share in cash for total consideration of $2,000,400.
 
    In November 1996, the Company issued a total of 162,624 shares of Common
Stock to the co-chairmen of its Scientific Advisory Board upon the exercise of
options at the exercise price of $0.03 per share for total consideration of
$5,000.
 
    In February 1997, the Company issued 48,787 shares of Common Stock to its
acting President and Chairman of the Board upon the exercise of options at the
exercise price of $0.15 per share for total consideration of $7,500.
 
    In May 1997, the Company issued warrants to purchase up to 22,500 shares of
Series C Preferred Stock at an exercise price of $1.80 per share (to purchase up
to 7,318 shares of Common Stock at an exercise price of $5.53 per share
following the Offering) to Comdisco in consideration for Comdisco (i) executing
and delivering certain lease agreements and schedules thereto and (ii) making
available $250,000 of lease financing.
 
    In May 1997, the Company issued 294 shares of Common Stock to a former
employee upon the exercise of options at the exercise price of $0.15 per share
for total consideration of $45.15.
 
    In August 1997, the Company issued 33,956 shares of Common Stock to its
President and Chief Executive Officer upon the exercise of options at the
exercise price of $0.15 per share for total consideration of $5,220.
 
    In September 1997, the Company issued 326 shares of Common Stock to a former
employee upon the exercise of options at the exercise price of $0.15 per share
for total consideration of $50.00.
 
    In October 1997, the Company issued warrants to purchase up to 45,000 shares
of Series C Preferred Stock at an exercise price of $1.80 per share (to purchase
up to 14,636 shares of Common Stock at an exercise price of $5.53 per share
following the Offering) to Comdisco in consideration for Comdisco (i) executing
and delivering certain lease agreements and schedules thereto and (ii) making
available $500,000 of lease financing.
 
                                      II-3
<PAGE>
    In November 1997, the Company issued 578 shares of Common Stock to an
employee upon the exercise of options at the exercise price of $0.15 per share
for total consideration of $88.75.
 
    In December 1997, the Company issued 5,713,034 shares of Series D Preferred
Stock (convertible into 1,858,145 shares of Common Stock) to BioChem at $3.50
per share in cash for total consideration of $20,000,000. In addition, the
Company issued a warrant to purchase 464,537 shares of Common Stock at an
exercise price of $13.47 per share.
 
    In December 1997, the Company issued 488 shares of Common Stock to an
employee upon the exercise of options at the exercise price of $0.15 per share
for total consideration of $75.00.
 
    In December 1997, the Company issued 248 shares of Common Stock to an
employee upon the exercise of options at the exercise price of $0.15 per share
for total consideration of $38.00.
 
    In December 1997, the Company issued 64 shares of Common Stock to an
employee upon the exercise of options at the exercise price of $0.15 per share
for total consideration of $9.75.
 
    In December 1997, the Company issued 58 shares of Common Stock to an
employee upon the exercise of options at the exercise price of $0.15 per share
for total consideration of $8.90.
 
    In December 1997, the Company issued 101 shares of Common Stock to an
employee upon the exercise of options at the exercise price of $0.15 per share
for total consideration of $15.50.
 
    In December 1997, the Company issued 245 shares of Common Stock to an
employee upon the exercise of options at the exercise price of $0.15 per share
for total consideration of $37.60.
 
    In December 1997, the Company issued 82 shares of Common Stock to an
employee upon the exercise of options at the exercise price of $0.15 per share
for total consideration of $12.50.
 
    In December 1997, the Company issued 62 shares of Common Stock to an
employee upon the exercise of options at the exercise price of $0.15 per share
for total consideration of $9.40.
 
    In December 1997, the Company issued 82 shares of Common Stock to an
employee upon the exercise of options at the exercise price of $0.15 per share
for total consideration of $12.50.
 
    In December 1997, the Company issued 61 shares of Common Stock to an
employee upon the exercise of options at the exercise price of $0.15 per share
for total consideration of $9.35.
 
    In December 1997, the Company issued 1,036 shares of Common Stock to an
employee upon the exercise of options at the exercise price of $0.15 per share
for total consideration of $159.20.
 
    In December 1997, the Company issued 578 shares of Common Stock to an
employee upon the exercise of options at the exercise price of $0.15 per share
for total consideration of $88.75.
 
    In January 1998, the Company issued 82 shares of Common Stock to an employee
upon the exercise of options at the exercise price of $0.15 per share for total
consideration of $12.50.
 
    In January 1998, the Company issued 537 shares of Common Stock to a
consultant upon the exercise of options at the exercise price of $0.15 per share
for total consideration of $82.50.
 
    In January 1998, the Company issued 27 shares of Common Stock to a former
employee upon the exercise of options at the exercise price of $0.15 per share
for total consideration of $4.20.
 
    In February 1998, the Company issued 102 shares of Common Stock to an
employee upon the exercise of options at the exercise price of $0.15 per share
for total consideration of $15.75.
 
    In February 1998, the Company issued 646 shares of Common Stock to an
employee upon the exercise of options at the exercise price of $0.15 per share
for total consideration of $99.25.
 
    As of December 31, 1997, the Company has outstanding options to purchase an
aggregate of 792,299 shares of Common Stock at exercise prices ranging from
$0.03 to $8.76.
 
    No underwriters were engaged in connection with the foregoing sales of
securities. Such sales of Common Stock and Preferred Stock were made in reliance
upon the exemption from registration set forth
 
                                      II-4
<PAGE>
in Section 4(2) of the Securities Act of 1933 and Rule 506 of Regulation D
promulgated thereunder for transactions not involving a public offering, and all
purchasers (except for certain of the purchasers described below) were
accredited investors as such term is defined in Rule 501(a) of Regulation D.
Issuances of options to the Company's employees, directors, consultants and
members of its Scientific Advisory Board were made pursuant to Rule 701
promulgated under the Securities Act of 1933.
 
ITEM 16. EXHIBITS AND FINANCIAL STATEMENT SCHEDULES
 
    (a) Exhibits.
 
   
<TABLE>
<CAPTION>
NO.                                                       DESCRIPTION
- ---------  ----------------------------------------------------------------------------------------------------------
<S>        <C>
1.1        Form of Underwriting Agreement**
3.1        Amended and Restated Certificate of Incorporation, as amended**
3.2        Amended and Restated Certificate of Incorporation**
3.3        By-Laws**
3.4        Form of Amended By-Laws**
3.5        Form of Amendment to Amended and Restated Certificate of Incorporation**
3.6        Form of Amended and Restated Certificate of Incorporation**
4.1        Specimen Common Stock Certificate**
5.1        Opinion of Fulbright & Jaworski L.L.P.**
10.1       Stock Purchase Agreement among the Company and the investors listed on the Schedule of Purchasers thereto
           dated September 16, 1993, as amended**
10.2       Loan and Stock Purchase Agreement among the Company and the purchasers listed on Schedule I thereto dated
           July 13, 1994**
10.3       Series B Stock Purchase Agreement among the Company, the investors listed on the Schedule of Purchasers
           thereto, Thomas Bologna and Barry Weinberg dated April 19, 1995**
10.4       Series C Stock Purchase Agreement among the Company, the investors listed on the Schedule of Purchasers
           thereto, Thomas Bologna and Barry Weinberg dated May 17, 1996**
10.5       Subsequent Series C Stock Purchase Agreement among the Company and Lombard, Odier & Cie dated November 15,
           1996**
10.6       Master Lease Agreement between the Company and Comdisco, Inc. dated November 22, 1993**
10.7       Warrant Agreement between the Company and Comdisco, Inc. dated January 17, 1994, as amended**
10.8       Warrant Agreement between the Company and Comdisco, Inc. dated May 18, 1996, as amended**
10.9       Collaboration and License Agreement between the Company and Hoechst Marion Roussel dated October 24,
           1997+**
10.10      Stock Purchase Agreement between the Company and Hoechst Marion Roussel dated October 24, 1997**
10.11      Registration Rights Agreement between the Company and Hoechst Marion Roussel dated October 24, 1997**
10.12      Heads of Agreement between the Company and Hoffmann-La Roche Inc. dated September 22, 1995, as amended+**
10.13      Collaboration Agreement between the Company and Eli Lilly and Company dated May 8, 1997+**
10.14      Compound Testing and Development Agreement between the Company and Monsanto Company dated November 17,
           1997+**
10.15      Assignment Agreement between the Company, Andrew Pakula and James Bowie effective March 15, 1994, as
           amended+**
10.16      Employment Agreement between the Company and Mark T. Weedon dated June 24, 1997**
10.17      Employment Agreement between the Company and Dr. Michael G. Palfreyman dated September 10, 1994**
</TABLE>
    
 
                                      II-5
<PAGE>
   
<TABLE>
<CAPTION>
NO.                                                       DESCRIPTION
- ---------  ----------------------------------------------------------------------------------------------------------
<S>        <C>
10.18      Employment Agreement between the Company and Karen A. Hamlin dated December 14, 1992**
10.19      Consulting Agreement between the Company and Dr. Michael R. Green dated January 30, 1998**
10.20      Consulting Agreement between the Company and Dr. Peter S. Kim dated February 2, 1998**
10.21      1994 Employee Stock Option Plan**
10.22      Commercial Real Property Lease between the Company and Cummings Properties Management, Inc. dated November
           2, 1993**
10.23      Stock Purchase Agreement by and between the Company and BioChem Pharma Inc. dated as of December 12,
           1997**
10.24      Research and License Agreement by and between the Company and BioChem Pharma Inc. dated as of December 12,
           1997+**
10.25      Registration Rights Agreement by and between the Company and BioChem Pharma Inc. dated as of December 12,
           1997**
10.26      Stockholders Agreement among the Company, BioChem Pharma Inc. and certain other security holders dated as
           of December 12, 1997**
10.27      Stock Purchase Warrant issued by the Company to BioChem Pharma Inc. dated December 12, 1997**
10.28      Warrant Agreement between the Company and BioChem Pharma Inc. dated as of December 12, 1997**
10.29      License Agreement by and between Trustees of Boston University and the Company dated January 1, 1998+**
10.30      1995 Stockholders' Agreement by and among the Company and certain Stockholders dated April 19, 1995**
10.31      Preferred Stockholders' Agreement by and among the Company and the Preferred Stock Purchasers dated May
           17, 1996**
10.32      Amendment No. 1 to Series B Preferred Stock Purchase Agreement and Series C Preferred Stock Purchase
           Agreement by and among the Company and the persons and entities listed on the signature page thereto dated
           August 8, 1997**
10.33      Employment Agreement between the Company and Michael Heslop dated November 26, 1997**
10.34      1997 Equity Incentive Plan**
10.35      Non-Employee Directors Stock Plan**
10.36      Form of Indemnification Agreement**
10.37      Material Transfer and Screening Agreement between the Company and ArQule, Inc. dated August 23, 1996**
11.1       Computation of Net Loss Per Share and Unaudited Pro Forma Net Loss Per Share**
23.1       Consent of Price Waterhouse LLP, Independent Accountants
23.2       Consent of Fulbright & Jaworski L.L.P. (included in Exhibit 5.1)**
23.3       Consent of Darby & Darby, P.C.**
24.1       Power of Attorney (included in signature page)
27.1       Financial Data Schedule**
</TABLE>
    
 
- ------------------------
 
*   TO BE FILED BY AMENDMENT
 
**  PREVIOUSLY FILED.
 
+   PORTIONS HAVE BEEN OMITTED PURSUANT TO A REQUEST FOR CONFIDENTIAL TREATMENT.
 
(b) Financial Statement Schedules. The following financial statement schedules
    are filed herewith:
 
    All other schedules are omitted because they are not required or are not
applicable or the information is included in the financial statements or notes
thereto.
 
                                      II-6
<PAGE>
ITEM 17. UNDERTAKINGS
 
    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 foregoing provisions, 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 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 of 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.
 
    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.
 
    The undersigned Registrant hereby undertakes that: (1) For purposes of
determining any liability under the Securities Act of 1933, 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 of 1933, 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.
 
                                      II-7
<PAGE>
                                   SIGNATURES
 
   
    Pursuant to the requirements of the Securities Act of 1933, the Registrant
has duly caused this Registration Statement to be signed on its behalf by the
undersigned, thereunto duly authorized, in the City of Medford, State of
Massachusetts, on February 11, 1998.
    
 
                                SCRIPTGEN PHARMACEUTICALS, INC.
 
                                BY:  /S/ MARK T. WEEDON
                                     -----------------------------------------
                                     Mark T. Weedon
                                     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.
 
   
          SIGNATURE                       TITLE                    DATE
- ------------------------------  --------------------------  -------------------
 
                                President, Chief Executive   February 11, 1998
                                  Officer and Director
                                  (Principal Executive
                                  Officer)
      /s/ MARK T. WEEDON
- ------------------------------
        Mark T. Weedon
 
                                Senior Director of           February 11, 1998
                                  Operations, Secretary
                                  and Treasurer (Principal
                                  Financial and Accounting
                                  Officer)
    *         /s/ KAREN A.
            HAMLIN
- ------------------------------
       Karen A. Hamlin
 
     *          /s/ BARRY       Chairman of the Board        February 11, 1998
           WEINBERG
- ------------------------------
        Barry Weinberg
 
 *      /s/ DAVID BALTIMORE,    Director                     February 11, 1998
            PH.D.
- ------------------------------
    David Baltimore, Ph.D.
 
    *        /s/ ALLAN R.       Director                     February 11, 1998
           FERGUSON
- ------------------------------
      Allan R. Ferguson
 
*      /s/ JASON S. FISHERMAN,  Director                     February 11, 1998
             M.D.
- ------------------------------
   Jason S. Fisherman, M.D.
 
    
 
*By:     /s/ MARK T. WEEDON
      -------------------------
           Mark T. Weedon
          ATTORNEY-IN-FACT
 
                                      II-8

<PAGE>
                                                                    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 10, 1998,
relating to the financial statements of Scriptgen Pharmaceuticals, Inc., which
appears in such Prospectus. We also consent to the references to us under the
headings "Experts" and "Selected Financial Data" in such Prospectus. However, it
should be noted that Price Waterhouse LLP has not prepared or certified such
"Selected Financial Data."
    
 
/s/ Price Waterhouse LLP
 
Price Waterhouse LLP
 
Boston, Massachusetts
 
   
February 10, 1998
    


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