AGOURON PHARMACEUTICALS INC
S-3, 1996-06-21
PHARMACEUTICAL PREPARATIONS
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<PAGE>
     AS FILED WITH THE SECURITIES AND EXCHANGE COMMISSION ON JUNE 21, 1996
                                                      REGISTRATION NO. 33-
- --------------------------------------------------------------------------------
- --------------------------------------------------------------------------------
                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549
                           --------------------------
                                    FORM S-3
                             REGISTRATION STATEMENT
                                     UNDER
                           THE SECURITIES ACT OF 1933
                         AGOURON PHARMACEUTICALS, INC.
             (Exact name of registrant as specified in its charter)
 
<TABLE>
<S>                              <C>
          CALIFORNIA                33-0061928
 (State or other jurisdiction    (I.R.S. Employer
     of incorporation or          Identification
        organization)                  No.)
</TABLE>
 
                           --------------------------
 
           10350 NORTH TORREY PINES ROAD, LA JOLLA, CALIFORNIA 92037
                                 (619) 622-8000
  (Address, including zip code, and telephone number, including area code, of
                   registrant's principal executive offices)
 
                                 PETER JOHNSON
                     PRESIDENT AND CHIEF EXECUTIVE OFFICER
                         AGOURON PHARMACEUTICALS, INC.
           10350 NORTH TORREY PINES ROAD, LA JOLLA, CALIFORNIA 92037
                                 (619) 622-8000
 (Name, address, including zip code, and telephone number, including area code,
                             of agent for service)
                           --------------------------
                                   COPIES TO:
 
<TABLE>
<S>                                       <C>
        Harry J. Proctor, Esq.                   Jeffrey S. Marcus, Esq.
  FERRIS, BRITTON & PROCTOR, A P.C.                Laura M. Perz, Esq.
         401 West "A" Street                     MORRISON & FOERSTER LLP
              Suite 1600                       1290 Avenue of the Americas
     San Diego, California 92101              New York, New York 10104-0012
</TABLE>
 
                           --------------------------
        APPROXIMATE DATE OF COMMENCEMENT OF PROPOSED SALE TO THE PUBLIC:
  As soon as practicable after this Registration Statement becomes effective.
 
    If  the  only securities  being registered  on this  Form are  being offered
pursuant to dividend or interest reinvestment plans, please check the  following
box. / /
 
    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, other than securities offered only in connection with dividend or interest
reinvestment plans, 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 Rule 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 delivery of the Prospectus is expected  to be made pursuant to Rule  434,
please check the following box. / /
 
                        CALCULATION OF REGISTRATION FEE
 
<TABLE>
<CAPTION>
                                                          PROPOSED      PROPOSED MAXIMUM
TITLE OF EACH CLASS OF SECURITIES                         MAXIMUM          AGGREGATE
              TO BE                   AMOUNT TO BE     OFFERING PRICE       OFFERING         AMOUNT OF
            REGISTERED               REGISTERED (1)    PER SHARE (2)       PRICE (2)      REGISTRATION FEE
<S>                                 <C>               <C>               <C>               <C>
Common Stock, no par value........     2,875,000           $39.25         $112,843,750        $38,912
<FN>
(1)  Includes  375,000 shares  of Common  Stock that  the Underwriters  have the
     option to purchase to cover over-allotments, if any.
(2)  Calculated in accordance with Rule 457(c) under the Securities Act of 1933.
</TABLE>
 
                           --------------------------
    THE REGISTRANT HEREBY  AMENDS THIS  REGISTRATION STATEMENT ON  SUCH DATE  OR
DATES AS MAY BE NECESSARY TO DELAY ITS EFFECTIVE DATE UNTIL THE REGISTRANT SHALL
FILE  A  FURTHER  AMENDMENT  WHICH SPECIFICALLY  STATES  THAT  THIS REGISTRATION
STATEMENT SHALL THEREAFTER BECOME EFFECTIVE  IN ACCORDANCE WITH SECTION 8(A)  OF
THE  SECURITIES ACT  OF 1933  OR UNTIL  THE REGISTRATION  STATEMENT SHALL BECOME
EFFECTIVE ON SUCH DATE  AS THE COMMISSION ACTING  PURSUANT TO 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 STATEMENT  BECOMES
EFFECTIVE.  THIS  PROSPECTUS  SHALL  NOT  CONSTITUTE AN  OFFER  TO  SELL  OR THE
SOLICITATION OF AN OFFER TO BUY NOR SHALL THERE BE ANY SALE OF THESE  SECURITIES
IN  ANY STATE IN WHICH SUCH OFFER,  SOLICITATION OR SALE WOULD BE UNLAWFUL PRIOR
TO REGISTRATION OR QUALIFICATION UNDER THE SECURITIES LAWS OF ANY SUCH STATE.
<PAGE>
                             SUBJECT TO COMPLETION
                   PRELIMINARY PROSPECTUS DATED JUNE 21, 1996
 
                                2,500,000 SHARES
 
                                     [LOGO]
 
                                  COMMON STOCK
 
                                ----------------
 
    All of the shares of Common Stock  offered hereby are being sold by  Agouron
Pharmaceuticals,  Inc. The  Common Stock  is traded  on The  Nasdaq Stock Market
under the symbol AGPH. On  June 19, 1996, the closing  sale price of the  Common
Stock  as reported by  Nasdaq was $39.25  per share. See  "Price Range of Common
Stock and Dividend Policy."
 
    THESE SECURITIES INVOLVE A HIGH DEGREE  OF RISK. SEE "RISK FACTORS" AT  PAGE
5.
 
                               -----------------
 
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>
                                                         UNDERWRITING
                                        PRICE TO         DISCOUNTS AND       PROCEEDS TO
                                         PUBLIC         COMMISSIONS(1)       COMPANY(2)
<S>                                 <C>                <C>                <C>
Per Share.........................          $                  $                  $
Total.............................          $                  $                  $
Total Assuming Full Exercise of             $                  $                  $
 Over-Allotment Option(3).........
</TABLE>
 
(1) See "Underwriting."
(2)  Before deducting expenses  estimated at $350,000, which  are payable by the
    Company.
(3) Assuming exercise in full of the 45-day option granted by the Company to the
    Underwriters to purchase up to 375,000 additional shares, on the same terms,
    solely to cover over-allotments. See "Underwriting."
 
                              -------------------
 
    The shares of Common Stock are offered by the Underwriters, subject to prior
sale, when, as and if delivered to and accepted by the Underwriters, and subject
to their  right to  reject orders  in  whole or  in part.  It is  expected  that
delivery  of the Common Stock offered hereby will be made in New York City on or
about          , 1996.
                              -------------------
 
PAINEWEBBER INCORPORATED                                      ALEX. BROWN & SONS
                                                                 INCORPORATED
 
                              -------------------
 
                THE DATE OF THIS PROSPECTUS IS           , 1996.
<PAGE>
    IN CONNECTION WITH THE OFFERING,  THE UNDERWRITERS MAY OVER-ALLOT OR  EFFECT
TRANSACTIONS WHICH STABILIZE OR MAINTAIN THE MARKET PRICE OF THE COMMON STOCK OF
THE  COMPANY AT  A LEVEL ABOVE  THAT WHICH  MIGHT OTHERWISE PREVAIL  IN THE OPEN
MARKET. SUCH  TRANSACTIONS  MAY  BE  EFFECTED ON  THE  NASDAQ  STOCK  MARKET  OR
OTHERWISE. SUCH STABILIZING, IF COMMENCED, MAY BE DISCONTINUED AT ANY TIME.
 
    IN  CONNECTION WITH THIS  OFFERING, CERTAIN UNDERWRITERS  (AND SELLING GROUP
MEMBERS) MAY ENGAGE IN PASSIVE MARKET MAKING TRANSACTIONS IN THE COMMON STOCK OF
THE COMPANY ON THE NASDAQ STOCK MARKET IN ACCORDANCE WITH RULE 10B-6A UNDER  THE
SECURITIES EXCHANGE ACT OF 1934. SEE "UNDERWRITING."
 
                             AVAILABLE INFORMATION
 
    The  Company is subject to the  informational requirements of the Securities
Exchange Act of 1934, as amended,  and, in accordance therewith, files  reports,
proxy  statements  and  other  information  with  the  Securities  and  Exchange
Commission  (the  "Commission").  Such  reports,  proxy  statements  and   other
information  filed by  the Company  may be  inspected and  copied at  the public
reference facilities maintained by the Commission at Room 1024, 450 Fifth Street
N.W., Judiciary Plaza, Washington, D.C. 20549, and at the Commission's  regional
offices:  Chicago Regional Office, Suite 1400, 500 West Madison Street, Chicago,
Illinois 60661; and  New York  Regional Office, Room  1400, 75  Park Place,  New
York,  New  York  10007.  Copies  of such  materials  can  also  be  obtained at
prescribed rates from  the Public  Reference Section  of the  Commission at  450
Fifth Street, N.W., Judiciary Plaza, Washington, D.C. 20549. The Common Stock of
the  Company is quoted on The Nasdaq Stock Market, and such material may also be
inspected  at  the  offices  of  Nasdaq  Operations,  1735  "K"  Street,   N.W.,
Washington, D.C. 20006.
 
    The  Company has filed with the  Commission a Registration Statement on Form
S-3 under the Securities  Act of 1933, as  amended (the "Securities Act"),  with
respect to the Common Stock offered hereby. This Prospectus does not contain all
of  the information  set forth in  the Registration Statement,  certain parts of
which  are  omitted  in  accordance  with  the  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  thereto, which may be inspected  without charge at, and copies thereof
may be obtained at  prescribed rates from, the  Public Reference Section of  the
Commission at 450 Fifth Street, N.W., Judiciary Plaza, Washington, D.C. 20549.
 
               INCORPORATION OF CERTAIN INFORMATION BY REFERENCE
 
    Agouron's  Annual Report  on Form  10-K for the  fiscal year  ended June 30,
1995, the  Company's Quarterly  Reports  on Form  10-Q  for the  quarters  ended
September  30, 1995, December 31, 1995 and March 31, 1996, and Current Report on
Form 8-K filed June 21, 1996, and the description of the Company's Common  Stock
contained  in  the  Company's  Registration  Statement  on  Form  8-A  having an
effective date of June 16, 1987  (file number 0-15609), are hereby  incorporated
by  reference in this  Prospectus, except as superseded  or modified herein. All
documents filed with  the Commission  pursuant to  Section 13(a),  13(c), 14  or
15(d) of the Securities Exchange Act of 1934 (the "Exchange Act") after the date
of this Prospectus and prior to the termination of the offering, shall be deemed
to  be incorporated by  reference into this  Prospectus and to  be a part hereof
from the  date of  filing of  such  documents. Any  statement contained  in  any
document  incorporated or deemed to be incorporated by reference herein shall be
deemed to  be modified  or superseded  for purposes  of this  Prospectus to  the
extent  that a  statement contained  herein or  in any  other subsequently filed
document which  also is  or is  deemed to  be incorporated  by reference  herein
modifies  or  supersedes  such  statement. Any  such  statement  so  modified or
superseded shall not be deemed, except as modified or superseded, to  constitute
a  part of this Prospectus. Agouron will  provide without charge to each person,
including any  beneficial owner,  to  whom this  Prospectus is  delivered,  upon
written  or oral request of such person, a  copy of any and all of the documents
that have been or may be  incorporated by reference herein (other than  exhibits
to such documents which are not specifically incorporated by reference into such
documents).  Such requests should be directed  to the Chief Financial Officer at
Agouron's executive  offices  at  10350  North  Torrey  Pines  Road,  La  Jolla,
California 92037; (619) 622-8000.
 
                                       2
<PAGE>
                               PROSPECTUS SUMMARY
 
    THE  FOLLOWING SUMMARY  IS QUALIFIED  IN ITS  ENTIRETY BY  THE MORE DETAILED
INFORMATION APPEARING ELSEWHERE IN THIS PROSPECTUS. UNLESS OTHERWISE  INDICATED,
THE INFORMATION IN THIS PROSPECTUS ASSUMES THAT THE UNDERWRITERS' OVER-ALLOTMENT
OPTION  WILL NOT BE  EXERCISED. EXCEPT FOR  THE HISTORICAL INFORMATION CONTAINED
HEREIN, THE DISCUSSION  IN THIS PROSPECTUS  CONTAINS FORWARD-LOOKING  STATEMENTS
THAT  INVOLVE RISKS AND UNCERTAINTIES. THE COMPANY'S ACTUAL RESULTS COULD DIFFER
MATERIALLY FROM THOSE DISCUSSED HEREIN.  FACTORS THAT COULD CAUSE OR  CONTRIBUTE
TO  SUCH DIFFERENCES, INCLUDE, BUT ARE NOT  LIMITED TO, THOSE DISCUSSED IN "RISK
FACTORS," "MANAGEMENT'S  DISCUSSION  AND  ANALYSIS OF  FINANCIAL  CONDITION  AND
RESULTS OF OPERATIONS" AND "BUSINESS."
 
                                  THE COMPANY
 
    Agouron  Pharmaceuticals, Inc. ("Agouron" or the "Company") is a pioneer and
leader in technologies  for the  atom by atom  design of  novel synthetic  drugs
based  upon the molecular structures of target  proteins which play key roles in
human disease. The  Company is conducting  phase II/III clinical  trials of  two
drugs generated by these design technologies: VIRACEPT-TM- (nelfinavir mesylate)
for  treatment of HIV infection and  THYMITAQ-TM- (formerly AG337) for treatment
of malignant  solid  tumors. In  addition,  eight preclinical  programs  are  in
progress  for  discovery or  development of  other  new drugs  in the  fields of
cancer, viral disease and inflammatory disease.
 
    Viracept, an orally administered  inhibitor of the  enzyme HIV protease,  is
the  subject of pivotal  phase II/ III clinical  studies evaluating the anti-HIV
activity and  safety  of  two alternative  doses  of  the drug  for  six  months
principally  in  combination  with  approved anti-HIV  drugs  in  more  than 700
HIV-infected subjects in the United  States. If successful, these studies  could
lead  to the submission of  a New Drug Application ("NDA")  to the U.S. Food and
Drug Administration ("FDA") for Viracept in the first quarter of calendar  1997.
In  a series of  shorter, smaller, pilot  phase II studies,  comparable doses of
Viracept taken alone or in combination with the approved anti-HIV drug stavudine
(d4T) produced profound reductions in the amount of HIV detectable in the  blood
of  patients and significant increases in their CD4+ T cell counts. Viracept was
reported to  be  safe  and well  tolerated  in  the pilot  studies.  Agouron  is
presently  preparing to market  and sell Viracept  in North America  if and when
approved by FDA.
 
    Agouron is  developing Viracept  in  collaboration with  the  pharmaceutical
division  of Japan  Tobacco, Inc. ("JT").  In collaboration with  JT, Agouron is
also engaged in  the discovery of  drugs for treatment  of infections caused  by
hepatitis  C and  by herpes viruses.  Under agreements with  JT, Agouron retains
exclusive commercial rights to these  anti-viral products in the United  States,
Canada  and Mexico, generally  subject to the  payment either of  royalties or a
share of profits to JT.
 
    Thymitaq, an  inhibitor  of  the  enzyme  thymidylate  synthase  ("TS"),  is
presently the subject of phase II/ III clinical studies evaluating the drug as a
chemotherapeutic  agent for treatment of  malignant solid tumors associated with
cancer of  the liver  (hepatocellular carcinoma)  and cancer  of the  head/neck.
Previously,  six  small phase  II clinical  studies  evaluated 5-day  courses of
treatment with Thymitaq  administered intravenously in  patients with  malignant
solid  tumors  associated  with  cancer of  the  colon,  lung,  liver, pancreas,
prostate or head/neck.  Tumor reductions of  greater than 50%  were observed  in
patients  with head/neck  cancer, liver  cancer, lung  cancer and  colon cancer.
Stabilization of disease was observed in  a majority of the remaining  evaluable
patients  in all groups studied.  An oral formulation of  Thymitaq is also being
developed by  the Company.  If  successful, the  phase II/III  pivotal  clinical
trials  could lead to submission of a NDA for Thymitaq in calendar 1998. Agouron
intends to engage in the sales and marketing of Thymitaq in North America if and
when approved by FDA.
 
    In  June   1996,  Agouron   signed   a  binding   letter  of   intent   with
Hoffmann-LaRoche  Inc.  and  F.  Hoffmann-La Roche  Ltd,  subsidiaries  of Roche
Holding  Ltd  ("Roche"),  providing   for  the  collaborative  development   and
commercialization of Thymitaq and of the Agouron anti-cancer compound designated
AG3340  currently under preclinical development. Under provisions of this letter
of intent, Agouron is to receive initial license fees and additional development
milestone payments from Roche. Roche has agreed  to bear 80% of future costs  of
developing  these drugs.  Agouron and  Roche will  cooperatively market  the two
compounds for cancer indications and share profits in North America, while Roche
has exclusive marketing rights for cancer indications to these compounds outside
North America, subject to the payment of royalties to Agouron. Roche also is  to
provide  annual research  funding support  and subsequent  milestone payments to
Agouron for similar commercial rights for all indications in compounds which are
generated in a collaborative research program focused on cell cycle control.
 
                                       3
<PAGE>
                                  THE OFFERING
 
<TABLE>
<S>                                 <C>
Common Stock Offered by the
 Company..........................  2,500,000 shares of Common  Stock, no par value  (Common
                                    Stock)
Common Stock to be Outstanding
 after the Offering...............  13,170,000 shares (1)
Use of Proceeds...................  To fund the manufacturing, marketing and working capital
                                    requirements  associated with the anticipated commercial
                                    launch of Viracept; for preclinical and clinical product
                                    development activities;  and for  capital  expenditures,
                                    working  capital and other corporate purposes.See Use of
                                    Proceeds.
Nasdaq Stock Market Symbol........  AGPH
</TABLE>
 
- ------------------------
(1) Based on the shares outstanding at June 14, 1996. Excludes (i) approximately
    3,375,800 shares  of Common  Stock  issuable upon  the exercise  of  options
    outstanding  at June  14, 1996 under  the Company's stock  option plans (ii)
    257,851 shares of Common Stock available for future grants under such  plans
    and (iii) 172,789 shares available for purchase under the Company's Employee
    Stock Purchase Plan.
 
                         SUMMARY FINANCIAL INFORMATION
                    (IN THOUSANDS, EXCEPT PER SHARE AMOUNTS)
 
<TABLE>
<CAPTION>
                                                                                                             NINE MONTHS
                                                              FISCAL YEAR ENDED JUNE 30,                   ENDED MARCH 31,
                                                ------------------------------------------------------  ---------------------
                                                  1991       1992       1993       1994        1995       1995        1996
                                                ---------  ---------  ---------  ---------  ----------  ---------  ----------
<S>                                             <C>        <C>        <C>        <C>        <C>         <C>        <C>
STATEMENT OF OPERATIONS DATA:
Revenues......................................  $   4,795  $   6,847  $   9,970  $  17,651  $   27,961  $  20,263  $   30,985
Research and development costs and expenses...      9,353     13,142     17,404     23,957      36,317     24,352      43,780
Net loss......................................     (6,621)    (9,132)    (9,829)    (9,462)    (12,939)    (7,285)    (17,661)
Net loss per common share.....................      (1.42)     (1.47)     (1.40)     (1.31)      (1.77)     (1.00)      (1.84)
Shares used in computing net loss per common
 share........................................      4,674      6,199      6,997      7,241       7,296      7,286       9,574
</TABLE>
 
<TABLE>
<CAPTION>
                                                                                              MARCH 31, 1996
                                                                                        --------------------------
                                                                                          ACTUAL    AS ADJUSTED(1)
                                                                                        ----------  --------------
<S>                                                                                     <C>         <C>
BALANCE SHEET DATA:
Cash, cash equivalents and short-term investments.....................................  $  104,656    $  196,543
Working capital.......................................................................      72,116       164,003
Total assets..........................................................................     113,191       205,078
Long-term liabilities.................................................................       1,863         1,863
Stockholders' equity (2)..............................................................      76,196       168,083
</TABLE>
 
- ------------------------
 
(1)  As adjusted to give effect to the  sale of 2,500,000 shares of Common Stock
    in this offering assuming  a public offering price  of $39.25 per share  and
    net proceeds of approximately $91,887,000.
 
(2) The Company has never declared or paid dividends on its Common Stock.
 
                                       4
<PAGE>
                                  RISK FACTORS
 
    AN  INVESTMENT IN THE SHARES BEING OFFERED  HEREBY INVOLVES A HIGH DEGREE OF
RISK.  PROSPECTIVE  INVESTORS  SHOULD  CAREFULLY  CONSIDER  THE  FOLLOWING  RISK
FACTORS,  IN ADDITION  TO THE  OTHER INFORMATION  CONTAINED IN  THIS PROSPECTUS,
BEFORE PURCHASING THE  SHARES OF  COMMON STOCK OFFERED  HEREBY. THIS  PROSPECTUS
CONTAINS  FORWARD-LOOKING STATEMENTS  THAT INVOLVE RISKS  AND UNCERTAINTIES. THE
COMPANY'S ACTUAL RESULTS COULD DIFFER  MATERIALLY FROM THOSE DISCUSSED IN  THESE
FORWARD-LOOKING  STATEMENTS.  FACTORS THAT  COULD  CAUSE OR  CONTRIBUTE  TO SUCH
DIFFERENCES INCLUDE, BUT ARE  NOT LIMITED TO, THOSE  DISCUSSED IN THE  FOLLOWING
"RISK FACTORS" SECTION AND IN "MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL
CONDITION AND RESULTS OF OPERATIONS" AND "BUSINESS."
 
EARLY STAGE OF PRODUCT DEVELOPMENT; UNCERTAINTY OF PRODUCT DEVELOPMENT AND
MARKET ACCEPTANCE; TECHNOLOGICAL UNCERTAINTY
 
    The Company has not yet completed the development of any products. While the
Company  has received  regulatory approval to  begin human  clinical testing for
certain of its compounds, these and other compounds currently being developed by
the Company will require further  research and development, including  extensive
additional  preclinical and human  clinical testing, prior  to submission of any
regulatory application for commercial  sale of such compounds.  There can be  no
assurance  that  further research  and development  will  be successful  or will
result in drugs  that will qualify  for approval by  regulatory authorities  for
commercial  sale. In addition,  clinical testing of  a pharmaceutical product is
itself subject to approvals by  various governmental regulatory authorities.  No
assurance  can  be  given  that  the Company  will  be  permitted  by regulatory
authorities to  conduct planned  additional clinical  testing of  the  Company's
compounds  in any particular country of  the world, including the United States,
or that, if  permitted, such additional  clinical testing will  prove that  such
drugs  are safe and efficacious to the extent necessary to permit the Company to
obtain marketing approvals for them from regulatory authorities. The Company may
encounter problems or  delays relating to  research and development,  regulatory
approval  and manufacturing and  the failure to address  such problems or delays
could have a material  adverse effect on the  Company's business and  prospects.
Even  if FDA and foreign regulatory approvals  for the marketing of any products
being developed by the Company are obtained, there can be no assurance that such
products will be accepted and successful in the marketplace.
 
    While the Company believes it has demonstrated the utility of certain of its
potential products in  preclinical testing  and in phase  I and  phase II  human
clinical  trials, extensive further clinical testing of these potential products
is required  before the  Company  can seek  marketing approval  from  regulatory
authorities.  Furthermore, results obtained in preclinical studies or in phase I
and phase II  human clinical trials  are not necessarily  indicative of  results
that  will be obtained  in subsequent or more  extensive preclinical or clinical
testing. Furthermore, one of the  Company's potential products, Viracept, is  an
HIV  protease inhibitor which is currently  being tested in large-scale clinical
trials. Technological uncertainty exists regarding the development of resistance
to HIV protease  inhibitors by human  subjects. There can  be no assurance  that
disease  resistance will  not limit the  efficacy of the  Company's HIV protease
inhibitor.  Within  the  pharmaceutical  industry,  treatment  of  the   disease
indications  being pursued  by the Company,  especially HIV  infection, AIDS and
cancer, has proven  difficult. There can  be no assurance  that drugs  resulting
from the approach of protein structure-based drug design employed by the Company
will  overcome the  difficulties of drug  discovery and development  in these or
other fields or result in  commercially successful products. No drug  discovered
by  use  of structure-based  drug design  has  yet been  successfully developed,
approved by FDA or marketed.
 
UNCERTAINTY ASSOCIATED WITH PRECLINICAL AND CLINICAL TESTING
 
    Before seeking regulatory approvals  for the commercial sale  of any of  its
products,  Agouron must undertake extensive  preclinical and clinical testing to
demonstrate their  safety and  efficacy  in humans.  To  date, the  Company  has
conducted  preclinical  testing of  certain of  its  drugs including  AG3340 and
AG2034 and has tested  Viracept and Thymitaq  in phase I  and phase II  clinical
studies  in Europe and the  United States. The results  of such testing of these
and other  products  under  development  by  the  Company  are  not  necessarily
predictive  of results that  will be obtained from  subsequent or more extensive
preclinical and clinical testing. Additionally, the Company has made and may  in
the future make changes to the formulation
 
                                       5
<PAGE>
of  its drugs  and/or to  the processes  for manufacturing  its drugs.  Any such
changes in  formulation or  manufacturing processes  could result  in delays  in
conducting  further  preclinical  and clinical  testing,  in  unexpected adverse
results in  further  preclinical  and clinical  testing,  and/or  in  additional
development  expenses.  Furthermore, there  can  be no  assurance  that clinical
studies of products under development  will demonstrate the safety and  efficacy
of  such  products  at all  or  to  the extent  necessary  to  obtain regulatory
approvals of such products. Companies in the industry have suffered  significant
setbacks  in advanced clinical  trials, even after  promising results in earlier
trials. The  failure to  adequately demonstrate  the safety  and efficacy  of  a
therapeutic product under development could delay or prevent regulatory approval
of the product, and would have a material adverse effect on the Company.
 
    Any drug is likely to produce some toxicities or undesirable side effects in
animals  and in humans  when administered at sufficiently  high doses and/or for
sufficiently long  periods of  time. In  an attempt  to evaluate  the  potential
toxicities  or side effects of Viracept  and Thymitaq, the Company has conducted
toxicology studies of  these compounds in  animals. On the  basis of results  to
date  from  such  toxicological  studies, the  Company  has  selected  for human
clinical testing dose levels of its drugs  and periods of exposure to its  drugs
which,   in  the  Company's  judgment,  are  unlikely  to  produce  unacceptable
toxicities or side effects  in humans. However, there  can be no assurance  that
unacceptable  toxicities or side effects will not occur at any dose level at any
time in the course of toxicological studies  or of human clinical trials of  the
Company's  drugs. The  appearance of  any such  unacceptable toxicities  or side
effects in  toxicology studies  or  in human  clinical  trials could  cause  the
Company  or  regulatory  authorities to  interrupt,  limit, delay  or  abort the
development of any  of the Company's  drugs and could  ultimately prevent  their
being  approved by FDA or foreign regulatory authorities for any or all targeted
indications. Even after being approved by FDA or foreign regulatory authorities,
products may later exhibit adverse effects that prevent their widespread use  or
necessitate their withdrawal from the market. There can be no assurance that any
products  under development  by the  Company will  be safe  when administered to
patients.
 
    The rate of  completion of clinical  trials is dependent  upon, among  other
factors,  the rate of enrollment  of patients. Patient accrual  is a function of
many factors, including  the size of  the patient population,  the proximity  of
patients  to  clinical sites,  the eligibility  criteria for  the study  and the
existence of competitive clinical trials.  Delays in planned patient  enrollment
in  the  Company's  current  trials  or future  clinical  trials  may  result in
increased costs, program  delays or both,  which could have  a material  adverse
effect  on the Company.  There can be  no assurance that  if clinical trials are
completed the Company will be able to submit a NDA as scheduled or that any such
application will be reviewed and approved by FDA in a timely manner, or at all.
 
HISTORY OF OPERATING LOSSES
 
    To date, most  of the Company's  revenues have consisted  of funds  received
pursuant to collaborative research and development arrangements, grants from the
National  Institutes of Health ("NIH") and  interest income. The Company has not
generated revenues from the commercialization  of any products. The Company  has
had  net operating losses since its inception and,  as of March 31, 1996, had an
accumulated deficit of  $81,183,000. The  Company expects to  continue to  incur
substantial and increasing net operating losses for at least the next two years.
Such  losses may fluctuate from quarter  to quarter depending on several factors
including the status of the  Company's research, development and clinical  trial
programs and on the timing and receipt of fees from collaborative relationships.
Such  losses will continue unless  and until such time  as product approvals are
obtained and product sales  generate sufficient revenue  to offset expenses  and
generate  sufficient  cash flow  to  fund continuing  operations.  The Company's
ability to achieve a profitable level of operations is dependent on successfully
completing the development of certain of its products. There can be no assurance
that any or all of these events will occur or that the Company will ever achieve
product revenues or profitable operations.
 
ADDITIONAL FINANCING REQUIREMENTS AND ACCESS TO CAPITAL
 
    The Company has expended more than $160,000,000 on research and  development
activities  and intends in the future  to expend substantial additional funds to
continue research and development activities,
 
                                       6
<PAGE>
conduct preclinical studies and tests, conduct human clinical trials,  establish
manufacturing,   sales  and  marketing  capabilities  and  market  any  approved
products. Additional  funds may  be required  in connection  with  collaborative
arrangements  with others  and for working  capital and  other general corporate
needs.
 
    The  Company  believes   that  its  current   capital  resources,   existing
contractual  commitments and the net proceeds of this offering will enable it to
maintain its current  and planned operations  through at least  fiscal 1998.  No
assurance  can be given that there will be no change in the Company's operations
that would consume available resources more rapidly than anticipated. Additional
funding may  be  required before  the  commercialization of  any  products.  The
Company's future capital requirements will depend on many factors, including the
progress  of  research and  development, the  scope  and results  of preclinical
studies and clinical trials, the cost, timing and outcome of regulatory reviews,
the rate  of  technological advances,  the  market acceptance  of  any  approved
Company  products, administrative and legal expenses and competitive factors. To
the extent the Company's capital resources  are insufficient to meet current  or
planned operating requirements, the Company will seek to obtain additional funds
through  equity  or debt  financings, collaborative  or other  arrangements with
corporate partners, licensees and others, and from other sources, which may have
the effect of diluting the holdings  of existing shareholders. No assurance  can
be  given that additional  financing will be  available when needed  or on terms
acceptable to the Company. If adequate funds are not available, the Company  may
be required to delay or eliminate expenditures for certain of its programs or to
license third parties to commercialize products or technologies that the Company
would  otherwise seek  to develop and  commercialize itself, any  of which would
have a material adverse effect on the Company. See "Use of Proceeds."
 
DEPENDENCE ON OTHERS
 
    The Company's strategy for development  and commercialization of certain  of
its products entails entering into various arrangements with corporate partners,
licensees  and  others,  and  upon the  subsequent  success  of  these partners,
licensees and others in performing  preclinical and clinical testing,  obtaining
regulatory  approvals,  manufacturing  and  marketing.  These  arrangements  may
require the  Company  to transfer  certain  material rights  to  such  corporate
partners,  licensees and others. In the  event the Company determines to license
or sublicense certain of its commercial  rights, there can be no assurance  such
arrangements  will not result  in reduced product revenue  to the Company. While
the Company believes its  partners, licensees and others  will have an  economic
motivation  to  succeed in  performing  their contractual  responsibilities, the
amount and  timing  of resources  to  be devoted  to  these activities  will  be
controlled  by others. Consequently, there can be no assurance that any revenues
or profits will  be derived from  such arrangements, that  any of the  Company's
current strategic arrangements will be continued or not terminated early or that
the Company will be able to enter into future collaborations.
 
    Under  the provisions of certain agreements entered into between the Company
and JT, JT has agreed to  collaborate on the development, commercialization  and
marketing  of certain novel therapeutic drugs including Viracept, anti-hepatitis
C and anti-herpes  drugs and  to make certain  payments related  thereto to  the
Company.  In the  event JT  fails to  make any  of the  anticipated payments, or
otherwise delays in the making of any  of the payments, such event could have  a
material   adverse  effect  on  the  Company.  See  "Business  --  Research  and
Development Agreements -- Japan Tobacco Inc."
 
    Additionally, under  the provisions  of the  binding letter  of intent  with
Roche,  Roche  and Agouron  have agreed  to collaborate  on the  development and
commercialization of Thymitaq  and the Agouron  anti-cancer compound  designated
AG3340  and in a  collaborative research program focused  on cell cycle control.
Roche is obligated to make certain payments under the provisions of the  binding
letter  of intent to the Company. Additional terms of this collaboration must be
negotiated by the  parties. In the  event Roche  and the Company  are unable  to
reach  agreement on  significant terms of  this collaboration or  Roche fails to
make any of the anticipated payments, or  otherwise delays in the making of  any
of the payments, such event could have a material adverse effect on the Company.
See "Business -- Research and Development Agreements -- Roche."
 
                                       7
<PAGE>
LACK OF MANUFACTURING EXPERIENCE
 
    The  Company has  not yet manufactured  at a commercial  scale and currently
does not have the facilities to manufacture its product candidates in commercial
quantities under current good manufacturing practices ("GMP") prescribed by FDA.
However,  the   Company  intends   to  fulfill   its  commercial   manufacturing
requirements  through contract manufacturing relationships. To be successful, if
approved by  FDA, the  Company's  products must  be manufactured  in  commercial
quantities  under GMP and at acceptable costs. Although the Company is producing
clinical quantities of certain chemical  compounds in certain of its  laboratory
facilities that have undergone GMP inspections and been approved by the State of
California,   and  has  business  relationships  with  manufacturers  to  supply
significant portions of  its clinical trial  material requirements, the  current
facilities  and  existing manufacturing  relationships  of the  Company  are not
adequate to meet anticipated commercial production needs. Therefore, the Company
will be  dependent  upon  its  collaborators  and  licensees  or  upon  contract
manufacturers  for the  commercial manufacture of  products it  may develop. The
Company has no experience in  such commercial manufacturing and related  matters
and  no assurance  can be  given that the  Company will  be able  to arrange for
contract manufacturing  or  that adequate  supplies  of raw  materials  will  be
available.  In the event the Company  is unable to obtain contract manufacturing
on acceptable terms, its ability to commercialize or timely deliver its products
at acceptable cost may be adversely affected.
 
LACK OF SALES AND MARKETING CAPABILITIES
 
    While the Company is  currently developing a sales  and marketing force,  it
has  no experience  in the sales,  marketing and  distribution of pharmaceutical
products and may have to rely on collaborators and licensees or on  arrangements
with others to provide for the sales, marketing and distribution of any products
approved  by FDA  or foreign regulatory  authorities. There can  be no assurance
that the Company  will be able  to establish sales,  marketing and  distribution
capabilities or make arrangements with its collaborators, licensees or others to
perform  such activities or that such efforts will be successful. Further, there
can be no assurance that any products, if approved, will gain market acceptance.
The Company's results of operations and cash flows will be highly dependent upon
the timing and extent of Viracept sales.
 
PATENTS AND PROPRIETARY TECHNOLOGY
 
    The Company seeks to protect its proprietary technology by means of patents,
trade secrets and unpatented proprietary know-how. The Company has applied  for,
and  will in the future apply for  United States and foreign patents for certain
of its technology and products. Most  of the Company's products are expected  to
be  synthetic chemical compounds, the patentability  of which will be determined
under principles and  procedures well  established by the  United States  Patent
Office  under  United States  patent law.  No  assurance can  be given  that the
Company's patent applications will issue as patents or that any patents that may
be issued will provide Agouron with adequate protection for the covered products
or technology.
 
    Many of  the  processes  and much  of  the  know-how of  importance  to  the
Company's  technology are dependent upon the skills, knowledge and experience of
its scientific and  technical personnel; such  skills, knowledge and  experience
are  not  patentable.  To help  protect  its  rights, the  Company  requires all
employees, significant consultants and advisors, and collaborators to enter into
confidentiality agreements with  Agouron. There  can be  no assurance,  however,
that  these agreements will provide adequate  protection for the Company's trade
secrets,  know-how  or  other  proprietary  information  in  the  event  of  any
unauthorized  use  or  disclosure.  Further,  the  Company  may  be  exposed  to
competitors who  independently develop  substantially equivalent  technology  or
otherwise  gain  access  to  the  Company's  trade  secrets,  know-how  or other
proprietary information. The commercial success of the Company will also  depend
in  part  on not  infringing  patent or  proprietary  rights of  others  and not
breaching any licenses granted  to the Company. There  can be no assurance  that
the  Company's activities will not infringe on the patents or proprietary rights
of others. Furthermore, there can be no assurance that the Company will be  able
to  obtain  a license  to  any technology  that it  may  require to  conduct its
business or that, if obtainable, such technology can be licensed at a reasonable
cost. Failure by the Company to obtain  a license to any technology that it  may
require  to commercialize any of its products may have a material adverse effect
on the Company.
 
                                       8
<PAGE>
    The cost  of obtaining  and enforcing  patent protection  and of  protecting
proprietary  technology may  involve a  substantial commitment  of the Company's
resources. Any such  commitment may  divert resources  from other  areas of  the
Company.
 
TECHNOLOGICAL CHANGE AND INTENSE COMPETITION
 
    The  pharmaceutical  and  biotechnology industries  are  subject  to intense
competition  and  rapid   technological  change.  The   Company  believes   that
industry-wide interest in the application of protein structure-based drug design
and  related  technology  will continue  and  may accelerate  as  the technology
becomes more widely understood. Competitors of the Company in the United  States
and abroad are numerous and include, among others, pharmaceutical, biotechnology
and  chemical  companies,  universities and  other  research  organizations. For
example, HIV protease inhibitors developed by Abbott Laboratories, Inc., Merck &
Co., Inc. and Roche are currently being marketed. There can be no assurance that
these and other  competitors will  not have  products or  succeed in  developing
technologies  and products that are  more effective than any  which have been or
are being  developed  by  the  Company  or  which  would  render  the  Company's
technology and products obsolete and noncompetitive.
 
    Many  of the Company's competitors  have substantially greater financial and
technical resources  and production  and marketing  capabilities and  experience
than   the  Company.  In  addition,  many  of  the  Company's  competitors  have
significantly greater  experience than  the  Company in  conducting  preclinical
testing  and  human  clinical  trials  of  new  pharmaceutical  products  and in
obtaining FDA and other regulatory  approvals of products. Accordingly,  certain
of  the Company's competitors  may succeed in  obtaining regulatory approval for
products more rapidly or effectively than the Company. If the Company  commences
commercial  sales of  its products,  it will also  be competing  with respect to
manufacturing efficiency and sales and marketing capabilities, areas in which it
currently has no experience.
 
GOVERNMENT REGULATION
 
    Preclinical studies, clinical trials and the production and marketing of the
Company's products  and  its ongoing  research  and development  activities  are
subject  to regulation by numerous governmental authorities in the United States
and other countries.  Rigorous preclinical  and clinical  testing and  obtaining
regulatory  approvals  can  take  many  years  and  require  the  expenditure of
substantial resources. Failures or delays by the Company or its collaborators or
licensees in obtaining regulatory approvals would adversely affect the marketing
of products  developed by  the  Company and  the  Company's ability  to  receive
product  revenues  or royalties.  Further, there  can be  no assurance  that the
Company or  its collaborators  or licensees  will be  able to  obtain  necessary
regulatory  approvals.  There can  be no  assurance that  clinical data  will be
accepted by  regulatory agencies  or that  any approvals  will be  granted on  a
timely  basis,  if  at  all.  Any  significant  delays  or  requests  to provide
additional data in the approval process could have a material adverse effect  on
the Company. See "Business -- Government Regulation."
 
    If  regulatory approval  of a  drug is  obtained, such  approval may involve
limitations and restrictions on the drug's  use. In addition, any marketed  drug
and  its  manufacturer  are subject  to  continual governmental  review  and any
subsequent  discovery  of  previously  unrecognized  problems  could  result  in
restrictions  on  the product  or  manufacturer, including,  without limitation,
withdrawal of the product from the market. Failure of the Company to comply with
applicable regulatory requirements  can, among  other things,  result in  fines,
suspension  of  regulatory  approvals,  product  recalls,  seizure  of products,
operating restrictions or criminal prosecution.
 
    Additionally, the Company is or may become subject to various federal, state
and local  laws,  regulations  and  recommendations  relating  to  safe  working
conditions,  laboratory  and manufacturing  practices,  the experimental  use of
animals  and  the  use  and  disposal  of  hazardous  or  potentially  hazardous
substances,  including radioactive compounds and infectious disease agents, used
in connection  with Agouron's  research  and development  work. The  Company  is
unable  to  predict  the  extent  of  restrictions  that  might  arise  from any
governmental or administrative action.
 
                                       9
<PAGE>
UNCERTAINTY OF THIRD-PARTY REIMBURSEMENT AND PRODUCT PRICING
 
    The Company's ability to commercialize products successfully will depend  in
part  on the  availability of  reimbursement of the  costs of  such products 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 foreign  countries  will be  available  for any  products the
Company 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, the
Company's products, thereby adversely affecting the Company's business.
 
    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 and the effect of any health care reform could materially  adversely
affect  the Company's ability to sell its products if successfully developed and
approved. 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.
 
PRODUCT LIABILITY; LIMITED INSURANCE COVERAGE
 
    The testing, marketing  and sale  of human  health care  products entail  an
inherent  risk of allegations of product liability and there can be no assurance
that product liability  claims will  not be  asserted against  the Company,  its
collaborators  or its licensees. The Company  currently has only limited amounts
of product liability insurance for clinical  trials and currently does not  have
product liability insurance for commercial sales. There can be no assurance that
the  Company will be able  to obtain or maintain  product liability insurance on
acceptable terms or that such  insurance will provide adequate coverage  against
any   potential  claims.  Furthermore,  there  can  be  no  assurance  that  any
collaborators and licensees of Agouron will  agree to indemnify the Company,  be
sufficiently  insured or have a sufficient net worth to protect the Company from
any product liability claims.
 
USE OF HAZARDOUS MATERIALS
 
    The Company's research and development activities involve the controlled use
of hazardous materials,  chemicals, viruses and  various radioactive  compounds.
Although  the  Company  believes that  its  safety procedures  for  handling and
disposing of such materials  comply with the standards  prescribed by state  and
federal  regulations, 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 liability could
have a material adverse effect on the Company.
 
ATTRACTION AND RETENTION OF PERSONNEL
 
    The future success of the Company will  depend in large part on its  ability
to  continue to  attract and retain  highly qualified  scientific, technical and
managerial personnel. Competition for such personnel is intense and there can be
no assurance  that Agouron  will be  able to  attract and  retain the  personnel
necessary for the development of its business. In addition, much of the know-how
developed  by the Company resides in  its scientific and technical personnel and
such know-how  is not  readily transferable  to other  scientific and  technical
personnel.  Further, the Company's  anticipated growth and  expansion into areas
and  activities  requiring  additional  expertise,  such  as  manufacturing  and
marketing,  will require the addition of  new technical and management personnel
and the development of additional expertise  by existing personnel. The loss  of
or  failure to recruit scientific, technical and managerial personnel could have
a material adverse effect on the Company.
 
DILUTION; ABSENCE OF DIVIDENDS
 
    Purchasers of  shares  of Common  Stock  in this  offering  will  experience
immediate  and  substantial dilution  in the  net tangible  book value  of their
shares. Further dilution will occur upon the exercise of
 
                                       10
<PAGE>
outstanding stock options,  the expiration  dates of which  do not  occur for  a
number  of years. The Company has never declared or paid dividends on its Common
Stock to date and  does not anticipate paying  any dividends in the  foreseeable
future. See "Dilution."
 
VOLATILITY OF STOCK PRICE
 
    The  market  price  of  the  Common Stock  has  in  recent  years fluctuated
significantly and it is likely that the price of the Common Stock will fluctuate
in the future.  Announcements by the  Company or others  regarding existing  and
future  collaborations,  results  of  clinical  trials,  scientific discoveries,
technological innovations, commercial products, patents or proprietary rights or
regulatory actions may have a significant adverse effect on the market price  of
the  Common Stock. Fluctuations  in financial performance  from period to period
also may have a significant impact on the market price of the Common Stock.
 
                                USE OF PROCEEDS
 
    The net proceeds to be received by Agouron from the sale of the Common Stock
offered hereby, after deducting estimated underwriting discounts and commissions
and offering  expenses, are  estimated to  be $91,887,000  ($105,720,000 if  the
Underwriters'  over-allotment option is exercised in  full) at an assumed public
offering price of $39.25 per share. The Company currently intends to use the net
proceeds in  the  following  approximate amounts:  manufacturing  and  inventory
commitments for the commercial launch of Viracept, $40,000,000; Viracept product
development   and   clinical   testing,   $20,000,000;   sales   and   marketing
infrastructure,  $15,000,000;  capital   equipment  and  facilities,   including
scientific  equipment  and computers,  $5,000,000; and  the  balance of  the net
proceeds, if  any, will  be added  to  the Company's  working capital  and  made
available for general corporate purposes. The amounts actually expended for each
purpose may vary significantly depending upon a number of factors, including the
status  of  competitive  products,  the progress  of  the  Company's development
programs,  timing   of   regulatory  approvals,   technological   advances   and
determinations  as to  the commercial potential  of the  Company's products. The
Company reserves  the right  to  reallocate the  proceeds  of this  offering  in
response to these and related contingencies. To the extent the offering proceeds
are  less than estimated herein, the Company would expect to reduce the proceeds
allocated to the sales and  marketing infrastructure and capital equipment.  The
Company  believes  that  its  current  capital  resources,  existing contractual
commitments and the net proceeds of this offering will enable it to maintain its
current and planned operations through at least fiscal 1998. Additional  funding
may  be required  before the Company  generates significant  positive cash flows
from  commercial  activities.   See  "Risk  Factors   --  Additional   Financing
Requirements and Access to Capital."
 
    Until applied to any of the foregoing uses, the net proceeds of the offering
will   be  invested  by  the   Company  in  interest-bearing  deposit  accounts,
certificates of  deposit  or similar  financial  instruments. The  Company  will
invest  its liquid  assets in a  manner that  will not subject  it to regulation
under the Investment Company Act of 1940.
 
                                       11
<PAGE>
                                 CAPITALIZATION
 
    The following table sets forth the capitalization of the Company as of March
31, 1996 and  as adjusted  to reflect  the issuance and  sale of  the shares  of
Common Stock offered hereby. See "Use of Proceeds."
 
<TABLE>
<CAPTION>
                                                                                     MARCH 31, 1996
                                                                                 -----------------------
                                                                                   ACTUAL    AS ADJUSTED
                                                                                 ----------  -----------
                                                                                     (IN THOUSANDS)
<S>                                                                              <C>         <C>
Long-term liabilities..........................................................  $    1,863   $   1,863
Stockholders' equity:
  Common Stock, no par value, 75,000,000 shares authorized; 10,622,800 shares
   issued and outstanding actual; and 13,122,800 shares issued and outstanding
   as adjusted (1).............................................................     157,379     249,266
  Accumulated deficit..........................................................     (81,183)    (81,183)
                                                                                 ----------  -----------
      Total stockholders' equity...............................................      76,196     168,083
                                                                                 ----------  -----------
          Total capitalization.................................................  $   78,059   $ 169,946
                                                                                 ----------  -----------
                                                                                 ----------  -----------
</TABLE>
 
- ------------------------
(1)  Excludes 3,680,670 shares  reserved for issuance  under the Company's Stock
    Option Plans (of which 2,622,107 shares were subject to outstanding options)
    and 45,000  shares  reserved  for  issuance  under  an  outstanding  warrant
    (subsequently exercised in June 1996).
 
                PRICE RANGE OF COMMON STOCK AND DIVIDEND POLICY
 
    The  Common Stock trades on  The Nasdaq Stock Market  under the symbol AGPH.
The following table  sets forth  the high  and low  sale prices  as reported  by
Nasdaq for the fiscal periods indicated.
 
<TABLE>
<S>                                                                    <C>         <C>
FISCAL 1994
  Quarter ended September 30.........................................  $      101/4 $       73/4
  Quarter ended December 31..........................................         121/2         83/4
  Quarter ended March 31.............................................         163/4         91/2
  Quarter ended June 30..............................................         141/4         93/4
 
FISCAL 1995
  Quarter ended September 30.........................................         133/4         93/4
  Quarter ended December 31..........................................         131/4        10
  Quarter ended March 31.............................................         19          107/8
  Quarter ended June 30..............................................         271/4        15
 
FISCAL 1996
  Quarter ended September 30.........................................         391/4        223/4
  Quarter ended December 31..........................................         357/8        221/2
  Quarter ended March 31.............................................         475/8        323/4
  Quarter ending June 30 (through June 19)...........................         47          32
</TABLE>
 
    On June 19, 1996, the last sale price of the Common Stock as reported by The
Nasdaq  Stock  Market  was  $39.25 per  share.  There  were  approximately 5,000
beneficial owners of the Common Stock as of such date.
 
    The Company has not declared any dividends on the Common Stock and does  not
intend  to declare  any cash  dividends on the  Common Stock  in the foreseeable
future.
 
                                       12
<PAGE>
                                    DILUTION
 
    As of  March 31,  1996,  the net  tangible book  value  of the  Company  was
$76,196,000,  or $7.17 per share. Net tangible  book value per share is equal to
net tangible  assets (tangible  assets of  the Company  less total  liabilities)
divided  by  the 10,622,800  shares of  Common  Stock outstanding.  After giving
effect to the sale  of the 2,500,000  shares of Common Stock  by the Company  in
this  offering and the  receipt of the  estimated net proceeds  therefrom (at an
assumed offering price  of $39.25 per  share), the pro  forma net tangible  book
value  of the  Company as  of March  31, 1996  would have  been $168,083,000, or
$12.81 per share.  This represents an  immediate increase in  net tangible  book
value  of $5.64 per share to existing  shareholders and an immediate dilution of
$26.44 per share to new investors. The following table illustrates the pro forma
dilution of a new investor's equity in a  share of Common Stock as of March  31,
1996:
 
<TABLE>
<S>                                                            <C>        <C>
Assumed public offering price................................             $   39.25
  Net tangible book value before offering....................  $    7.17
  Increase attributable to new investors.....................       5.64
                                                               ---------
                                                               ---------
Pro forma net tangible book value after offering.............                 12.81
                                                                          ---------
                                                                          ---------
Dilution of net tangible book value to new investors.........             $   26.44
                                                                          ---------
                                                                          ---------
</TABLE>
 
                                       13
<PAGE>
                            SELECTED FINANCIAL DATA
                    (IN THOUSANDS, EXCEPT PER SHARE AMOUNTS)
 
    The  following data for the years ended  June 30, 1991, 1992, 1993, 1994 and
1995 have been  derived from  financial statements audited  by Price  Waterhouse
LLP,  independent accountants. The data as of  March 31, 1995 and 1996 have been
derived from unaudited financial statements which, in the opinion of management,
include all  adjustments  which  the  Company considers  necessary  for  a  fair
presentation  of  such  data.  Interim  operating  results  are  not necessarily
indicators of operating results for the full year. The information presented for
the fiscal year  ended June  30, 1995  should be  read in  conjunction with  the
Company's  Annual Report on Form  10-K for the year ended  June 30, 1995 and the
information presented for the nine months  ended March 31, 1995 and 1996  should
be  read in conjunction with the quarterly  reports on Form 10-Q for the periods
ended March 31,  1995 and  1996. See  "Incorporation of  Certain Information  by
Reference."
 
<TABLE>
<CAPTION>
                                                                                              NINE MONTHS ENDED
                                                     YEAR ENDED JUNE 30,                          MARCH 31,
                                    ------------------------------------------------------  ---------------------
                                      1991       1992       1993       1994        1995       1995        1996
                                    ---------  ---------  ---------  ---------  ----------  ---------  ----------
<S>                                 <C>        <C>        <C>        <C>        <C>         <C>        <C>
STATEMENT OF OPERATIONS DATA:
Revenues:
  Contract........................  $   3,781  $   5,307  $   8,266  $  16,301  $   26,722  $  19,285  $   27,465
  Interest........................      1,014      1,540      1,704      1,350       1,239        978       3,520
                                    ---------  ---------  ---------  ---------  ----------  ---------  ----------
    Total revenues................      4,795      6,847      9,970     17,651      27,961     20,263      30,985
                                    ---------  ---------  ---------  ---------  ----------  ---------  ----------
Costs and Expenses:
  Research and development........      9,353     13,142     17,404     23,957      36,317     24,352      43,780
  General and administrative......      1,880      2,519      2,127      2,961       4,358      3,027       4,679
  Interest........................        183        318        268        195         225        169         187
                                    ---------  ---------  ---------  ---------  ----------  ---------  ----------
    Total expenses................     11,416     15,979     19,799     27,113      40,900     27,548      48,646
                                    ---------  ---------  ---------  ---------  ----------  ---------  ----------
Net loss..........................  $  (6,621) $  (9,132) $  (9,829) $  (9,462) $  (12,939) $  (7,285) $  (17,661)
                                    ---------  ---------  ---------  ---------  ----------  ---------  ----------
                                    ---------  ---------  ---------  ---------  ----------  ---------  ----------
Net loss per common share.........  $   (1.42) $   (1.47) $   (1.40) $   (1.31) $    (1.77) $   (1.00) $    (1.84)
                                    ---------  ---------  ---------  ---------  ----------  ---------  ----------
                                    ---------  ---------  ---------  ---------  ----------  ---------  ----------
Shares used in computing net loss
 per common share.................      4,674      6,199      6,997      7,241       7,296      7,286       9,574
BALANCE SHEET DATA:
Working capital...................  $   8,978  $  35,115  $  29,933  $  21,039  $    8,837  $  13,821  $   72,116
Total assets......................     15,672     45,625     41,721     37,178      27,097     34,529     113,191
Long-term liabilities.............      1,179      3,050      2,613      2,285       1,884      2,015       1,863
Stockholders' equity..............     10,620     37,517     33,757     24,852      12,591     17,812      76,196
Dividends per common share (1)....     --         --         --         --          --         --          --
</TABLE>
 
- ------------------------
(1) The Company has never declared or paid dividends on the Common Stock.
 
                                       14
<PAGE>
          MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION
                           AND RESULTS OF OPERATIONS
 
    EXCEPT  FOR  THE  HISTORICAL  INFORMATION  CONTAINED  HEREIN,  THE FOLLOWING
"MANAGEMENT'S DISCUSSION  AND ANALYSIS  OF FINANCIAL  CONDITION AND  RESULTS  OF
OPERATIONS"  SECTION CONTAINS FORWARD-LOOKING STATEMENTS  THAT INVOLVE RISKS AND
UNCERTAINTIES. THE COMPANY'S ACTUAL RESULTS  COULD DIFFER MATERIALLY FROM  THOSE
DISCUSSED  HERE.  FACTORS THAT  COULD CAUSE  OR  CONTRIBUTE TO  SUCH DIFFERENCES
INCLUDE, BUT  ARE  NOT LIMITED  TO,  THOSE  DISCUSSED IN  "BUSINESS"  AND  "RISK
FACTORS."
 
OVERVIEW
 
    The  Company has been  primarily engaged in the  research and development of
human pharmaceuticals utilizing  protein structure-based drug  design since  its
inception  in  1984. Such  research  and development  has  been funded  from the
Company's equity-derived  working  capital, through  collaborative  arrangements
with  other companies and through grants from the National Institutes of Health.
The Company's  net operating  losses incurred  since inception  are primarily  a
result  of  the Company's  independent research  and development  activities and
continued increasing investment in clinical development activities  concentrated
on  the Company's lead compounds  in cancer and AIDS.  Net losses for the fiscal
years ended June 30,  1993, 1994 and  1995 and the nine  months ended March  31,
1996 were $9,829,000, $9,462,000, $12,939,000 and $17,661,000. It is anticipated
that  substantial net operating losses will  continue and will possibly increase
through at least the next two years.
 
RESULTS OF OPERATIONS
 
  NINE MONTHS ENDED MARCH 31, 1995 AND 1996
 
    The increase  in the  net loss  for the  nine months  ended March  31,  1996
compared  to  the  year-earlier  period  is  due  principally  to  the Company's
commitment to support expanding clinical  activities and establish a  commercial
infrastructure  associated with  the Company's  two leading  product candidates.
These spending increases were only partially offset by increased revenues.
 
    Contract revenues in the current  nine-month period have increased  compared
to  the year-earlier  period due mainly  to the anti-HIV  collaboration with JT.
Interest income  has  increased  significantly from  the  prior-year  nine-month
period  due to a higher average  investment portfolio balance resulting from the
receipt of a milestone payment from JT  in August 1995 and a public offering  of
common stock in September 1995.
 
    Research  and development costs  and expenses increased  from the prior-year
nine-month period due generally to  increasing average research and  development
staff  levels  (approximately  20%)  and  staff-related  expenditures, including
occupancy, and  significantly increased  expenditures for  human clinical  trial
activities associated with Thymitaq and Viracept.
 
    The increase in general and administrative costs and expenses in the current
nine-month   period  is   due  chiefly   to  increasing   average  staff  levels
(approximately 25%) and staff related expenditures and certain costs  associated
with a growing sales and marketing infrastructure.
 
    Interest  expense in the current-year period  is generally decreasing as the
level of debt  and capital  lease obligations declines.  However, these  general
decreases  were  offset  by the  exercise  costs associated  with  certain lease
buy-out options.
 
  FISCAL YEARS ENDED JUNE 30, 1993, 1994 AND 1995
 
    Collaborative research and  development agreements with  Japan Tobacco  Inc.
("JT"),  Syntex (U.S.A.) Inc. (now a subsidiary of Roche Holding Ltd) ("Roche"),
Schering-Plough Corporation  ("Schering") and  Eli Lilly  and Company  ("Lilly")
accounted  for approximately  94%, 94% and  97% of the  Company's total contract
revenue for  1993, 1994  and 1995.  Total contract  revenue for  1994  increased
approximately  97% over  1993 due principally  to the  effect of a  full year of
activities on the collaborative programs covered  by the 1992 agreement with  JT
("JT 1992"), the June 1993 collaborative agreement with Roche and the initiation
of  work on  additional collaborative programs  with JT  under expanded research
arrangements established  in February  1994  ("JT 1994").  Partially  offsetting
these  increases was the  absence of any funding  in 1994 from  Lilly due to the
completion of a  collaborative research  program in April  1993. Total  contract
revenues for 1995
 
                                       15
<PAGE>
increased   approximately  64%  over   1994  due  principally   to  an  anti-HIV
collaboration with JT  initiated in December  1994 ("JT HIV"),  the effect of  a
full year of program activities associated with JT 1994 and increased activities
for  the research program  with Roche. These increases  were partially offset by
the absence  of  funding in  1995  from Schering  due  to the  completion  of  a
collaborative  research program in April 1994.  The Company anticipates that its
contract revenues for 1996 will exceed the level of such revenues recognized  in
1995.
 
    Interest income decreased by approximately 21% from 1993 to 1994 and 8% from
1994  to 1995, primarily  due to a  generally declining portfolio  of cash, cash
equivalents and short-term investments which  were utilized to fund  operations.
The Company anticipates that interest income will increase in 1996.
 
    Research  and development spending increased  by approximately 38% from 1993
to 1994  and  by  approximately  52%  from 1994  to  1995,  due  principally  to
staff-related   expenses  and  third-party   costs  associated  with  increasing
preclinical and clinical  development activities associated  with the  Company's
leading  product candidates: Thymitaq  for the treatment  of cancer and Viracept
for the  treatment  of  HIV infections  and  AIDS.  Collaborator-funded  program
expenditures  representing 55%,  45% and 65%  of total  research and development
costs and expenses in  1993, 1994 and 1995  generated a significant majority  of
the  increases in  research and  development costs  and expenses.  The Company's
self-funded research and development  programs generated approximately 45%,  55%
and  35% of total research and development  costs and expenses in 1993, 1994 and
1995. Of such self-funded costs during  1993, 1994 and 1995, approximately  60%,
44%  and  49%  was dedicated  to  the  preclinical and  clinical  development of
anti-proliferative drugs in  the Company's most  advanced programs. The  Company
anticipates that total research and development costs and expenses will increase
in  1996 in response  to expanding drug  design efforts on  various projects and
increasing preclinical  and  clinical studies  associated  with several  of  the
Company's product development programs.
 
    General  and administrative costs and expenses represented approximately 11%
of total costs  and expenses in  each of 1993,  1994 and 1995.  The increase  in
absolute  dollar spending  for such costs  from 1993  to 1994 was  due mainly to
certain administrative costs associated with the JT collaborations and increased
occupancy costs related to additional leased facilities. The increase from  1994
to  1995  was due  to increasing  average staff  levels (approximately  36%) and
staff-related expenditures and certain administrative costs associated with  the
JT collaborations. The Company anticipates that total general and administrative
costs  and  expenses  will  increase  in 1996  due  to  additional  staff, costs
associated with planned facility expansion and increasing commercial development
and sales and marketing activities.
 
    Interest expense  declined  by  approximately  27% from  1993  to  1994  and
increased by approximately 15% from 1994 to 1995 due to fluctuations in interest
rates and the level of debt and capital lease obligations from year to year.
 
LIQUIDITY AND CAPITAL RESOURCES
 
    Since  its  inception, the  Company's  cash expenditures  have substantially
exceeded its revenues and the Company has relied primarily on equity, lease  and
debt financing and various collaborative arrangements to fund its operations and
capital  expenditures. To  date, the Company  has raised net  equity proceeds of
approximately $157,400,000,  principally  from  corporate  and  venture  capital
investors  and through  its public  offerings in  calendar 1987,  1989, 1991 and
1995.  The  Company  believes  that  its  current  capital  resources,  existing
contractual commitments and the net proceeds of this offering, will enable it to
maintain  its current and planned operations  through at least fiscal 1998. This
belief is based on current research and clinical development plans,  anticipated
working  capital requirements associated with the commercial launch of Viracept,
the current  regulatory  environment,  historical  industry  experience  in  the
development  of therapeutic drugs  and general economic  conditions. The Company
believes that additional  funding may  be required  before significant  positive
cash  flows are generated  from commercial activities. As  a result, the Company
anticipates  pursuing  various  financing  alternatives  such  as  collaborative
arrangements  and  additional  public  offerings or  private  placements  of the
Company's securities. If such alternatives are not
 
                                       16
<PAGE>
available, the Company may  be required to delay  or eliminate expenditures  for
certain  of its potential products under development or to license third parties
to commercialize products or technologies that the Company would otherwise  seek
to develop or commercialize itself.
 
    During   1995,  capital   expenditures  totaled   $2,032,000  compared  with
$1,829,000 and $3,186,000 during  1994 and 1993, of  which $17,000, $58,000  and
$85,000  were financed through  capital lease obligations.  Of the total capital
expenditures during 1993, 1994 and 1995, approximately $1,202,000, $119,000  and
$130,000  represented leasehold improvement costs associated with certain of the
Company's scientific and  administrative facilities. With  the exception of  the
leasehold  improvement costs incurred during 1993,  1994 and 1995, virtually all
of the capital expenditures  during 1993, 1994  and 1995 represented  laboratory
equipment  and  scientific  instrumentation necessary  to  support  an expanding
research and development effort.
 
    Capital expenditures during 1996 are expected to be approximately $2,500,000
to support  product  manufacturing,  development and  research  activities.  The
Company  may  utilize  lease  or  debt  financing  for  certain  expenditures if
available on acceptable terms.
 
NEW ACCOUNTING PRONOUNCEMENT
 
    In October 1995, the Financial  Accounting Standards Board issued  Statement
of  Financial Accounting Standards  (SFAS) No. 123,  "Accounting for Stock-Based
Compensation." This Statement defines a fair  value method of accounting for  an
employee  stock option or  similar equity instrument  and encourages adoption of
that method. The Statement also requires that an employer's financial statements
include  certain   disclosures  about   stock-based  compensation   arrangements
regardless  of the method used  to account for them.  The Statement is effective
for financial statements for  fiscal years that begin  after December 15,  1995.
The  Company  is  currently  evaluating  the  financial  impact  and  disclosure
requirements associated with the adoption of SFAS No. 123.
 
                                       17
<PAGE>
                                    BUSINESS
 
    EXCEPT FOR  THE  HISTORICAL  INFORMATION  CONTAINED  HEREIN,  THE  FOLLOWING
"BUSINESS"  SECTION CONTAINS  FORWARD-LOOKING STATEMENTS THAT  INVOLVE RISKS AND
UNCERTAINTIES. THE COMPANY'S ACTUAL RESULTS  COULD DIFFER MATERIALLY FROM  THOSE
DISCUSSED  HEREIN. FACTORS THAT  COULD CAUSE OR  CONTRIBUTE TO SUCH DIFFERENCES,
INCLUDE, BUT ARE NOT LIMITED TO, THOSE DISCUSSED IN THIS "BUSINESS" SECTION  AND
IN  "RISK  FACTORS"  AND  "MANAGEMENT'S  DISCUSSION  AND  ANALYSIS  OF FINANCIAL
CONDITION AND RESULTS OF OPERATIONS."
 
OVERVIEW
 
    Agouron is a pioneer and leader in technologies for the atom by atom  design
of  novel synthetic drugs based upon the molecular structures of target proteins
which play key roles  in human disease. The  Company is conducting phase  II/III
clinical   trials  of  two   drugs  generated  by   these  design  technologies:
VIRACEPT-TM-  (nelfinavir  mesylate)   for  treatment  of   HIV  infection   and
THYMITAQ-TM-  (formerly  AG337)  for  treatment of  malignant  solid  tumors. In
addition,  eight  preclinical  programs  are   in  progress  for  discovery   or
development  of  other new  drugs in  the  fields of  cancer, viral  disease and
inflammatory disease.
 
    Viracept, an orally administered  inhibitor of the  enzyme HIV protease,  is
the  subject of pivotal  phase II/ III clinical  studies evaluating the anti-HIV
activity and  safety  of  two alternative  doses  of  the drug  for  six  months
principally  in  combination  with  approved anti-HIV  drugs  in  more  than 700
HIV-infected subjects in the United  States. If successful, these studies  could
lead  to the submission of  a New Drug Application ("NDA")  to the U.S. Food and
Drug Administration ("FDA") for Viracept in the first quarter of calendar  1997.
In  a series of  shorter, smaller, pilot  phase II studies,  comparable doses of
Viracept taken alone or in combination with the approved anti-HIV drug stavudine
(d4T) produced profound reductions in the amount of HIV detectable in the  blood
of  patients and significant increases in their CD4+ T cell counts. Viracept was
reported to  be  safe  and well  tolerated  in  the pilot  studies.  Agouron  is
presently  preparing  to market  and  sell Viracept  in  North America  upon its
approval by FDA.
 
    Agouron is  developing Viracept  in  collaboration with  the  pharmaceutical
division  of Japan  Tobacco, Inc. ("JT").  In collaboration with  JT, Agouron is
also engaged in  the discovery of  drugs for treatment  of infections caused  by
hepatitis  C and  by herpes viruses.  Under agreements with  JT, Agouron retains
exclusive commercial rights to these  anti-viral products in the United  States,
Canada  and Mexico, generally  subject to the  payment either of  royalties or a
share of profits to JT.
 
    Thymitaq, an  inhibitor  of  the  enzyme  thymidylate  synthase  ("TS"),  is
presently the subject of phase II/ III clinical studies evaluating the drug as a
chemotherapeutic  agent for treatment of  malignant solid tumors associated with
cancer of  the liver  (hepatocellular carcinoma)  and cancer  of the  head/neck.
Previously,  six  small phase  II clinical  studies  evaluated 5-day  courses of
treatment with Thymitaq  administered intravenously in  patients with  malignant
solid  tumors  associated  with  cancer of  the  colon,  lung,  liver, pancreas,
prostate or head/neck.  Tumor reductions of  greater than 50%  were observed  in
patients  with head/neck  cancer, liver  cancer, lung  cancer and  colon cancer.
Stabilization of disease was observed in  a majority of the remaining  evaluable
patients  in all groups studied.  An oral formulation of  Thymitaq is also being
developed by  the Company.  If  successful, the  phase II/III  pivotal  clinical
trials  could lead to submission of a NDA for Thymitaq in calendar 1998. Agouron
intends to engage in the sales and  marketing of Thymitaq in North America  upon
its approval by FDA.
 
    In   June   1996,  Agouron   signed  a   binding   letter  of   intent  with
Hoffmann-LaRoche Inc.  and  F.  Hoffmann-La Roche  Ltd,  subsidiaries  of  Roche
Holding   Ltd  ("Roche"),  providing  for   the  collaborative  development  and
commercialization of Thymitaq and of the Agouron anti-cancer compound designated
AG3340 currently under preclinical development. Under provisions of this  letter
of intent, Agouron is to receive initial license fees and additional development
milestone  payments from Roche. Roche has agreed  to bear 80% of future costs of
developing these  drugs. Agouron  and Roche  will cooperatively  market the  two
compounds for cancer indications and share profits in North America, while Roche
has exclusive marketing rights for cancer indications to these compounds outside
North   America,   subject   to   the   payment   of   royalties   to   Agouron.
 
                                       18
<PAGE>
Roche also  is  to  provide  annual  research  funding  support  and  subsequent
milestone   payments  to  Agouron  for  similar  commercial  rights  for  cancer
indications in compounds which are generated in a collaborative research program
focused on cell cycle control.
 
RESEARCH AND DEVELOPMENT PROGRAMS
 
    Agouron's research and  development programs concentrate  in three areas  of
human  disease: cancer, viral disease and inflammatory disease. All of Agouron's
drug discovery programs apply  the Company's core technologies  for the atom  by
atom  design of small synthetic drug  molecules based upon the three dimensional
molecular architecture of  proteins that play  key roles in  human disease.  See
"Drug Design Technology."
 
    The following table outlines Agouron's preclinical and clinical research and
development  programs.  Some  of these  programs  are being  pursued  by Agouron
independently while  others are  being undertaken  in collaboration  with  other
companies.
 
<TABLE>
<CAPTION>
                                                                       DEVELOPMENT
       PROGRAM             INDICATION           PROTEIN TARGET            STAGE         PARTNER
- ---------------------  -------------------  -----------------------  ----------------  ----------
<S>                    <C>                  <C>                      <C>               <C>
CANCER
  Thymitaq- i.v.       Solid Tumors         TS                       Phase II/III      Roche
  Thymitaq- oral       Solid Tumors         TS                       Phase I           Roche
  AG2034               Solid Tumors         GART                     Preclinical       None
  AG3340               Metastasis           MMPs                     Preclinical       Roche
  AICART               Solid Tumors         AICART                   Research          None
  cdk4                 Solid Tumors         cdk4                     Research          Roche
  VEGF Receptor        Solid Tumors         kdr                      Research          None
VIRAL DISEASE
  Viracept             HIV Infection        HIV Protease             Phase II/III      JT
  Rhinovirus           Common Cold          RhV 3C Protease          Research          None
  Cytomegalovirus      CMV Infection        CMV Protease             Research          JT
  Herpes simplex       Herpes Infection     HSV-1 Protease           Research          JT
  Hepatitis C          Viral Diseases       Hepatitis C Protease     Research          JT
INFLAMMATORY DISEASE
  MMP                  Arthritis            MMPs                     Research          Roche
  AICART               Inflammation         AICART                   Research          None
</TABLE>
 
CANCER
 
  OVERVIEW
 
    The development of new drugs for treatment of cancer is a primary scientific
and commercial focus of the Company. Cancer is the second leading cause of death
in  the United States and  most developed nations. While  much progress has been
made in the  treatment of  certain forms  of cancer,  most existing  anti-cancer
drugs  display limited efficacy  and significant toxicities  that restrict their
clinical usefulness. As a result, there remains a critical need for  anti-cancer
drugs   which  are  less  toxic  and  more  efficacious  either  as  tumoricidal
(tumor-killing) or tumoristatic (tumor-controlling) agents.
 
    Agouron believes that  the next generation  of agents for  treatment of  the
most  common human cancers should  have a target other  than DNA, should be more
capable  of  evading  drug  resistance   and  should  retain  activity   against
non-proliferating  tumor  cells. The  Company's  anti-cancer drug  discovery and
development programs are  aimed at  meeting these  criteria by  focusing on  the
discovery  and development of  inhibitors of the  following enzymes: thymidylate
synthase  (TS);   glycinamide   ribotide  formyltransferase   ("GART");   matrix
metalloproteases (MMPs); aminoimidazole carboxamide ribonucleotide
formyltransferase ("AICART"); cyclin dependent kinase 4 ("cdk4"); and a receptor
for  Vascular Endothelial Growth Factor ("VEGF").  Three of these enzyme targets
(TS, GART  and  AICART)  have  a  common  structural  motif  that  permits  lead
inhibitors from one program to be useful potentially in others.
 
                                       19
<PAGE>
  TS INHIBITORS: THYMITAQ
 
    The  enzyme TS  catalyzes a  critical step  in the  synthesis of  DNA and is
especially  crucial  to  cancer  cells  undergoing  uncontrolled  proliferation.
Independent  research has established  that the efficacy  of the anti-tumor drug
5-fluorouracil derives from its ability to inactivate TS. Inhibition of TS kills
tumor cells by  inducing programmed  cell death --  a form  of natural  cellular
suicide  by which normal cell growth is usually regulated. It has been Agouron's
goal to  design highly  specific  inhibitors of  TS  that overcome  the  several
limitations  of 5-fluorouracil. In particular, Agouron has focused on the design
of TS inhibitors of novel chemical character that it believes may be capable  of
penetrating  fatty membranes and tissues, circumventing  some of the more common
forms of drug resistance and passing into and out of cells by passive diffusion,
allowing for  much  greater clinical  control  of  toxicity and  for  a  broader
spectrum  of anti-tumor  activity. Agouron's  lead compound  in the  TS program,
Thymitaq, is in phase II/III clinical testing.
 
    Phase I studies of Thymitaq initially  conducted at the medical hospital  of
the  University of Newcastle upon Tyne in  England, under the sponsorship of the
British Cancer  Research  Campaign,  evaluated  first  an  intravenous  ("i.v.")
formulation  and then an oral formulation of Thymitaq. In these phase I studies,
which were ultimately extended into the United States and involved a total of 45
advanced cancer  patients, the  maximum  tolerated 5-day  dose of  Thymitaq  was
determined  through a series of dose escalations. On the basis of these studies,
a dose of 1000mg/m(2)/day was determined to be appropriate for phase II efficacy
studies. The phase I studies demonstrated that Thymitaq i.v. was well tolerated:
at the maximum tolerated dose, the predominant toxicities were determined to  be
myelosuppression  (suppression of  bone marrow  activity) of  short duration and
mucositis (mouth  sores)  which could  frequently  be mitigated  with  a  simple
mouthwash.  A  subsequent  phase  I  study  involving  32  patients  in  England
demonstrated that oral administration of Thymitaq resulted in a  pharmacokinetic
and safety profile similar to that of the i.v. formulation.
 
    The  Company has conducted six small phase II trials of the i.v. formulation
of Thymitaq. The  six studies  have evaluated  5-day courses  of treatment  with
Thymitaq  in patients with malignant solid  tumors associated with cancer of the
colon, lung, liver, pancreas, prostate or head/neck. Tumor reductions of greater
than 50% were  observed in patients  with head/neck cancer,  liver cancer,  lung
cancer  and colon cancer. Stabilization of disease was observed in a majority of
the remaining evaluable patients in all groups studied. Of 19 evaluable patients
with head/neck cancer, four  experienced reductions in  tumor mass greater  than
50%,  including  two  patients with  reductions  of  100%. Of  18  patients with
hepatocellular (liver)  cancer, two  experienced tumor  reductions greater  than
50%;  two  others experienced  tumor  reductions sufficient  to  permit surgical
removal of tumors previously deemed to be inoperable.
 
    Pivotal phase II/III clinical trials have recently been initiated at several
clinical sites in the United States for evaluation of Thymitaq as a single agent
treatment in  cancer of  the head/neck  and in  liver cancer.  For treatment  of
head/neck  cancer,  Thymitaq is  being  compared to  the  chemotherapeutic agent
methotrexate in patients who  have failed first-line  therapy. For treatment  of
liver  cancer, Thymitaq is being evaluated  in a non-comparative clinical trial,
as no drugs are  currently approved for  use as single  agents in this  disease.
Complete  enrollment of these studies is expected to require several months. The
Company intends to supplement  the U.S. clinical trials  of Thymitaq by  opening
additional  clinical studies  in Europe  (head/neck cancer)  and in  Asia (liver
cancer). If enrolled in  a timely manner and  if successful, the pivotal  trials
could  permit the Company to file a  NDA covering for Thymitaq in calendar 1998.
See "Risk Factors -- Uncertainty Associated with Clinical Trials."
 
    The binding  letter of  intent signed  by  Agouron and  Roche in  June  1996
provides  for the  collaborative further  development and  commercialization for
cancer indications  of Thymitaq.  Under  provisions of  this letter  of  intent,
Agouron is to receive license fees and subsequent development milestone payments
from Roche. Roche has agreed to bear 80% of future costs of developing Thymitaq.
Agouron  and Roche will cooperatively market Thymitaq for cancer indications and
share profits  from sales  of the  drug in  North America.  Roche has  exclusive
marketing  rights  to Thymitaq  for  cancer indications  outside  North America,
subject to certain co-promotion rights and the payment of royalties to  Agouron.
See "Research and Development Agreement -- Roche."
 
                                       20
<PAGE>
  GART INHIBITORS: AG2034
 
    An  Agouron research program has resulted in the design of AG2034. AG2034 is
a potent,  selective  inhibitor  of  glycinamide  ribonucleotide  transformylase
(GART)  -- a  key enzyme  in the biochemical  pathway through  which tumor cells
synthesize purines, essential  components of  DNA. With the  exception of  liver
cells,  all normal human  tissues obtain purines  through an alternative pathway
(the purine salvage pathway). The Company believes that inhibitors of GART  will
show  a high  degree of  selectivity for tumor  cells and  less significant bone
marrow toxicity than other chemotherapeutic agents.
 
    AG2034 has  demonstrated preclinical  anti-tumor  activity against  a  broad
panel  of tumor types in preclinical models at various dosing schedules. In cell
culture experiments, AG2034 selectively kills  tumor cells missing certain  cell
cycle  checkpoints,  but  is  inactive  against  cells  with  normal  checkpoint
functions. Because  it  has become  technically  possible to  determine  whether
biopsied tumor cells are deficient in checkpoint functions, the Company believes
that  physicians may be able  to determine in advance  of treatment which tumors
are most likely to respond to AG2034.
 
    Agouron has completed  initial chemical scale-up  of AG2034 and  preclinical
toxicology  studies  are in  progress.  The Company  plans  to initiate  phase I
clinical studies of AG2034 in late calendar 1996. The Company presently  retains
all commercial rights to any compounds resulting from this program.
 
  MMP INHIBITORS: AG3340
 
    Independent  research has shown MMPs to  be involved in many disease states.
Certain MMPs have  been associated with  tumor growth, the  metastasis of  tumor
cells  to secondary sites  within the body  and the growth  of new blood vessels
(angiogenesis) through which  tumor cells obtain  nutrients and growth  factors.
The  Company believes that MMPs represent a new opportunity for the discovery of
novel tumoristatic  agents.  The Company  further  believes that  orally  active
inhibitors of certain combinations of MMPs, but not of all MMPs, are most likely
to  have  the  optimal safety  and  efficacy profiles  of  superior tumoristatic
agents.
 
    A  three-year  program   of  drug   discovery  undertaken   by  Agouron   in
collaboration  with Roche  ("Roche 1993") has  resulted in the  selection of the
compound designated  AG3340 for  development by  the Company  as an  anti-cancer
agent.  AG3340  selectively  inhibits the  MMPs  known  as Gelatinase  A  and B,
Stromelysin-1 and Collagenase-3, but  is relatively inactive against  Fibroblast
Collagenase.  In preclinical tests, AG3340 has demonstrated excellent anti-tumor
in vivo activity  following oral administration  in both mouse  and human  tumor
xenograft  models. Significant tumor growth delays in all models and significant
reductions of spontaneous  metastases in the  mouse Lewis lung  model have  been
reported  at  recent  scientific  meetings.  Toxicology  studies  are  currently
underway to support  initiation of phase  I clinical studies  of AG3340 in  late
calendar 1996.
 
    Other  compounds from the Roche 1993 collaboration on MMP inhibitors are the
subjects of preclinical evaluation  including certain compounds being  evaluated
by  Roche as agents for treatment of arthritis. See "Inflammatory Disease -- MMP
Inhibitors."
 
    The binding  letter of  intent signed  by  Agouron and  Roche in  June  1996
provides  for the  collaborative further  development and  commercialization for
cancer indications of AG3340  and certain other  compounds. Under provisions  of
this  agreement, Agouron is  to receive license  fees and subsequent development
milestone payments from Roche. Roche has agreed  to bear 80% of future costs  of
developing AG3340. Agouron and Roche will cooperatively market AG3340 for cancer
indications and share profits from sales of the drug in North America. Roche has
exclusive  marketing  rights  to  AG3340 for  cancer  indications  outside North
America, subject to certain co-promotion rights and the payment of royalties  to
Agouron.  See "Inflammatory Disease" and "Research and Development Agreements --
Roche."
 
  AICART INHIBITORS
 
    The  enzyme  AICART  catalyzes  a   rate-determining  step  in  the   purine
biosynthetic  pathway and represents a second target for anti-cancer drugs which
are active  by virtue  of their  anti-purine effects.  Research has  shown  that
inhibiting  the  rate-limiting  enzyme  in  such  a  pathway  produces  the most
significant effects  on the  growth  of cells  dependent  on that  pathway.  The
scientific   rationale  for   GART  as  a   target  for   new  anti-tumor  drugs
 
                                       21
<PAGE>
applies equally to AICART. Agouron scientists believe that two inhibitors of the
purine  pathway --  an inhibitor of  GART and an  inhibitor of AICART  -- may be
highly  synergistic  in  producing  anti-tumor  activity  when  administered  in
combination.
 
    The   Company's  scientists  have  solved  the  three-dimensional  molecular
structure of  AICART and  are engaged  in design,  synthesis and  evaluation  of
AICART  inhibitors intended  to be efficacious  in the treatment  of cancer. The
Company presently retains all commercial rights to any compounds resulting  from
this program.
 
  CELL CYCLE CONTROL: CDK4
 
    Cyclin  dependent  kinases are  enzymes that  play  roles in  regulating the
transitions between phases in  the life cycles  of all cells.  A member of  this
family  of enzymes known as cdk4 has  been implicated by independent research in
driving  cells  from  a  quiescent  phase  to  the  highly  proliferative  phase
characteristic of malignancies -- particularly in familial melanomas, esophageal
carcinomas  and pancreatic cancers. Agouron has been engaged in a drug discovery
program aimed at the design of selective small molecule drugs with the potential
to inhibit the  activity of cdk4  and therefore block  the transition of  cancer
cells into their proliferative phase.
 
    Under provisions of the binding letter of intent signed by Agouron and Roche
in  June 1996, Roche is to pay to  Agouron annual research funding in support of
the cdk4 program. Commercial rights for  all indications in compounds which  are
generated  in  the program  are similar  to those  which Roche  has for  the MMP
inhibitor AG3340. See "Research and Development Agreement -- Roche."
 
  VEGF RECEPTOR
 
    The process known as angiogenesis, the formation of new blood vessels, is  a
key  factor  in  the  maintenance  and  progression  of  several  disease states
including the metastasis  of malignant tumors.  The ability of  cancer cells  to
carry  out angiogenesis depends in part upon  the activity of a protein known as
Vascular Endothelial Growth Factor (VEGF) which, by binding to a receptor  known
as  kdr, triggers the growth of endothelial  cells. Agouron is engaged in a drug
discovery program whose  objective is  the design of  drugs that  block the  kdr
receptor  for VEGF and therefore compromise the ability of tumors to carry out a
key process in angiogenesis. The Company presently retains all commercial rights
to any compounds resulting from this program.
 
VIRAL DISEASE
 
  OVERVIEW
 
    The development of new drugs for the treatment of certain viral diseases  is
another scientific and commercial focus of the Company. The Company is presently
conducting  programs aimed  at discovery and/or  development of  four classes of
anti-viral drugs  which  block  viral proteases,  enzymes  required  by  several
families of pathogenic viruses to carry out replication and infection. Agouron's
anti-viral  drug programs include HIV protease inhibitors (Viracept), rhinovirus
3C protease  inhibitors,  herpes  virus  protease  inhibitors  and  hepatitis  C
protease  inhibitors. Agouron is  developing certain of  its anti-viral drugs in
collaboration with JT. See "Research and Development Agreements -- Japan Tobacco
Inc."
 
  HIV PROTEASE INHIBITOR: VIRACEPT
 
    Research and development of drugs for treatment of HIV infection and AIDS in
the  pharmaceutical  industry   has  thus  far   produced  both  successes   and
disappointments.   Initially,  scientists  were  optimistic  that  blocking  the
essential HIV  enzyme reverse  transcriptase ("RT")  would prove  sufficient  to
defeat the replication of HIV and curb the progression of HIV infection to AIDS.
As  a  result  of research  and  development efforts  by  several pharmaceutical
companies, several RT inhibitors are now approved for use in the United  States.
However,  the clinical usefulness of this first generation of anti-HIV drugs has
generally been limited by  their toxicity and  by the ability  of HIV to  mutate
into  forms that  are resistant  to them. For  this reason,  it has  been a high
priority at Agouron, as well as  at other pharmaceutical companies, to  discover
and  develop new anti-HIV  drugs that work  by a mechanism  of action other than
inhibition of RT.
 
    Inhibitors of the enzyme HIV protease are widely regarded as one of the most
promising new classes of anti-HIV drugs. HIV protease is an enzyme that performs
an essential role in the infectious cycle of HIV.
 
                                       22
<PAGE>
Research shows that inhibition of the protease enzyme renders HIV unable to form
new infectious virus. Three  HIV protease inhibitors have  been approved by  FDA
for  marketing in the United States during  the last year. Agouron believes that
its HIV protease  inhibitor, Viracept,  has properties  that will  permit it  to
compete  effectively  with these  approved  drugs. See  "Competition"  and "Risk
Factors -- Technological Change and Competition."
 
    A series  of small,  short-term pilot  phase II  clinical studies  has  been
completed  evaluating the  safety and acute  anti-HIV efficacy  of several daily
oral doses of Viracept  administered orally to  HIV-infected subjects. In  these
studies, Viracept taken alone or in combination with the approved drug stavudine
(d4T),  produced profound decreases in the amount of HIV detectable in the blood
of patients and significant increases in their CD4+ T cell counts. Pivotal phase
II/III clinical  studies  of daily  doses  of 500  mg  and 750  mg  of  Viracept
administered   three  times  daily  in  a  tablet  formulation,  principally  in
combination with other  anti-HIV drugs,  are currently  in progress  at a  large
number  of sites in the United States. In the pilot phase II studies, such doses
of Viracept were  safe and  well tolerated,  the most  common side-effect  being
loose stool/diarrhea.
 
    If  the current phase II/III clinical trials  of Viracept are completed on a
timely basis and if results from these trials are satisfactory, Agouron plans to
file a NDA in the first quarter of calendar 1997 and, if the NDA is approved  on
a  timely basis,  to launch  Viracept in North  America later  in calendar 1997.
However, there can  be no assurance  that any  of these events  will occur.  See
"Risk Factors -- Uncertainty Associated with Clinical Trials," and "Research and
Development Agreements -- Japan Tobacco Inc."
 
  RHINOVIRUS 3C PROTEASE INHIBITORS
 
    Rhinoviruses are believed to be the single most frequent cause of the common
cold.  While  rhinovirus  infections are  a  periodic annoyance  to  most normal
individuals, they  produce more  severe and  prolonged symptoms  in people  with
asthma,  emphysema  and chronic  obstructive  pulmonary disease.  The  family of
rhinoviruses has eluded attempts to develop a useful vaccine because it contains
more than 100 serotypes. However, all known strains of rhinoviruses depend on  a
critical  enzyme, the  3C protease,  at several  stages of  their life-cycle for
production of new  infectious viruses.  It has  been shown  both by  independent
research   and  by  Agouron  scientists  that  inactivating  this  enzyme  halts
rhinovirus production IN VITRO.  Because there is  no known natural  counterpart
for  the  3C protease  enzyme  in humans,  Agouron  scientists believe  that the
potential for toxicity from selective  inhibitors of the rhinovirus 3C  protease
is low.
 
    Agouron's rhinovirus protease research has resulted in the design of potent,
selective  rhinovirus  3C  protease  inhibitors  currently  being  evaluated  in
preclinical pharmacological studies  of anti-viral  activity, cellular  toxicity
and  oral bioavailability. It is the Company's goal to select one such inhibitor
for development within 12 months.  The Company presently retains all  commercial
rights to any compounds resulting from this program.
 
  CMV AND HSV-1 PROTEASE INHIBITORS
 
    Among  the  most  clinically significant  members  of the  family  of herpes
viruses are herpes simplex virus-1  (HSV-1) and cytomegalovirus (CMV). Like  HIV
and  rhinoviruses, HSV-1  and CMV each  contain a protease  enzyme essential for
virus maturation and  infection. Agouron  believes that  these protease  enzymes
represent targets for a new class of anti-viral drugs with the potential for low
toxicity.   Agouron  scientists  have   recently  solved  the  three-dimensional
molecular structure of the targeted protease enzyme from CMV and are seeking  to
solve the HSV-1 protease in preparation for application of Agouron's drug design
technologies.  However, no inhibitor  of HSV-1 or  CMV has yet  been selected by
Agouron for  development.  See "Research  and  Development Agreements  --  Japan
Tobacco Inc."
 
  HEPATITIS C PROTEASE INHIBITORS
 
    The ability to treat infection by hepatitis C virus represents a significant
unmet  clinical need, particularly in Asian countries. Hepatitis C virus depends
upon a key protease enzyme for the  production of new infectious viruses. As  no
human  counterpart  of  the  hepatitis  C  protease  enzyme  is  known,  Agouron
scientists believe  that the  potential for  toxicity of  selective hepatitis  C
protease inhibitors is low. Agouron's anti-hepatitis C project is an early stage
research  program in which  no inhibitor has been  selected for development. See
"Research and Development Agreements -- Japan Tobacco Inc."
 
                                       23
<PAGE>
INFLAMMATORY DISEASE
 
  OVERVIEW
 
    Another scientific and commercial focus of the Company is the development of
drugs for treatment of  inflammatory disease. These  include MMP inhibitors  for
use   against   degenerative   diseases  such   as   rheumatoid   arthritis  and
osteoarthritis and AICART  inhibitors for  use as  anti-inflammatory agents  and
immuno-suppressive agents for treatment of various neuro-degenerative disorders.
 
  MMP INHIBITORS
 
    In addition to their role in the growth and metastasis of solid tumors, MMPs
display  high  levels of  enzymatic activity  in  such degenerative  diseases as
rheumatoid arthritis and osteoarthritis. Certain  members of the MMP family  are
associated  most closely with these disease  states and, Agouron believes, offer
targets for  orally  active  drugs  with potential  for  minimal  toxicity.  The
development  of MMP  inhibitors associated with  these disease  states are being
pursued by  an  affiliate of  Roche.  If  successfully developed  by  the  Roche
affiliate,  the Company believes such selective  inhibitors of certain MMPs have
the potential to interrupt  the progression of  arthritic disease itself  rather
than  just to treat the symptoms. The Company will receive a royalty on sales by
Roche  of  any  anti-inflammatory  products  resulting  from  the  collaborative
program. See "Research and Development Agreements -- Roche."
 
  AICART INHIBITORS
 
    AICART  is  being  pursued  by  Agouron  scientists  as  a  target  for  the
development of novel  anti-inflammatory drugs.  It is widely  believed that  the
anti-inflammatory  effects observed following administration of low doses of the
anti-cancer drug  methotrexate result  from the  drug's indirect  inhibition  of
AICART.  Used for  chronic therapy,  methotrexate accumulates  in the  liver and
other tissues and  frequently results  in serious  toxicity. Agouron  scientists
believe  that inhibitors of AICART designed to avoid accumulation in tissues may
be superior  anti-inflammatory  drugs  for conditions  such  as  arthritis.  The
Company's initial lead compounds in this program are being used to validate this
assertion. Having solved the three-dimensional molecular structure of the AICART
enzyme,  Agouron  scientists believe  they are  uniquely positioned  to initiate
protein structure-based drug  design of  novel inhibitors of  the AICART  enzyme
intended  to  be  efficacious  in  the  treatment  of  inflammatory  disease. No
candidate for development has yet been  identified in this program. The  Company
presently  retains all  commercial rights to  any compounds  resulting from this
program.
 
DRUG DESIGN TECHNOLOGY
 
    Common to all of  Agouron's drug discovery programs  is the design of  novel
drugs  based  upon the  structure  of proteins  which  play key  roles  in human
disease. It  is  the centrality  of  this protein  structure-based  approach  to
rational   drug  design  which   distinguishes  the  Company   from  most  other
pharmaceutical and biotechnology companies.
 
  BACKGROUND: CONVENTIONAL DRUG DISCOVERY
 
    Historically, the pharmaceutical industry has relied upon drug discovery  by
screening-sifting  through vast inventories  of naturally-occurring and man-made
chemicals in search of previously undiscovered substances with therapeutic uses.
While screening has  been the  basis for the  discovery of  virtually all  drugs
currently   in  use,  the  Company  believes   it  has  become  an  increasingly
unsatisfactory approach as  it is both  costly and inefficient  and the rate  of
discovery  of new therapeutic compounds has  declined over the last decade. Most
importantly,  there   remain  many   important  therapeutic   needs  for   which
screening-based  research  has failed  to  yield acceptably  safe  and effective
drugs.
 
  THE IDEA OF DESIGNING DRUGS
 
    With  the  ability  to   synthesize  chemical  compounds  of   predetermined
composition, came the desire to overcome the limitations and unpredictability of
screening  by building  molecules specifically  designed to  perform therapeutic
tasks. This vision  of "rational  drug design" was  made more  plausible by  the
discovery  that, despite many differences between  them, drugs work according to
the same general scheme.
 
    Nearly every drug  molecule works  through a structural  interaction with  a
"target"  or  "receptor"  molecule  or  protein  which  play  key  roles  in all
biological processes. In the most common model for this
 
                                       24
<PAGE>
interaction, the  drug molecule  inserts itself  into a  functionally  important
crevice  of its  target protein  like a key  in a  lock, binds  there and either
induces  or,  more  commonly,  inhibits  the  protein's  normal  function.  This
universal  drug-target scheme suggested a  powerful alternative approach to drug
discovery: if it were  possible to identify in  advance the appropriate  protein
target  for  a  given  therapeutic  need and  if  enough  were  known  about the
distinguishing structure of  that target  protein, it  ought to  be feasible  to
design the structure of an ideal drug to interact with it.
 
  PROTEIN STRUCTURE-BASED DRUG DESIGN
 
    Agouron's  scientists have  developed an  approach for  drug discovery which
exploits the three-dimensional structures of molecular targets. At the heart  of
the   Company's  strategy   is  the   analytical  technique   of  protein  x-ray
crystallography,   which   enables   Agouron   scientists   to   determine   the
three-dimensional  atomic structures of target proteins and the drugs which bind
to them. The Company's  approach to drug  design integrates genetic  engineering
techniques,  which allow  the identification,  purification and  modification of
appropriate target proteins, with  innovations in protein x-ray  crystallography
and  the use of increasingly sophisticated  programs run on high speed computers
which permit chemists to predict and simulate molecular structure, dynamics  and
energetics.
 
  GENETIC ENGINEERING
 
    In   contrast  to  the  biotechnology   industry,  Agouron  employs  genetic
engineering techniques to produce proteins not as products, but as drug targets.
Genetic engineering techniques can assist scientists in identifying  appropriate
molecular targets for particular therapeutic objectives, produce target proteins
in  sufficient amounts to permit structural studies and modify proteins to probe
the connections between a target protein's structure and function.
 
  PROTEIN X-RAY CRYSTALLOGRAPHY
 
    The only  method  which  has  been successful  in  determining  the  precise
three-dimensional  atomic structure of  large proteins is  an analytic technique
known as protein x-ray  crystallography. Agouron believes  it has assembled  the
largest   and  most  experienced  group  of  protein  crystallographers  in  the
pharmaceutical industry.
 
    X-ray  crystallographic  studies  require  that  a  target  protein  be   in
crystalline form. Once such crystals are obtained, a single crystal is bombarded
with  a powerful x-ray  beam. The protein  crystal diffracts the  x-ray beam and
generates  a  definitive  diffraction  pattern.  A  complex  analytical  process
involving  extensive mathematical  computations is  then performed  on the x-ray
diffraction data. From  the results  of these  calculations, it  is possible  to
determine  the exact  three-dimensional structure of  the target  protein. It is
this  elusive  information  which  provides  the  critical  starting  point  for
three-dimensional drug design.
 
  DRUG DESIGN
 
    Having    determined   the   architecture   of   the   target   protein   in
three-dimensional atomic detail and having identified its functionally  critical
regions,  Agouron  chemists,  crystallographers  and  molecular  biologists  are
positioned to begin  the process  of drug design.  The structure  of the  target
protein  along with  representations of  its chemical  and electronic properties
(most of which can be computed accurately if the protein structure is known) are
displayed on an interactive computer graphics system. Ideas for the structure of
a  drug  molecule  which  complements   the  unique  structure  and   electronic
environment  of the target protein  are developed by members  of the design team
and are then simulated and evaluated on  the computer with the aid of more  than
100 specialized analytical software programs.
 
    The  most  promising  computer  designs of  drug  candidates  are chemically
synthesized by  the  Company's  medicinal  chemists.  As  in  conventional  drug
development  strategies, experimental measurements  are taken of  the ability of
such a newly synthesized drug candidate to produce the intended effect upon  the
target protein. Company crystallographers then re-determine the structure of the
protein  target, now  in combination with  the candidate drug  molecule, and are
able to  see in  detail the  structural interactions  actually achieved  by  the
candidate  drug with its target. Agouron scientists are positioned to relate the
performance of such a  compound measured by  familiar biochemical techniques  to
its  structural interactions  with the target  as revealed crystallographically.
The design team can  then incorporate the results  of this specialized  analysis
into the next generation of its compounds.
 
                                       25
<PAGE>
    In  summary, Agouron's drug design  methodology consists of iterative cycles
of design, simulation, synthesis, structural assessment and redesign. Its  power
lies  in the ability of  Agouron's drug design team to  see the primary event in
drug action -- the  interaction of the  drug with its target  -- as it  actually
occurs  and to be guided in the design  and optimization of drugs by the details
of this interaction. This "look" at the heart of drug and target interaction  is
provided  by Agouron's protein  x-ray crystallography research  group, which the
Company believes to be  unique in the pharmaceutical  industry by virtue of  its
configuration and experience.
 
RESEARCH AND DEVELOPMENT AGREEMENTS
 
    The  Company has funded its research  and development primarily from working
capital generated  from  both  private  and  public  sales  of  Agouron  equity,
corporate  collaborative  arrangements and  federal grants.  The Company  has an
ongoing program of business  development which may,  from time-to-time, lead  to
the establishment of corporate collaborations in addition to those noted below.
 
  JAPAN TOBACCO INC.
 
    In  December  1992,  the  Company  entered  into  an  agreement  with  JT to
collaborate  on  the  discovery,  development  and  commercialization  of  novel
therapeutic  drugs which act on key proteins  related to the human immune system
(JT 1992). In February 1994, the Company expanded its strategic alliance with JT
into the field  of anti-viral drugs  for the treatment  of infections caused  by
hepatitis  C,  the  herpes family  of  viruses  and rhinoviruses  (JT  1994). In
December 1994,  the  Company  added  its anti-HIV  drug,  Viracept,  to  the  JT
collaboration  with  the  execution  of a  worldwide  development  and licensing
agreement (JT HIV). In  January 1995, JT 1992  was canceled by mutual  agreement
and  JT 1992 resources were  reallocated to JT 1994  programs. In February 1996,
the portion of  the JT  1994 collaboration  targeting rhinovirus  was ended  and
program resources were reallocated to other JT 1994 programs.
 
    Under  the provisions  of JT  1994, JT has  agreed to  make certain research
payments of  not less  than $8,000,000  to the  Company over  a two-year  period
ending December 1996. Such payments could approximate more than $21,000,000 over
a four-year period if certain technical milestones are achieved. In addition, JT
made an up-front payment of $7,778,000, which is being amortized to revenue over
a twenty-four month period. Under the provisions of JT HIV, JT has made payments
of  $30,000,000  to Agouron  representing an  initial  payment of  $2,500,000, a
milestone payment of $3,500,000 in recognition of the satisfactory completion of
a phase  I  clinical  study  and second  milestone  payment  of  $24,000,000  in
recognition of the satisfactory completion of a pilot phase II clinical study of
Viracept.  Agouron and  JT are  currently sharing  equally the  costs of further
development of Viracept.
 
    Under the provisions of JT 1994,  the Company will have exclusive rights  to
develop,  manufacture and market  anti-hepatitis C and  anti-herpes drugs in the
United States, Canada  and Mexico.  JT will  have exclusive  rights to  develop,
manufacture and market these drugs in Japan, Taiwan and South Korea. Outside the
countries  in which they respectively have exclusive rights, Agouron and JT will
have  co-exclusive   rights  to   manufacture  and   market  jointly   developed
anti-hepatitis  C and anti-herpes drugs. Each  company will pay royalties to the
other based  upon their  respective sales  of anti-hepatitis  C and  anti-herpes
drugs.  Under the provisions of JT HIV, Agouron will retain exclusive commercial
rights to Viracept (with the right to sublicense, subject to JT's right of first
refusal) in  the  United States,  Canada  and  Mexico. JT  will  have  exclusive
commercial  rights to  Viracept (with  the right  to sublicense,  subject to the
Company's right of first refusal) in Japan and certain other countries of  Asia.
Exclusive  commercial rights  (with the right  to sublicense) in  Europe and all
remaining countries of the world will be  held by a joint venture owned  equally
by  Agouron and JT.  The two companies  will share royalties  or profits equally
from the worldwide commercialization of Viracept.
 
    Under a separate agreement dated December 1992, JT purchased 155,844  shares
of newly issued Common Stock for an aggregate purchase price of $3,000,000. Such
purchase represented approximately 2% of the then outstanding Common Stock.
 
                                       26
<PAGE>
  ROCHE
 
    In June 1996, the Company completed a three-year agreement entered into with
Syntex (U.S.A.) Inc. (now a subsidiary of Roche) to collaborate on the discovery
of  novel matrix metalloprotease inhibitor  drugs. Roche has exclusive worldwide
commercial rights  in any  MMP  inhibitors used  to  treat arthritis  and  other
degenerative  bone diseases,  subject to  the payment  of royalties  to Agouron.
Under the terms of the  agreement, the Company will  have a royalty position  in
certain  other agreement products, if any,  and other development and commercial
rights in other agreement products, if any.
 
    Under a  separate  agreement dated  June  1993, Syntex  Corporation  (now  a
subsidiary  of Roche) purchased 155,844 shares  of newly issued Common Stock for
an  aggregate   purchase  price   of  $3,000,000.   Such  purchase   represented
approximately 2% of the then outstanding Common Stock.
 
    In   June   1996,  Agouron   signed  a   binding   letter  of   intent  with
Hoffmann-LaRoche Inc.  and  F. Hoffmann-La  Roche  Ltd, subsidiaries  of  Roche,
providing  for the  collaborative development and  commercialization of Thymitaq
and of  the  Agouron  anti-cancer compound  designated  AG3340  currently  under
preclinical   development.  Agouron  is  to  receive  initial  license  fees  of
$15,000,000 and additional development milestone  payments of up to  $40,000,000
from  Roche. Roche has  agreed to bear  80% of future  costs of developing these
drugs. Agouron and Roche will cooperatively market the two compounds for  cancer
indications  and  share  profits in  North  America, while  Roche  has exclusive
marketing rights  for  cancer  indications  to  these  compounds  outside  North
America,  subject to certain co-promotion rights and the payment of royalties to
Agouron. Roche is  to provide annual  research support of  $3,000,000 for  three
years  as well as subsequent milestone payments  of up to $20,000,000 to Agouron
for similar  commercial  rights  for  all indications  in  compounds  which  are
generated in a collaborative research program focused on cell cycle control. See
"Research and Development Programs -- Cancer -- Cell Cycle Control: cdk4."
 
  SCHERING-PLOUGH CORPORATION
 
    In April 1994, the Company and Schering completed a three-year collaborative
research  agreement providing for  the discovery and  development of anti-cancer
drugs which  target oncogenic  RAS  proteins. Each  company may  pursue  further
discovery or development efforts in this program area at its sole discretion and
expense with no subsequent obligations to the other company.
 
  ELI LILLY AND COMPANY
 
    In  April 1993,  the Company and  Lilly completed  a five-year collaborative
research program in several therapeutic  categories. Further development of  any
discoveries  made  in the  program  will be  undertaken  at each  company's sole
discretion  and  expense.  Agouron  has  continuing  commercial  rights   and/or
financial interests in certain of these discoveries.
 
  NATIONAL INSTITUTES OF HEALTH
 
    The  Company is  the grantee  organization for  two grants  from the  NIH to
conduct research related to HIV.
 
COMPETITION
 
    The pharmaceutical  and  biotechnology  industries are  subject  to  intense
competition  and rapid and significant  technological change. Many companies and
organizations,  including  major  pharmaceutical,  biotechnology  and   chemical
companies,  universities  and  other  research  organizations,  are  engaged  in
discovery and development  of drugs for  diseases targeted by  the Company.  For
example,  the Company is aware of several pharmaceutical companies that have HIV
protease inhibitors, some of which are currently being marketed, including those
of Abbott Laboratories, Inc., Merck & Co., Inc. and Roche. Certain companies and
organizations have substantially greater  financial and other resources,  larger
research  and  development staffs  and more  extensive production  and marketing
organizations, experience and capabilities than  the Company. In addition,  many
companies  have significantly greater experience than the Company in preclinical
testing and  in conducting  human clinical  trials of  potential  pharmaceutical
products  and  in obtaining  FDA and  other regulatory  approvals. All  of these
companies  and  other  research  organizations  compete  with  the  Company   in
recruiting and retaining highly qualified scientific and management personnel.
 
                                       27
<PAGE>
    Agouron  was  the first  company  to devote  itself  to the  development and
application of  protein  structure-based  drug  design.  As  such,  the  Company
believes   that  it  has  achieved   certain  competitive  advantages  including
developmental  lead  time,  level  of  commitment  to  the  technology  and  the
development  of certain practical or  technical capabilities. However, in recent
years several pharmaceutical companies have undertaken to establish capabilities
in  protein  x-ray  crystallography,  either  internally  or  through   academic
collaborations,  and can be presumed to be engaged in the use of such technology
for the same  purposes as is  the Company. Certain  biotechnology companies  and
other companies have also entered into the field of protein structure-based drug
design.  For example,  Abbott Laboratories,  Ciba-Geigy Limited,  Glaxo Wellcome
plc, Merck and  Roche have  developed programs focused  on structure-based  drug
design. The Company expects that the technology for protein structure-based drug
design  will become more widely implemented over time and will ultimately become
more common in the pharmaceutical industry.
 
    The Company believes that its ability to compete successfully will be  based
on  its  ability  to  create and  maintain  scientifically  advanced technology,
attract and retain scientific personnel with a broad range of expertise,  obtain
patent  protection  or  otherwise  develop  proprietary  products  or processes,
conduct clinical trials  and obtain  required government approvals  on a  timely
basis,  select and  pursue drug  design projects  in areas  in which significant
market opportunities exist or are likely to develop, manufacture its products on
a cost-effective basis and successfully market  its products either alone or  in
conjunction  with others. Many  of the Company's  competitors have substantially
greater financial resources, clinical  and regulatory experience,  manufacturing
capabilities  and  sales and  marketing  organizations than  Agouron.  See "Risk
Factors -- Technological Change and Competition" and "Risk Factors -- Attraction
and Retention of Personnel."
 
PATENTS AND TRADE SECRETS
 
    The Company  seeks  patent protection  for  its proprietary  technology  and
potential  products in the United  States and in foreign  countries. Most of the
Company's products are expected to be synthetic chemical compounds which may  be
afforded  patent protection under principles  and procedures well established by
the United States Patent and Trademark Office under United States patent law.
 
    The Company's strategy is  to pursue a strong  patent portfolio and  Agouron
holds  several patents, including a patent  covering the chemical composition of
Viracept. The Company is currently  prosecuting a number of patent  applications
in  the  United States  and in  various other  countries seeking  protection for
certain series  of  compounds,  including, Thymitaq  and  Viracept  and  certain
proprietary technology. The Company will continue to file patent applications on
its  evolving  technology,  processes  and products.  The  Company  has recently
received one  United States  patent covering  processes of  making Thymitaq  and
related  compounds and  intermediates thereof.  The Company's  failure to obtain
patent protection for its products could have an adverse impact on the Company.
 
    Many of  the  processes  and much  of  the  know-how of  importance  to  the
Company's  technology are dependent upon the skills, knowledge and experience of
its scientific and technical personnel,  which skills, knowledge and  experience
are  not patentable. To protect its rights  in these areas, the Company requires
all employees, significant consultants and advisors, and collaborators to  enter
into  confidentiality  agreements  with  Agouron.  There  can  be  no assurance,
however, that  these  agreements  will provide  meaningful  protection  for  the
Company's  trade secrets, know-how or other proprietary information in the event
of any  unauthorized  use or  disclosure  of  such trade  secrets,  know-how  or
proprietary  information.  Further, in  the  absence of  patent  protection, the
Company may be  exposed to competitors  who independently develop  substantially
equivalent  technology or otherwise gain access  to the Company's trade secrets,
knowledge or other  proprietary information.  See "Risk Factors  -- Patents  and
Proprietary Technology."
 
GOVERNMENT REGULATION
 
    The  production  and marketing  of the  Company's  products and  its ongoing
research and  development  activities  are subject  to  regulation  for  safety,
efficacy  and quality by numerous governmental  authorities in the United States
and other countries.  Pharmaceutical products  intended for  therapeutic use  in
humans  are principally governed by FDA regulations  in the United States and by
comparable government regulations in  foreign countries. Various federal,  state
and   local   statutes   and   regulations   also   govern   or   influence  the
 
                                       28
<PAGE>
research   and   development,   manufacturing,   safety,   labeling,    storage,
recordkeeping,  distribution  and marketing  of  such products.  The  process of
completing preclinical and clinical  testing and obtaining  the approval of  FDA
and similar health authorities in foreign countries to market a new drug product
requires  a  significant  number of  years  and the  expenditure  of substantial
resources. Failures or delays by the  Company or its collaborators or  licensees
in  obtaining  regulatory  approvals  would adversely  affect  the  marketing of
products being developed  by the Company  and the Company's  ability to  receive
product revenues or royalties.
 
    The  steps required by FDA before a  new human pharmaceutical product may be
marketed in the United States include: (a) preclinical laboratory tests, IN VIVO
preclinical studies and  formulation studies;  (b) the  submission to  FDA of  a
request  for authorization to conduct clinical  trials on an Investigational New
Drug Application  ("IND"), which  must become  effective before  human  clinical
trials  may commence; (c) adequate and  well-controlled human clinical trials to
establish the  safety  and  efficacy of  the  drug  for its  intended  use;  (d)
submission to FDA of a NDA; and (e) review and approval of the NDA by FDA before
the  drug product may  be shipped or  sold commercially. Prior  to obtaining FDA
approval for each product, each  manufacturing establishment for new drugs  must
be registered with and receive appropriate approval by FDA.
 
    Preclinical  tests include  laboratory evaluation  of product  chemistry and
formulation, as well as animal studies to assess the safety and efficacy of  the
product.  Preclinical test results  are submitted to  FDA as a  part of the IND.
Clinical trials are typically conducted in three sequential phases, although the
phases may overlap. Phase I represents the initial administration of the drug to
a small group  of humans,  either healthy volunteers  or patients,  to test  for
safety,  dosage tolerance,  absorption, distribution,  metabolism, excretion and
clinical pharmacology  and, if  possible,  early indications  of  effectiveness.
Phase  II involves  studies in  a small  sample of  the actual  intended patient
population to assess  the efficacy of  the investigational drug  for a  specific
clinical  indication, to ascertain dose tolerance and the optimal dose range and
to collect  additional clinical  information relating  to safety  and  potential
adverse effects. Once an investigational drug is found to have some efficacy and
an  acceptable clinical safety profile in the targeted patient population, phase
III studies are often initiated to further establish safety and efficacy of  the
investigational  drug in a broader sample  of the target patient population. The
results of the  clinical trials  together with  the results  of the  preclinical
tests  and complete manufacturing information are submitted  in a NDA to FDA for
approval. See "Risk Factors -- Uncertainty Associated with Clinical Trials."
 
    If a  NDA  is  submitted  to  FDA, there  can  be  no  assurance  that  such
application  will be reviewed and approved by FDA in a timely manner, if at all.
Even after initial FDA  approval has been  obtained, further studies,  including
post-market  studies, may be required to provide additional information. Results
of such post-market programs  may limit or expand  the further marketing of  the
product.
 
    The  Company is  also subject  to foreign  regulatory requirements governing
development, manufacturing and sales of pharmaceutical products that vary widely
from country to country. Approval of a drug by applicable regulatory agencies of
foreign countries must be secured prior to  the marketing of such drug in  those
countries.  The regulatory  approval process may  be more or  less rigorous from
country to country and the time required  for approval may be longer or  shorter
than that required in the United States.
 
    In   addition  to  the  regulatory   framework  for  pharmaceutical  product
approvals, the Company  is and  may become  subject to  various federal,  state,
local and foreign laws, regulations and recommendations relating to safe working
conditions,  laboratory  and manufacturing  practices,  the experimental  use of
animals  and  the  use  and  disposal  of  hazardous  or  potentially  hazardous
substances,  including radioactive compounds and infectious disease agents, used
in connection  with Agouron's  research  and development  work. The  Company  is
unable  to  predict  the  extent  of  restrictions  that  might  arise  from any
governmental  or  administrative  action.   See  "Risk  Factors  --   Government
Regulation."
 
MANUFACTURING
 
    The  Company  currently has  no manufacturing  facilities for  production of
commercial quantities  of  any  compounds under  development  as  pharmaceutical
products.  The Company's facilities  include scale-up laboratories  in which the
Company intends to produce,  under GMP, amounts of  its drug product  candidates
 
                                       29
<PAGE>
sufficient  for use in certain early clinical trials. The Company is and will be
relying upon third parties to manufacture its products in quantities  sufficient
to  meet both clinical and commercial needs.  The Company will be dependent upon
these manufacturers to comply with GMP and to meet its production  requirements.
There  can  be  no  assurance  that  these  manufacturers  will  timely  deliver
sufficient quantities of  the Company's products  or that the  Company would  be
able  to find substitute manufacturers, if  necessary. See "Risk Factors -- Lack
of Manufacturing Experience."
 
MARKETING
 
    The Company  does  not  currently market  any  pharmaceutical  products  but
intends  to market  any approved cancer  and anti-HIV products  in North America
through its  own sales  and marketing  organization. The  Company has  begun  to
establish its sales and marketing organization by hiring key sales and marketing
management personnel who possess significant pharmaceutical industry experience.
Additional sales and marketing personnel will be hired and certain programs will
be   implemented  upon  the  achievement  of  clinical  development  milestones,
including  the  successful  completion  of  pivotal  clinical  trials  and   the
submission  of a NDA.  The Company intends  to possess the  capability to launch
products concurrent  with  their  approval  by  FDA.  The  Company's  sales  and
marketing  efforts will utilize a field  sales organization focused primarily on
office and  hospital  based physicians  including  key medical  thought  leaders
Additionally, the Company will seek to ensure market access and availability for
its  products in part  by establishing relationships  within key market segments
including health maintenance organizations, third-party payers and  governmental
agencies. See "Risk Factors -- Lack of Sales and Marketing Capabilities."
 
HUMAN RESOURCES
 
    As  of May 31, 1996, the Company had 353 employees, 91 of whom hold Ph.D. or
M.D. degrees. Two  hundred eighty-three  employees are engaged  in, or  directly
support,  research  and product  development.  The Company's  employees  are not
covered by  a collective  bargaining  agreement and  the Company  considers  its
relations  with  its employees  to be  excellent. The  Company has  entered into
confidentiality agreements with all of its employees.
 
FACILITIES
 
    The Company leases space in three facilities located in La Jolla, California
which provide  a  total of  approximately  110,000  square feet  of  office  and
laboratory  space.  The Company's  corporate headquarters  are located  at 10350
North Torrey  Pines Road,  Suite  100, La  Jolla,  California 92037,  where  the
Company  occupies  approximately 42,000  square  feet under  three  leases which
expire in April 1997. Research and development activities are conducted at  3565
General  Atomics Court,  San Diego, California  92121 (where the  Company is the
sole tenant and occupies  approximately 43,500 square feet  under a lease  which
expires  September  2001)  and  at  11099 North  Torrey  Pines  Road,  La Jolla,
California 92037 (where  the Company occupies  approximately 24,500 square  feet
under  a  lease  which  expires  in  September  2000).  These  two  research and
development buildings provide state-of-the-art facilities designed  specifically
to  implement  and support  the Company's  innovative  approach to  drug design.
Included in the facilities are approved scale-up laboratories in which  kilogram
quantities of Company-designed drug compounds are manufactured under current GMP
for use in clinical trials. Additionally, the Company leases approximately 1,000
square  feet of  office space in  the United  Kingdom which it  utilizes for its
European clinical  staff. While  the Company  believes that  its facilities  are
adequate  for its current operations, it is negotiating two further leases for a
total of approximately 70,000 square  feet to provide additional laboratory  and
administrative  space. Additional  facilities will  be necessary  if the Company
undertakes commercial manufacturing.
 
LEGAL PROCEEDINGS
 
    The Company is involved in certain legal proceedings generally incidental to
its normal business activities. While the outcome of any such proceedings cannot
be accurately predicted, the Company does not believe the ultimate resolution of
any such existing matters should have a material adverse effect on its financial
position or results of operations.
 
                                       30
<PAGE>
                                   MANAGEMENT
 
OFFICERS AND DIRECTORS
 
    The executive officers and directors of the Company are as follows:
 
<TABLE>
<CAPTION>
NAME                                                      AGE     POSITION
- -----------------------------------------------------     ---     -----------------------------------------------------
<S>                                                    <C>        <C>
Peter Johnson (2)(4).................................     51      President, Chief Executive Officer and Director
 
Neil J. Clendeninn, M.D., Ph.D.......................     47      Vice President, Clinical Affairs
 
Steven S. Cowell (2).................................     47      Vice President, Finance and Chief Financial Officer
 
Gary E. Friedman (2).................................     49      Vice President, General Counsel, Secretary and
                                                                   Director
 
Robert C. Jackson, Ph.D..............................     53      Vice President, Research and Development
 
Barry D. Quart, Pharm.D..............................     39      Vice President, Regulatory Affairs
 
R. Kent Snyder.......................................     42      Vice President, Commercial Affairs
 
Glenn R. Zinser......................................     52      Vice President, Operations
 
John N. Abelson, Ph.D. (1)...........................     56      Director
 
Patricia M. Cloherty (3)(4)..........................     54      Director
 
A.E. Cohen (1)(4)....................................     60      Director
 
Michael E. Herman (1)(4).............................     55      Director
 
Irving S. Johnson, Ph.D. (4).........................     71      Director
 
Antonie T. Knoppers, M.D., Ph.D. (3).................     81      Director
 
Melvin I. Simon, Ph.D. (3)...........................     59      Director
</TABLE>
 
- ------------------------
(1) Member of Directors Compensation Committee
(2) Member of Management Compensation Committee
(3) Member of Audit Committee
(4) Member of Executive Committee
 
    PETER JOHNSON, a founder  of the Company,  has served as  a director and  as
president  and chief  executive officer  of the  Company since  its inception in
1984. Through  1989,  Mr.  Johnson  held  various  positions  with  The  Agouron
Institute,  including executive director.  Mr. Johnson received  a M.A. from the
University of California, San Diego.
 
    NEIL J. CLENDENINN joined  the Company in February  1993 as vice  president,
clinical  affairs.  From 1985  until joining  the  Company, Dr.  Clendeninn held
various  positions  with   Burroughs  Wellcome  Co.,   including  head  of   the
chemotherapy  section from 1988.  From 1981 through  1985, Dr. Clendeninn worked
with the  clinical oncology  and clinical  pharmacology groups  at the  National
Institutes of Health. Dr. Clendeninn received a M.D. and a Ph.D. in pharmacology
from New York University.
 
    STEVEN  S.  COWELL joined  the  Company in  August  1991 as  vice president,
finance and chief financial  officer. From 1982 until  joining the Company,  Mr.
Cowell  held various positions, the most recent  of which was vice president and
controller at  Cetus  Corporation,  a  public  biotechnology  company  primarily
engaged   in  the  development,  manufacture  and  marketing  of  pharmaceutical
products. Mr. Cowell is a Certified Public Accountant in California and received
a B.S. in business administration from the University of California, Berkeley.
 
                                       31
<PAGE>
    GARY E. FRIEDMAN, a founder of the  Company, has served as a director  since
its  inception,  as the  secretary of  the Company  since May  1986 and  as vice
president and general counsel since  December 1991. Previously, from 1982  until
December  1991, Mr. Friedman was a principal of  the law firm of Friedman, Jay &
Cramer, a  Professional  Corporation. Mr.  Friedman  is a  California  Certified
Specialist  in Taxation.  Mr. Friedman  received a  J.D. and  a M.B.A.  from the
University of California, Berkeley, and a L.L.M. in taxation from the University
of San Diego.
 
    ROBERT C.  JACKSON joined  the  Company in  March  1991 as  vice  president,
research and development. From June 1990 to February 1991, Dr. Jackson was group
director  of  the  anti-cancer  drug  discovery  program  at  The  DuPont  Merck
Pharmaceutical Company and, from 1982 to June 1990, held various positions  with
the  Parke-Davis Pharmaceutical Research Division of the Warner-Lambert Company,
including director of tumor biology and director of the chemotherapy department.
Dr. Jackson received a Ph.D. in biochemistry from the University of London.
 
    BARRY D. QUART joined the Company in June 1993 as vice president, regulatory
affairs. From 1983 until joining the Company, Dr. Quart held various  management
positions with the Bristol-Myers Squibb Company, including executive director of
international  regulatory affairs  from 1992. Dr.  Quart received  a Pharm.D. in
clinical pharmacy from the University of California, San Francisco.
 
    R. KENT SNYDER joined the Company  in July 1991 as vice president,  business
development.  In June  1995, Mr. Snyder's  title was changed  to vice president,
commercial affairs. From 1982 until joining the Company, Mr. Snyder held various
positions with Marion Laboratories, Inc. and its successor organization,  Marion
Merrell   Dow  Inc.  (now   Hoechst  Marion  Roussel),   including  director  of
U.S./European licensing. Prior to his employment  at Marion, from 1978 to  1982,
he  held various sales and marketing  positions with Hoffmann-La Roche, Inc. Mr.
Snyder received a M.B.A. from Rockhurst College.
 
    GLENN R. ZINSER joined the Company in 1987 and, since July 1995, has  served
as  vice president,  operations. Previously,  from 1987  through June  1995, Mr.
Zinser held  various management  positions with  the Company,  including  senior
director,  operations from  July 1993 through  June 1995. Mr.  Zinser received a
M.B.A. from the University of California, Los Angeles.
 
    JOHN N. ABELSON, a founder  of the Company, has  served as a director  since
its  inception. Dr. Abelson, a molecular biologist,  is a member of the National
Academy of Sciences. Since 1982, Dr. Abelson has been a member of the faculty of
the Division of Biology  at the California Institute  of Technology where,  from
October 1989 until June 1995, he served as chairman. Previously, Dr. Abelson was
a  member of  the faculty in  the Department  of Chemistry at  the University of
California, San Diego. Dr. Abelson received a Ph.D. in biophysics from The Johns
Hopkins University and was a postdoctoral fellow at the Laboratory of  Molecular
Biology  in Cambridge,  England. Dr.  Abelson also serves  as a  director of The
Agouron Institute.
 
    PATRICIA M. CLOHERTY  joined the  Board in  December 1988.  Since 1970,  Ms.
Cloherty  has been associated with Patricof  & Co. Ventures, Inc. (formerly Alan
Patricof Associates, Inc.), a  New York venture  capital firm ("Patricof"),  and
has  been a general  partner of its funds  since 1973. In  1993, she was elected
president of Patricof. Ms. Cloherty also served as deputy administrator for  the
U.S. Small Business Administration in 1977 and 1978. Ms. Cloherty also serves on
the  board of directors of several private  companies and is the chairman of the
National Venture Capital Association.
 
    A.E. COHEN  joined the  Board in  March 1992.  Mr. Cohen  is an  independent
management consultant. From 1957 until his retirement in January 1992, Mr. Cohen
held various positions at Merck & Co., Inc., including senior vice president and
president  of the  Merck Sharp  & Dohme  International Division.  Currently, Mr.
Cohen is the chairman of the board of Neurobiological Technologies, Inc. and  is
a  member of the board of directors  of Akzo N.V., Immunomedics, Inc., Macrochem
Corporation, Teva Pharmaceutical Industries Ltd.  and Vasomedical, Inc., all  of
which  are public companies. Mr. Cohen also  serves on the board of directors of
several private companies.
 
    MICHAEL E. HERMAN joined the Board in October 1992. Mr. Herman is a  private
investor,  as well as president  and chief operating officer  of the Kansas City
Royals Baseball Team. From October 1974 until his retirement in 1990, Mr. Herman
held  various  positions  at  Marion  Laboratories,  Inc.  (now  Hoechst  Marion
 
                                       32
<PAGE>
Roussel),  including  executive  vice  president  and  chief  financial officer.
Currently, Mr. Herman serves as chairman  of the finance committee of the  Ewing
Marion  Kauffman Foundation, a private foundation  located in Kansas City, where
from 1985 through 1990,  he was the president  and chief operating officer.  Mr.
Herman  is also  a member of  the board  of directors of  Cerner Corporation and
Seafield Capital, both of which are public companies, and serves on the board of
directors of several private companies.
 
    IRVING S.  JOHNSON  joined  the  Board  in  May  1989.  Dr.  Johnson  is  an
independent  consultant  in biomedical  research  working with  numerous private
companies. From 1953  until his retirement  in November 1988,  Dr. Johnson  held
various positions at Lilly, including vice president of research from 1973 until
1988.  Dr. Johnson also served on several  committees of the National Academy of
Sciences, the Office  of Technology  Assessment and the  National Institutes  of
Health.  Currently,  he  is  a  member of  the  board  of  directors  of Allelix
Biopharmaceuticals Inc., Athena Neurosciences,  Inc. and Ligand  Pharmaceuticals
Incorporated, all of which are public companies. Dr. Johnson received a Ph.D. in
developmental biology from the University of Kansas.
 
    ANTONIE  T.  KNOPPERS joined  the Board  in  July 1991.  Dr. Knoppers  is an
independent management consultant. From 1952  until his retirement in 1975,  Dr.
Knoppers held various positions at Merck & Co., Inc., including vice chairman of
the board and president and chief operating officer. Dr. Knoppers is a member of
the  board of  directors of Centocor,  Inc., a public  biotechnology company. In
addition, he is a member of the board of trustees of the Salk Institute, was the
former chairman of the U.S. Council of the International Chamber of Commerce and
a member  of  the advisory  board  of PaineWebber  Development  Corporation,  an
affiliate  of PaineWebber Incorporated, a  representative of the Underwriters in
this offering. Dr. Knoppers received a M.D. from the University of Amsterdam and
a Ph.D. from the University of Leiden, The Netherlands.
 
    MELVIN I. SIMON, a founder  of the Company, has  served as a director  since
its  inception. Dr. Simon, a  molecular geneticist, is a  member of the National
Academy of Sciences. Currently, Dr. Simon is chairman of the Division of Biology
at the California  Institute of Technology  where he  has been a  member of  the
faculty  since 1982. Previously,  Dr. Simon was  a member of  the faculty in the
Department of Biology  at the  University of  California, San  Diego. Dr.  Simon
received a Ph.D. in biochemistry from Brandeis University. Dr. Simon also serves
as a director of The Agouron Institute.
 
    The  Board consists of nine  directors elected by the  holders of the Common
Stock. All directors of the Company hold office until the next annual meeting of
the shareholders  and  the  election  and  qualification  of  their  successors.
Non-officer  members  of the  Board  of Directors  of  the Company  receive cash
compensation in the amount of $250 per meeting attended for their services as  a
director.
 
                                       33
<PAGE>
                           DESCRIPTION OF SECURITIES
 
    The authorized capital stock of the Company consists of 75,000,000 shares of
Common  Stock,  without  par value,  and  2,000,000 shares  of  preferred stock,
without par value ("Preferred Stock"). There is no Preferred Stock  outstanding.
The  Board of Directors is authorized to determine the dividend rights, dividend
rate,  conversion  rights,  voting  rights,  rights  and  terms  of  redemption,
liquidation  preferences and sinking  fund terms on any  series of the Preferred
Stock, the  number  of  shares  constituting such  series  and  the  designation
thereof.  The Company  has no  present plans  to issue  any shares  of Preferred
Stock. The issuance of Preferred Stock could have the effect of aiding the Board
of Directors in opposing takeover attempts and could adversely affect the voting
power of the holders of the Common Stock.
 
COMMON STOCK
 
    At May 31, 1996, there were approximately 10,670,000 shares of Common  Stock
outstanding held by approximately 5,000 beneficial owners. The holders of shares
of  Common Stock are entitled to elect  all directors. The bylaws of the Company
provide that there are nine directors. Upon giving notice of intent to cumulate,
holders of Common  Stock may  cumulate votes in  the election  of directors.  In
general,  the  approval  of proposals  submitted  to shareholders  at  a meeting
requires a favorable vote of  the majority of the holders  of the shares of  the
Common  Stock represented and voting at the meeting on which the matter is to be
adopted.  Each  share  of  Common  Stock   entitles  its  owner  to  one   vote.
Additionally,  under California  law, certain fundamental  matters affecting the
Company may require  a favorable vote  of a greater  percentage. As an  example,
sale  or transfer of all Company assets  or merger or dissolution of the Company
would each require the affirmative vote of a majority of the outstanding shares.
Holders of  Common Stock  are entitled  to  receive dividends  when, as  and  if
declared   by  the  Board   of  Directors.  Under   the  Company's  articles  of
incorporation,  holders  of  Common  Stock  have  no  preemptive,  subscription,
redemption  or conversion rights  and there are no  sinking fund provisions with
respect to the Common Stock. All of the outstanding shares of Common Stock  are,
and the shares to be issued in this offering will be, validly issued, fully paid
and non-assessable.
 
    As  of June  14, 1996, options  to purchase  a total of  3,375,800 shares of
Common Stock were  outstanding. Certain of  the Company's current  shareholders,
including  all directors and executive officers, have agreed not to offer, sell,
contract to sell or grant any option to purchase or otherwise dispose of any  of
the  Common Stock owned by them  for a period of 90  days after the date of this
Prospectus without  the prior  written  consent of  the Representatives  of  the
Underwriters. See "Underwriting."
 
PREFERRED STOCK
 
    The  Board of  Directors has  the authority,  without further  action by the
stockholders, to issue up to 2,000,000 shares of Preferred Stock in one or  more
series, and to fix the rights, preferences, privileges and restrictions thereof,
including,  but  not  limited  to, dividend  rights,  conversion  rights, voting
rights, rights  and  terms  of  redemption,  and  liquidation  preferences.  The
issuance  of  Preferred Stock  may  have the  effect  of delaying,  deferring or
preventing a change in control of the Company without any further action by  the
stockholders.  The Board of  Directors, without stockholder  approval, can issue
Preferred Stock, with voting and conversion rights which could adversely  affect
the  voting power of  the holders of  Common Stock. In  addition, such Preferred
Stock may have  other rights, including  economic rights, senior  to the  Common
Stock  and, as  a result,  the issuance  thereof could  have a  material adverse
affect on the market value of the Common Stock. The Company has no present  plan
to  issue any  shares of  Preferred Stock.  However, the  Board of  Directors is
evaluating the appropriateness of adopting a shareholder rights agreement  which
would  provide certain  protections for  the Company  and its  shareholders from
certain changes  in  control  of  the  Company not  approved  by  the  Board  of
Directors.  If  adopted,  such an  agreement  could  result in  the  issuance of
warrants to acquire shares of Preferred Stock.
 
TRANSFER AGENT AND REGISTRAR
 
    The transfer agent and  registrar for the Common  Stock is Wells Fargo  Bank
N.A., Los Angeles, California.
 
                                       34
<PAGE>
                                  UNDERWRITING
 
    Upon  the terms and subject to  the conditions of the Underwriting Agreement
(the "Underwriting  Agreement") among  the Company  and the  Underwriters  named
below  (the "Underwriters"), for whom PaineWebber Incorporated and Alex. Brown &
Sons Incorporated  are acting  as Representatives  (the "Representatives"),  the
Underwriters  severally have agreed to purchase from the Company and the Company
has agreed to sell to the Underwriters, 2,500,000 shares of Common Stock,  which
in the aggregate equal the number of shares set forth opposite the names of such
Underwriters below:
 
<TABLE>
<CAPTION>
                                                         NUMBER OF
UNDERWRITERS                                              SHARES
- -------------------------------------------------------  ---------
<S>                                                      <C>
PaineWebber Incorporated...............................
Alex. Brown & Sons Incorporated........................
                                                         ---------
    Total..............................................  2,500,000
</TABLE>
 
    In the Underwriting Agreement, the several Underwriters have agreed, subject
to  certain conditions, to purchase all of the shares of Common Stock being sold
pursuant to  such Agreement  (other  than those  covered by  the  over-allotment
option  described  below),  if  any are  purchased.  The  Underwriting Agreement
provides that,  in  the  event  of  a default  by  an  Underwriter,  in  certain
circumstances,  the purchase  commitments of non-defaulting  Underwriters may be
increased or the Underwriting Agreement may be terminated.
 
    The Company has been  advised by the  Representatives that the  Underwriters
propose  to offer the shares of Common Stock  in part to the public at the price
to the public set  forth on the cover  page of this Prospectus,  and in part  to
certain securities dealers (who may include the Underwriters) at such price less
a concession not in excess of $    per share; and that the Underwriters and such
dealers may reallow a discount not in excess of $    per share to other dealers,
including  the Underwriters. After the commencement  of the public offering, the
public offering price, the  concession to selected dealers  and the discount  to
other dealers may be changed by the Representatives and the Managers.
 
    The  Company has granted  to the Underwriters  an option, exercisable during
the  45-day  period  after  the  date  of  this  Prospectus,  under  which   the
Underwriters  may purchase up to 375,000  additional shares of Common Stock from
the Company at  the price  to the public,  less the  underwriting discounts  and
commissions set forth on the cover page of this Prospectus. The Underwriters may
exercise  the option only  to cover over-allotments, if  any, made in connection
with the offering of the  shares of Common Stock  offered hereby. To the  extent
such  option is  exercised, each Underwriter  will become  obligated, subject to
certain conditions,  to  purchase  approximately the  same  percentage  of  such
additional  shares of Common Stock  as it was obligated  to purchase pursuant to
the Underwriting Agreement.
 
    The Company and certain of the Company's current shareholders, including all
directors and executive officers of the Company, have agreed not to offer, sell,
contract to sell or otherwise dispose of  any shares of Common Stock, or  rights
to  acquire shares of  Common Stock, for a  period of 90 days  after the date of
this Prospectus without the prior written consent of the Representatives.
 
    The Company  has  agreed  to  indemnify  the  Underwriters  against  certain
liabilities, including liabilities under the Securities Act, or to contribute to
payments the Underwriters may be required to make in respect thereof.
 
    PaineWebber  Incorporated  was a  representative  of the  underwriters  in a
public offering by the Company of 3,000,000 shares of Common Stock in  September
1995,   for  which  PaineWebber  Incorporated  received  customary  underwriting
discounts and commissions.
 
    The rules  of  the Securities  and  Exchange Commission  (the  "Commission")
generally  prohibit the  Underwriters from making  a market in  the Common Stock
during the  two business  day period  prior  to commencement  of sales  in  this
offering  (the  "Cooling  Off  Period"). The  Commission  has,  however, adopted
 
                                       35
<PAGE>
Rule 10b-6A  under  the Securities  Exchange  Act  of 1934,  as  amended  ("Rule
10b-6A"),  which provides an exemption from such prohibition for certain passive
market making transactions. Such passive market making transactions must  comply
with applicable price and volume limits and must be identified as passive market
making transactions. In general, pursuant to Rule 10b-6A, a passive market maker
may  display its  bid for a  security at  a price not  in excess  of the highest
independent bid for the security. If all independent bids are lowered below  the
passive  market maker's bid, however, such bid must then be lowered when certain
purchase limits are exceeded. Further, net  purchases by a passive market  maker
on  each day  are generally  limited to  a specified  percentage of  the passive
market maker's average  daily trading volume  in a security  during a  specified
prior  period and must be  discontinued when such limit  is reached. Pursuant to
the exemption provided by Rule 10b-6A,  certain of the Underwriters and  selling
group members may engage in passive market making in the Common Stock during the
Cooling  Off Period. Passive market makers may stabilize the market price of the
Common Stock  at  a level  above  that which  might  otherwise prevail  and,  if
commenced, may be discontinued at any time.
 
                                 LEGAL MATTERS
 
    The  validity of the Common Stock being  offered hereby has been passed upon
for the Company by  Ferris, Britton & Proctor,  a Professional Corporation,  San
Diego,  California. A shareholder  of Ferris, Britton  & Proctor, a Professional
Corporation, owns  1,000 shares  of  Common Stock  of  the Company.  Morrison  &
Foerster  LLP, New York, New York, is  acting as counsel for the Underwriters in
connection with certain legal matters relating  to the sale of the Common  Stock
offered hereby.
 
                                    EXPERTS
 
    The  financial statements as of  June 30, 1995 and 1994  and for each of the
three years in the period  ended June 30, 1995  included in this Prospectus  and
the  financial statements  incorporated in this  Prospectus by  reference to the
Annual Report  on Form  10-K for  the  year ended  June 30,  1995 have  been  so
included  and incorporated  in reliance on  the report of  Price Waterhouse LLP,
independent accountants,  given on  the authority  of said  firm as  experts  in
auditing and accounting.
 
                                       36
<PAGE>
                         INDEX TO FINANCIAL STATEMENTS
 
<TABLE>
<CAPTION>
                                                         PAGE
                                                         ----
<S>                                                      <C>
Report of Price Waterhouse LLP, Independent
 Accountants...........................................  F-2
Financial Statements:
  Balance Sheet........................................  F-3
  Statement of Operations..............................  F-4
  Statement of Stockholders' Equity....................  F-5
  Statement of Cash Flows..............................  F-6
  Notes to Financial Statements........................  F-7
  Supplemental Financial Information (unaudited).......  F-15
</TABLE>
 
                                      F-1
<PAGE>
                       REPORT OF INDEPENDENT ACCOUNTANTS
 
To the Board of Directors and Stockholders
of Agouron Pharmaceuticals, Inc.:
 
    In our opinion, the accompanying balance sheet and the related statements of
operations,  of stockholders'  equity and of  cash flows present  fairly, in all
material respects, the  financial position of  Agouron Pharmaceuticals, Inc.  at
June 30, 1994 and 1995, and the results of its operations and its cash flows for
each  of the three years  in the period ended June  30, 1995, 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
 
San Diego, California
 July 25, 1995, except as to Notes 1, 4 and 9
 which are as of August 24, 1995
 
                                      F-2
<PAGE>
                         AGOURON PHARMACEUTICALS, INC.
                                 BALANCE SHEET
                             (DOLLARS IN THOUSANDS)
                                     ASSETS
 
<TABLE>
<CAPTION>
                                                                                       JUNE 30,
                                                                                  ------------------  MARCH 31,
                                                                                    1994      1995      1996
                                                                                  --------  --------  ---------
                                                                                                      (UNAUDITED)
<S>                                                                               <C>       <C>       <C>
Current assets:
  Cash and cash equivalents.....................................................  $  2,104  $  4,358   $14,547
  Short-term investments........................................................    27,757    15,886    90,109
  Accounts receivable...........................................................       328       344       350
  Other current assets..........................................................       891       871     2,242
                                                                                  --------  --------  ---------
  Total current assets..........................................................    31,080    21,459   107,248
Property and equipment, net.....................................................     6,098     5,638     5,943
                                                                                  --------  --------  ---------
                                                                                  $ 37,178  $ 27,097   $113,191
                                                                                  --------  --------  ---------
                                                                                  --------  --------  ---------
 
                                     LIABILITIES AND STOCKHOLDERS' EQUITY
 
Current liabilities:
  Accounts payable..............................................................  $  1,514  $  5,426   $ 8,752
  Accrued liabilities...........................................................       519       683     1,075
  Deferred revenue..............................................................     6,818     5,745    24,763
  Current portion of long-term debt.............................................     1,190       768       542
                                                                                  --------  --------  ---------
  Total current liabilities.....................................................    10,041    12,622    35,132
                                                                                  --------  --------  ---------
Long-term liabilities:
  Long-term debt, less current portion..........................................       992       580       606
  Accrued rent..................................................................     1,293     1,304     1,257
                                                                                  --------  --------  ---------
  Total long-term liabilities...................................................     2,285     1,884     1,863
                                                                                  --------  --------  ---------
Stockholders' equity:
  Common stock, no par value, 75,000,000 shares authorized, 7,278,488 and
   7,359,282 shares issued and outstanding at June 30, 1994 and 1995 and
   10,622,800 shares at March 31, 1996..........................................    75,435    76,113   157,379
  Accumulated deficit...........................................................   (50,583)  (63,522)  (81,183 )
                                                                                  --------  --------  ---------
  Total stockholders' equity....................................................    24,852    12,591    76,196
                                                                                  --------  --------  ---------
Commitments and contingencies (Note 8)..........................................     --        --        --
                                                                                  --------  --------  ---------
                                                                                  $ 37,178  $ 27,097   $113,191
                                                                                  --------  --------  ---------
                                                                                  --------  --------  ---------
</TABLE>
 
                See accompanying notes to financial statements.
 
                                      F-3
<PAGE>
                         AGOURON PHARMACEUTICALS, INC.
                            STATEMENT OF OPERATIONS
                (DOLLARS IN THOUSANDS, EXCEPT PER SHARE AMOUNTS)
 
<TABLE>
<CAPTION>
                                                                YEAR ENDED JUNE 30,                      NINE MONTHS
                                                    -------------------------------------------        ENDED MARCH 31,
                                                        1993           1994           1995       ----------------------------
                                                    -------------  -------------  -------------      1995           1996
                                                                                                 -------------  -------------
                                                                                                  (UNAUDITED)    (UNAUDITED)
Revenues:
<S>                                                 <C>            <C>            <C>            <C>            <C>
  Contract........................................  $       8,266  $      16,301  $      26,722  $      19,285  $      27,465
  Interest........................................          1,704          1,350          1,239            978          3,520
                                                    -------------  -------------  -------------  -------------  -------------
                                                            9,970         17,651         27,961         20,263         30,985
                                                    -------------  -------------  -------------  -------------  -------------
Costs and expenses:
  Research and development........................         17,404         23,957         36,317         24,352         43,780
  General and administrative......................          2,127          2,961          4,358          3,027          4,679
  Interest........................................            268            195            225            169            187
                                                    -------------  -------------  -------------  -------------  -------------
                                                           19,799         27,113         40,900         27,548         48,646
                                                    -------------  -------------  -------------  -------------  -------------
Net loss..........................................  $      (9,829) $      (9,462) $     (12,939) $      (7,285) $     (17,661)
                                                    -------------  -------------  -------------  -------------  -------------
                                                    -------------  -------------  -------------  -------------  -------------
Net loss per common share.........................  $       (1.40) $       (1.31) $       (1.77) $       (1.00) $       (1.84)
                                                    -------------  -------------  -------------  -------------  -------------
                                                    -------------  -------------  -------------  -------------  -------------
Shares used in computing net loss per common
 share............................................      6,997,000      7,241,000      7,296,000      7,286,000      9,574,000
                                                    -------------  -------------  -------------  -------------  -------------
                                                    -------------  -------------  -------------  -------------  -------------
</TABLE>
 
                See accompanying notes to financial statements.
 
                                      F-4
<PAGE>
                         AGOURON PHARMACEUTICALS, INC.
 
                       STATEMENT OF STOCKHOLDERS' EQUITY
 
                             (DOLLARS IN THOUSANDS)
 
<TABLE>
<CAPTION>
                                                                      COMMON STOCK
                                                                ------------------------  ACCUMULATED
                                                                   SHARES       AMOUNT      DEFICIT       TOTAL
                                                                ------------  ----------  ------------  ----------
<S>                                                             <C>           <C>         <C>           <C>
Balance at June 30, 1992......................................     6,903,933  $   68,809   $  (31,292)  $   37,517
Stock issuances:
  Private sales...............................................       311,688       5,940       --            5,940
  Exercise of stock options...................................         2,500          21       --               21
  Employee stock purchase plan................................         8,425          70       --               70
  Options granted for services provided.......................       --               38       --               38
Net loss......................................................       --           --           (9,829)      (9,829)
                                                                ------------  ----------  ------------  ----------
Balance at June 30, 1993......................................     7,226,546      74,878      (41,121)      33,757
Stock issuances:
  Exercise of stock options...................................        32,649         352       --              352
  Employee stock purchase plan................................        19,293         170       --              170
  Options granted for services provided.......................       --               35       --               35
Net loss......................................................       --           --           (9,462)      (9,462)
                                                                ------------  ----------  ------------  ----------
Balance at June 30, 1994......................................     7,278,488      75,435      (50,583)      24,852
Stock issuances:
  Exercise of stock options...................................        49,125         382       --              382
  Employee stock purchase plan................................        31,669         296       --              296
Net loss......................................................       --           --          (12,939)     (12,939)
                                                                ------------  ----------  ------------  ----------
Balance at June 30, 1995......................................     7,359,282      76,113      (63,522)      12,591
Stock issuances (unaudited):
  Public sale.................................................     3,000,000      78,579       --           78,579
  Exercise of stock options...................................       245,694       2,393       --            2,393
  Employee stock purchase plan................................        17,824         294       --              294
Net loss (unaudited)..........................................       --           --          (17,661)     (17,661)
                                                                ------------  ----------  ------------  ----------
Balance at March 31, 1996 (unaudited).........................    10,622,800  $  157,379   $  (81,183)  $   76,196
                                                                ------------  ----------  ------------  ----------
                                                                ------------  ----------  ------------  ----------
</TABLE>
 
                See accompanying notes to financial statements.
 
                                      F-5
<PAGE>
                         AGOURON PHARMACEUTICALS, INC.
 
                            STATEMENT OF CASH FLOWS
 
                             (DOLLARS IN THOUSANDS)
 
<TABLE>
<CAPTION>
                                                                                                           NINE MONTHS ENDED MARCH
                                                                                YEAR ENDED JUNE 30,                  31,
                                                                            ----------------------------  -------------------------
                                                                              1993      1994      1995       1995          1996
                                                                            --------  --------  --------  -----------   -----------
                                                                                                          (UNAUDITED)   (UNAUDITED)
<S>                                                                         <C>       <C>       <C>       <C>           <C>
Cash flows from operating activities:
  Cash received from contracts............................................  $  7,973  $ 20,307  $ 25,633   $ 21,018      $ 46,477
  Cash paid to suppliers, employees and service providers.................   (16,962)  (24,955)  (34,113)   (22,405)      (44,419)
  Interest received.......................................................     1,704     1,350     1,239        978         3,520
  Interest paid...........................................................      (268)     (195)     (225)      (169)         (187)
                                                                            --------  --------  --------  -----------   -----------
    Net cash provided (used) by operating activities......................    (7,553)   (3,493)   (7,466)      (578)        5,391
                                                                            --------  --------  --------  -----------   -----------
Cash flows from investing activities:
  Net (increase) decrease in short-term investments.......................     6,878      (840)   11,871      7,561       (74,223)
  Expenditures for property and equipment.................................    (2,655)   (1,783)   (1,978)    (1,749)       (1,588)
                                                                            --------  --------  --------  -----------   -----------
    Net cash provided (used) by investing activities......................     4,223    (2,623)    9,893      5,812       (75,811)
                                                                            --------  --------  --------  -----------   -----------
Cash flows from financing activities:
  Net proceeds from issuance of common stock..............................     6,031       522       678        245        81,266
  Principal payments under equipment leases...............................      (572)     (550)     (613)      (460)         (304)
  Increase (decrease) in long-term debt, net..............................      (312)      465      (238)       (68)         (353)
                                                                            --------  --------  --------  -----------   -----------
    Net cash provided (used) by financing activities......................     5,147       437      (173)      (283)       80,609
                                                                            --------  --------  --------  -----------   -----------
Net increase (decrease) in cash and cash equivalents......................     1,817    (5,679)    2,254      4,951        10,189
Cash and cash equivalents at beginning of period..........................     5,966     7,783     2,104      2,104         4,358
                                                                            --------  --------  --------  -----------   -----------
    Cash and cash equivalents at end of period............................  $  7,783  $  2,104  $  4,358   $  7,055      $ 14,547
                                                                            --------  --------  --------  -----------   -----------
                                                                            --------  --------  --------  -----------   -----------
Reconciliation of net loss to net cash provided (used) by operating
 activities:
  Net loss................................................................  $ (9,829) $ (9,462) $(12,939)  $ (7,285)     $(17,661)
  Depreciation and amortization...........................................     1,755     2,180     2,455      1,858         1,740
  Net (increase) decrease in accounts receivable and other current
   assets.................................................................      (172)     (635)        4        (53)       (1,377)
  Net increase (decrease) in accounts payable, accrued liabilities,
   deferred revenue and other liabilities.................................       655     4,389     3,014      4,902        22,689
  Options granted for services provided...................................        38        35     --        --            --
                                                                            --------  --------  --------  -----------   -----------
    Net cash provided (used) by operating activities......................  $ (7,553) $ (3,493) $ (7,466)  $   (578)     $  5,391
                                                                            --------  --------  --------  -----------   -----------
                                                                            --------  --------  --------  -----------   -----------
</TABLE>
 
                See accompanying notes to financial statements.
 
                                      F-6
<PAGE>
                         AGOURON PHARMACEUTICALS, INC.
                         NOTES TO FINANCIAL STATEMENTS
 (THE FINANCIAL INFORMATION AS OF MARCH 31, 1996 AND FOR THE NINE MONTHS ENDED
                     MARCH 31, 1995 AND 1996 IS UNAUDITED.)
 
NOTE 1 -- THE COMPANY AND ITS SIGNIFICANT ACCOUNTING POLICIES
 
THE COMPANY
 
    Agouron  Pharmaceuticals, Inc. ("Agouron" or the "Company") was incorporated
in the state  of California  on June  22, 1984. The  Company is  engaged in  the
development  of  human  pharmaceuticals utilizing  protein  structure-based drug
design.
 
UNAUDITED FINANCIAL INFORMATION
 
    In the opinion of management, the unaudited financial statement  information
included in these financial statements contains all adjustments (consisting only
of  normal, recurring items) necessary to  present fairly the financial position
of the Company as of March 31, 1996  and the results of its operations and  cash
flows  for the nine month periods ended March  31, 1995 and 1996. The results of
operations for the interim periods  presented are not necessarily indicative  of
the results to be expected for the full year.
 
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, liabilities, revenues
and expenses and related disclosures as of the date of the financial statements.
Actual results could differ from such estimates.
 
SHORT-TERM INVESTMENTS
 
    Short-term investments  consist  principally  of  government  or  government
agency  securities, corporate notes and bonds, commercial paper and certificates
of deposit with original maturities of  three to thirty-six months. Included  in
short-term investments at June 30, 1994 and 1995 and March 31, 1996 is $246,000,
$172,000 and $1,544,000 of accrued interest receivable.
 
    The  Company  adopted Statement  of Financial  Accounting Standards  No. 115
"Accounting for Certain Investments in  Debt and Equity Securities" ("FAS  115")
for  investments held  as of  or acquired  after July  1, 1994.  The Company has
classified its short-term investments as available-for-sale. The adoption of FAS
115 did  not have  a material  impact  on the  Company's financial  position  or
results of operations.
 
CONCENTRATION OF CREDIT AND MARKET RISK AND OFF BALANCE SHEET RISK
 
    The  Company invests  its excess  cash principally  in marketable securities
from a diversified portfolio of institutions with strong credit ratings and,  by
policy,  limits  the amount  of credit  exposure at  any one  institution. These
investments are generally  not collateralized  and primarily  mature within  one
year.  The Company has not realized any material losses from such investments in
1993, 1994 or 1995 or in the nine months ended March 31, 1996.
 
PROPERTY AND EQUIPMENT
 
    Property and equipment is recorded  at cost. Depreciation is computed  using
the  straight-line method  over estimated useful  lives of three  to five years.
Leasehold improvements are  amortized over  the life  of the  lease. Charges  to
costs and expenses for repairs and maintenance were $508,000, $534,000, $422,000
and  $433,500 for  the years  ended June 30,  1993, 1994  and 1995  and the nine
months ended March 31, 1996.
 
REVENUE RECOGNITION
 
    Contract revenues (including profit,  if any) are  earned and recognized  as
work  is performed.  Contract payments  received in  advance of  performance are
recorded as  deferred  revenue.  Subsequent  contract  revenues  are  recognized
according  to the  provisions of  each collaborative  agreement, generally  on a
percentage-of-completion basis over the life of the contract.
 
                                      F-7
<PAGE>
                         AGOURON PHARMACEUTICALS, INC.
                   NOTES TO FINANCIAL STATEMENTS (CONTINUED)
 (THE FINANCIAL INFORMATION AS OF MARCH 31, 1996 AND FOR THE NINE MONTHS ENDED
                     MARCH 31, 1995 AND 1996 IS UNAUDITED.)
 
NOTE 1 -- THE COMPANY AND ITS SIGNIFICANT ACCOUNTING POLICIES (CONTINUED)
STATEMENT OF CASH FLOWS
 
    For purposes of  the Statement of  Cash Flows, cash  equivalents are  highly
liquid  investments purchased with an original maturity of three months or less.
Non-cash financing activities were not significant  in 1993, 1994 or 1995 or  in
the nine months ended March 31, 1996.
 
INCOME TAXES
 
    Effective  July  1,  1993,  the Company  adopted,  on  a  prospective basis,
Statement of  Financial  Accounting Standards  No.  109 "Accounting  for  Income
Taxes"  ("FAS  109").  Under  FAS  109, deferred  tax  is  recognized  using the
liability  method,  whereby  tax  rates  are  applied  to  cumulative  temporary
differences  based on when and  how they are expected  to affect the tax return.
The adoption  of  FAS 109  did  not have  a  material impact  on  the  Company's
financial statements.
 
LIQUIDITY AND CAPITAL RESOURCES
 
    As  of  June  30,  1995,  the  Company  believes  that  its  current capital
resources, existing  contractual commitments  and the  JT milestone  payment  of
$24,000,000 (see Note 4), will be sufficient to meet its operating needs through
fiscal 1996.
 
    As  of  March  31,  1996,  the Company  believes  that  its  current capital
resources and existing contractual  commitments will be  sufficient to meet  its
operating  needs through fiscal  1996. This belief is  based on current research
and clinical development plans,  the current regulatory environment,  historical
industry experience in the development of therapeutic drugs and general economic
conditions.  However, the  Company will  need additional  financing to  meet the
planned operating needs of fiscal 1997 and beyond. Such needs would include  the
expenditure   of  substantial   funds  to  continue   research  and  development
activities, conduct existing and planned preclinical studies and tests,  conduct
human  clinical trials and establish  certain manufacturing, sales and marketing
capabilities. As a  result, the Company  anticipates pursuing various  financing
alternatives, such as collaborative arrangements and additional public offerings
or private placements of Company common or preferred stock. If such alternatives
are   not  available,  the  Company  may  be  required  to  delay  or  eliminate
expenditures for  certain of  its  potential products  under development  or  to
license third parties to commercialize products or technologies that the Company
would otherwise seek to develop itself.
 
NOTE 2 -- SHORT-TERM INVESTMENTS
    At  June 30, 1995, the amortized cost and estimated fair value of short-term
investments held as available-for-sale were as follows:
 
<TABLE>
<CAPTION>
                                                                     AMORTIZED     UNREALIZED     UNREALIZED      FAIR
                                                                       COST          GAINS          LOSSES        VALUE
                                                                     ---------     ----------     ----------     -------
                                                                                       (IN THOUSANDS)
<S>                                                                  <C>           <C>            <C>            <C>
United States government securities..............................     $10,236         $   5          $ (60)      $10,181
Corporate obligations............................................       3,037             2            (16)        3,023
Other interest bearing securities................................       2,613         --             --            2,613
                                                                                         --
                                                                     ---------                         ---       -------
                                                                      $15,886         $   7          $ (76)      $15,817
                                                                                         --
                                                                                         --
                                                                     ---------                         ---       -------
                                                                     ---------                         ---       -------
</TABLE>
 
                                      F-8
<PAGE>
                         AGOURON PHARMACEUTICALS, INC.
                   NOTES TO FINANCIAL STATEMENTS (CONTINUED)
 (THE FINANCIAL INFORMATION AS OF MARCH 31, 1996 AND FOR THE NINE MONTHS ENDED
                     MARCH 31, 1995 AND 1996 IS UNAUDITED.)
 
NOTE 2 -- SHORT-TERM INVESTMENTS (CONTINUED)
    At March 31, 1996, the amortized cost and estimated fair value of short-term
investments held as available-for-sale were as follows:
 
<TABLE>
<CAPTION>
                                                  AMORTIZED    UNREALIZED     UNREALIZED      FAIR
                                                    COST          GAINS         LOSSES        VALUE
                                                 -----------  -------------  -------------  ---------
                                                                    (IN THOUSANDS)
<S>                                              <C>          <C>            <C>            <C>
United States government securities............   $  72,770     $     110      $     (88)   $  72,792
Corporate obligations..........................      13,945            97             (2)      14,040
Other interest bearing securities..............       3,394        --             --            3,394
                                                 -----------        -----            ---    ---------
                                                  $  90,109     $     207      $     (90)   $  90,226
                                                 -----------        -----            ---    ---------
                                                 -----------        -----            ---    ---------
</TABLE>
 
    Realized gains and losses on  the disposal of available-for-sale  securities
during  1995 totaled  $3,000 and  $7,000, respectively.  During the  nine months
ended such gains totaled $22,000. The cost of securities sold is based upon  the
specific  identification  method. At  June  30, 1995,  scheduled  maturities for
available-for-sale securities  were  less  than one  year  for  $14,720,000  and
between one and two years for $1,166,000. At March 31, 1996 such maturities were
$59,699,000  and $30,410,000, respectively. At June 30, 1995 and March 31, 1996,
short-term investments are carried on the  balance sheet at amortized cost.  The
difference  between  amortized cost  and fair  value has  not been  reflected in
stockholders' equity as such difference is not material.
 
NOTE 3 -- COMPOSITION OF CERTAIN FINANCIAL STATEMENT CAPTIONS
 
<TABLE>
<CAPTION>
                                                        JUNE 30,        MARCH 31,
                                                    -----------------  -----------
                                                     1994      1995       1996
                                                    -------  --------  -----------
<S>                                                 <C>      <C>       <C>
                                                             (UNAUDITED)
                                                        (DOLLARS IN THOUSANDS)
Accounts receivable:
  Employee receivables............................  $   270  $    262   $    148
  Other receivables...............................       58        82        202
                                                    -------  --------  -----------
                                                    $   328  $    344   $    350
                                                    -------  --------  -----------
                                                    -------  --------  -----------
Property and equipment, net:
  Scientific instrumentation......................  $ 6,748  $  7,787   $  9,110
  Computer equipment..............................    4,838     5,453      5,704
  Leasehold improvements..........................    2,535     2,798      3,110
  Furniture and fixtures..........................      794       944      1,073
                                                    -------  --------  -----------
                                                     14,915    16,982     18,997
  Less accumulated depreciation and amortization..   (8,817)  (11,344)   (13,054)
                                                    -------  --------  -----------
                                                    $ 6,098  $  5,638   $  5,943
                                                    -------  --------  -----------
                                                    -------  --------  -----------
Accrued liabilities:
  Accrued vacation................................  $   489  $    623   $    789
  Other...........................................       30        60        286
                                                    -------  --------  -----------
                                                    $   519  $    683   $  1,075
                                                    -------  --------  -----------
                                                    -------  --------  -----------
</TABLE>
 
                                      F-9
<PAGE>
                         AGOURON PHARMACEUTICALS, INC.
                   NOTES TO FINANCIAL STATEMENTS (CONTINUED)
 (THE FINANCIAL INFORMATION AS OF MARCH 31, 1996 AND FOR THE NINE MONTHS ENDED
                     MARCH 31, 1995 AND 1996 IS UNAUDITED.)
 
NOTE 4 -- SIGNIFICANT CONTRACT AND GRANT ARRANGEMENTS
 
JAPAN TOBACCO INC.
 
    In December 1992, the Company entered  into an agreement with Japan  Tobacco
Inc.  ("JT") to collaborate on  the discovery, development and commercialization
of novel therapeutic drugs which act on key proteins related to the human immune
system ("JT  1992").  In  February  1994, the  Company  expanded  its  strategic
alliance  with  JT into  the  field of  anti-viral  drugs for  the  treatment of
infections caused  by  hepatitis  C,  the  herpes  family  of  viruses  and  the
rhinoviruses ("JT 1994"). In December 1994, the Company added its anti-HIV drug,
Viracept  (formerly AG1343),  to the  JT collaboration  with the  execution of a
worldwide development and licensing  agreement ("JT HIV").  In January 1995,  JT
1992  was canceled by mutual agreement and JT 1992 resources were reallocated to
JT 1994 programs. In February 1996, JT 1994 was modified to delete  rhinoviruses
from the strategic alliance.
 
    Under  the provisions  of JT  1994, JT has  agreed to  make certain research
payments to  the Company  of not  less than  $8,000,000 over  a two-year  period
ending December 1996. Such payments could approximate more than $21,000,000 over
a four-year period if certain technical milestones are achieved. In addition, JT
made an up-front payment of $7,778,000, which is being amortized to revenue over
a  twenty-four  month  period. Under  the  provisions  of JT  HIV,  JT  has made
milestone payments of $30,000,000 to Agouron representing an initial payment  of
$2,500,000, a milestone payment of $3,500,000 in recognition of the satisfactory
completion  of  a phase  I  clinical study  and  a second  milestone  payment of
$24,000,000 in recognition of  results from a pilot  phase II clinical study  of
Viracept.  Agouron and  JT will  ultimately share  equally the  costs of further
development of Viracept.
 
    Under the provisions of JT 1994,  the Company will have exclusive rights  to
develop,  manufacture and market  anti-hepatitis C and  anti-herpes drugs in the
United States, Canada  and Mexico.  JT will  have exclusive  rights to  develop,
manufacture and market these drugs in Japan, Taiwan and South Korea. Outside the
countries  in which they respectively have exclusive rights, Agouron and JT will
have  co-exclusive   rights  to   manufacture  and   market  jointly   developed
anti-hepatitis  C and anti-herpes drugs. Each  company will pay royalties to the
other based  upon their  respective sales  of anti-hepatitis  C and  anti-herpes
drugs.  Under the provisions of JT HIV, Agouron will retain exclusive commercial
rights to Viracept (with the right to sublicense, subject to JT's right of first
refusal) in  the  United States,  Canada  and  Mexico. JT  will  have  exclusive
commercial  rights  to  Viracept  (with  the  right  to  sublicense,  subject to
Agouron's right of first refusal) in Japan and certain other countries in  Asia.
Exclusive  commercial rights  (with the right  to sublicense) in  Europe and all
remaining countries of the world will be  held by a joint venture owned  equally
by  Agouron  and JT.  The  two companies  will  share profits  equally  from the
worldwide commercialization of Viracept.
 
    Under the combined terms of the  agreements, the Company has incurred  costs
of   $1,144,000,   $5,043,000,  $19,211,000   and  $28,514,000   and  recognized
corresponding revenues of $2,156,000,  $11,144,000, $22,880,000 and  $24,416,000
for the years ended June 30, 1993, 1994 and 1995 and the nine months ended March
31, 1996.
 
    Under  a separate agreement dated December 1992, JT purchased 155,844 shares
of newly issued common stock for an aggregate purchase price of $3,000,000. Such
purchase represented approximately 2% of the total outstanding common stock.
 
SYNTEX (U.S.A.) INC.
 
    In June 1993,  the Company entered  into an agreement  with Syntex  (U.S.A.)
Inc.  (now a subsidiary of  Roche Holding Ltd) ("Roche"),  to collaborate on the
discovery of novel matrix metalloprotease inhibitor drugs for use against cancer
and degenerative  diseases  such  as rheumatoid  arthritis  and  osteoarthritis.
 
                                      F-10
<PAGE>
                         AGOURON PHARMACEUTICALS, INC.
                   NOTES TO FINANCIAL STATEMENTS (CONTINUED)
 (THE FINANCIAL INFORMATION AS OF MARCH 31, 1996 AND FOR THE NINE MONTHS ENDED
                     MARCH 31, 1995 AND 1996 IS UNAUDITED.)
 
NOTE 4 -- SIGNIFICANT CONTRACT AND GRANT ARRANGEMENTS (CONTINUED)
Under the provisions of the agreement, Roche has agreed to make certain research
payments   to  the  Company  over  a  three-year  period  ending  June  1996  of
approximately $8,500,000. Under  the agreement, the  Company has incurred  costs
and  recognized corresponding  revenues of $120,000,  $2,307,000, $3,043,000 and
$2,465,000 during the  years ended June  30, 1993,  1994 and 1995  and the  nine
months  ended March 31, 1996. The Company is funding a portion of the activities
associated with this collaboration  on its own account.  Under the terms of  the
agreement,  the  Company  will  have a  royalty  position  in  certain agreement
products, if any, and other development and commercial rights in other agreement
products, if any.
 
    Under a  separate  agreement dated  June  1993, Syntex  Corporation  (Roche)
purchased  155,844 shares of newly issued common stock for an aggregate purchase
price of $3,000,000.  Such purchase  represented approximately 2%  of the  total
outstanding common stock.
 
SCHERING-PLOUGH CORPORATION
 
    In  April  1994, the  Company  and Schering-Plough  Corporation  completed a
three-year collaborative  research agreement  providing  for the  discovery  and
development  of  anti-cancer drugs  which  target oncogenic  ras  proteins. Each
company may pursue further discovery or development efforts in this program area
at its sole discretion and expense  with no subsequent obligations to the  other
company.  Under the  agreement, the  Company has  incurred costs  and recognized
corresponding revenues of $2,570,000 and $1,894,000 during the years ended  June
30, 1993 and 1994.
 
ELI LILLY AND COMPANY
 
    In  April 1993, the Company and Eli  Lilly and Company completed a five year
collaborative  research  program  in  several  therapeutic  categories.  Further
development  of any discoveries made  in the program will  be undertaken at each
company's sole discretion and expense. Agouron has continuing commercial  rights
and/or   financial  interests  in  certain  of  these  discoveries.  During  the
collaborative research  program, the  Company has  been reimbursed  for  certain
costs incurred and has recognized revenues of $2,941,000 during 1993.
 
NATIONAL INSTITUTES OF HEALTH
 
    The  Company is currently  the grantee organization for  two grants from the
National  Institutes  of  Health  to  conduct  research  related  to  the  Human
Immunodeficiency  Virus.  Costs  incurred  and  the  corresponding reimbursement
revenues recognized  under  various  grant  programs  were  $479,000,  $956,000,
$799,000  and $554,000 for the years ended June  30, 1993, 1994 and 1995 and the
nine months ended March 31, 1996.
 
                                      F-11
<PAGE>
                         AGOURON PHARMACEUTICALS, INC.
                   NOTES TO FINANCIAL STATEMENTS (CONTINUED)
 (THE FINANCIAL INFORMATION AS OF MARCH 31, 1996 AND FOR THE NINE MONTHS ENDED
                     MARCH 31, 1995 AND 1996 IS UNAUDITED.)
 
NOTE 5 -- LONG-TERM DEBT
    At June 30, 1994  and 1995 and  March 31, 1996,  long-term debt and  capital
lease obligations were as follows:
 
<TABLE>
<CAPTION>
                                                           JUNE 30,
                                                    -----------------------   MARCH 31,
                                                       1994         1995        1996
                                                    -----------  ----------  -----------
<S>                                                 <C>          <C>         <C>
                                                                             (UNAUDITED)
Notes payable, secured with personal property and
 a certificate of deposit for $400,000; interest
 at prime plus 1.5%; maturing September 1995, June
 1997 and November 1998...........................  $ 1,169,000  $  931,000  $   578,000
Capital leases, with interest rates between 6.00%
 and 16.5%, maturing at various dates through
 December 2000....................................    1,013,000     417,000      570,000
                                                    -----------  ----------  -----------
Total long-term debt and capital lease
 obligations......................................    2,182,000   1,348,000    1,148,000
Current portion of long-term debt.................   (1,190,000)   (768,000)    (542,000)
                                                    -----------  ----------  -----------
Long-term debt....................................  $   992,000  $  580,000  $   606,000
                                                    -----------  ----------  -----------
                                                    -----------  ----------  -----------
</TABLE>
 
    Maturities of long-term debt, excluding capital leases, are as follows: 1996
- -$445,000,  1997  - $344,000,  1998  - $100,000,  1999  - $42,000  and  2000 and
thereafter $0.
 
NOTE 6 -- INCOME TAXES
    At June 30, 1994 and  1995, the Company has  total deferred income taxes  of
$23,609,000 and $30,299,000, which have been fully reserved as follows:
 
<TABLE>
<CAPTION>
                                                                JUNE 30, 1994   JUNE 30, 1995
                                                                --------------  --------------
<S>                                                             <C>             <C>
Deferred revenue..............................................  $    2,737,000  $    2,358,000
Book and tax depreciation differences.........................       1,588,000       1,664,000
Accrued liabilities...........................................         715,000         790,000
Net operating loss carryforwards..............................      14,437,000      19,638,000
Foreign tax credits...........................................       1,237,000       1,913,000
Research and development tax credits..........................       2,895,000       3,936,000
                                                                --------------  --------------
                                                                    23,609,000      30,299,000
Valuation allowance...........................................     (23,609,000)    (30,299,000)
                                                                --------------  --------------
Deferred taxes, net...........................................  $     --        $     --
                                                                --------------  --------------
                                                                --------------  --------------
</TABLE>
 
    The  Company has not recorded provisions  for any United States income taxes
due to net operating losses  for tax reporting purposes.  At June 30, 1995,  the
Company  had net operating loss carryforwards for federal tax reporting purposes
of approximately $53,509,000, expiring from 2000 through 2010. The Company  also
has  federal  research  and development  credit  carryforwards  of approximately
$2,721,000 at  June  30, 1995,  expiring  from  2000 through  2010.  The  future
utilization of, or limitation as to the use of, net operating loss carryforwards
for  federal and state  income tax purposes  may be impacted  by the issuance of
additional equity securities.
 
                                      F-12
<PAGE>
                         AGOURON PHARMACEUTICALS, INC.
                   NOTES TO FINANCIAL STATEMENTS (CONTINUED)
 (THE FINANCIAL INFORMATION AS OF MARCH 31, 1996 AND FOR THE NINE MONTHS ENDED
                     MARCH 31, 1995 AND 1996 IS UNAUDITED.)
 
NOTE 6 -- INCOME TAXES (CONTINUED)
    As a  result  of California's  partial  conformity with  federal  provisions
regarding  net operating loss and research and development credit carryforwards,
the  Company  has  net  operating  loss  and  research  and  development  credit
carryforwards   of  approximately  $15,055,000  and  $1,215,000  for  state  tax
reporting purposes at June 30, 1995, expiring from 1996 through 2010.
 
    Included in general and administrative costs and expenses at June 30,  1993,
1994,  1995 and the nine months ended March 31, 1996, is approximately $116,000,
$611,000, $863,000  and $628,000  of  foreign tax  expense associated  with  the
contract research payments from JT.
 
NOTE 7 -- STOCKHOLDERS' EQUITY
 
STOCK OPTIONS
 
    The  Company has two  stock option plans whereby  4,220,000 shares of common
stock have been reserved for issuance to its officers, directors, employees  and
consultants.  The plans, as amended, are  administered by the Board of Directors
or its designees and  provide generally that, for  incentive stock options,  the
exercise price shall not be less than the fair market value of the shares at the
date  of grant and, for certain non-qualified stock options, the price shall not
be less than 85% of the fair market value of the shares at the date of grant and
may be at any price determined by the Board of Directors for others. The options
expire not later than ten years from the date of the grant and generally  become
exercisable  ratably over a four  year period beginning one  year from the grant
date. As  of  June  30, 1995,  293,636  of  these options  had  been  exercised,
1,107,922  were exercisable and 340,672 shares  of common stock remain available
for option  grant.  At  March  31,  1996, 539,330  of  these  options  had  been
exercised,  1,144,763 options  were exercisable  and 1,058,563  shares of common
stock remain available for  option grant. The  following table summarizes  stock
option activity for 1993 through March 31, 1996:
 
<TABLE>
<CAPTION>
                                                                  SHARES          PRICE
                                                                ----------  -----------------
<S>                                                             <C>         <C>
Outstanding June 30, 1992.....................................     803,278
Options granted...............................................     494,239  $   7.88 - $13.88
Options exercised.............................................      (2,500) $   7.38 - $ 9.15
Options canceled..............................................     (20,550) $   7.38 - $15.50
                                                                ----------
Outstanding June 30, 1993.....................................   1,274,467
Options granted...............................................     703,450  $   8.63 - $16.00
Options exercised.............................................     (32,649) $   5.40 - $12.00
Options canceled..............................................     (39,829) $   7.88 - $15.50
                                                                ----------
Outstanding June 30, 1994.....................................   1,905,439
Options granted...............................................     773,275  $  10.13 - $24.50
Options exercised.............................................     (49,125) $   5.40 - $15.50
Options canceled..............................................     (43,897) $   7.88 - $16.13
                                                                ----------
Outstanding June 30, 1995.....................................   2,585,692  $   5.40 - $24.50
Options granted (unaudited)...................................     314,125  $   23.56  $44.38
Options exercised (unaudited).................................    (245,694) $    5.40  $17.38
Options canceled (unaudited)..................................     (32,016) $    7.88  $39.13
                                                                ----------
Outstanding March 31, 1996 (unaudited)........................   2,622,107  $    5.40  $44.38
                                                                ----------
                                                                ----------
</TABLE>
 
                                      F-13
<PAGE>
                         AGOURON PHARMACEUTICALS, INC.
                   NOTES TO FINANCIAL STATEMENTS (CONTINUED)
 (THE FINANCIAL INFORMATION AS OF MARCH 31, 1996 AND FOR THE NINE MONTHS ENDED
                     MARCH 31, 1995 AND 1996 IS UNAUDITED.)
 
NOTE 7 -- STOCKHOLDERS' EQUITY (CONTINUED)
EMPLOYEE STOCK PURCHASE PLAN
 
    In  December 1992, the shareholders approved an Employee Stock Purchase Plan
("ESPP") which commenced on January 1,  1993. Under the ESPP, 250,000 shares  of
common  stock have been reserved for  issuance and 190,613 shares were available
for purchase at June 30, 1995  and 172,789 shares remain available for  purchase
at  March  31, 1996.  Eligible employees  may purchase  shares of  the Company's
common stock  through payroll  deductions at  prices equal  to 85%  of the  fair
market  value of the common stock on either  the first or last day of a purchase
period. During the nine months ended  March 31, 1996, 11,693 shares were  issued
at  a price of $19.98 per share and 6,131 shares were issued at a price of $9.88
per share. During 1995, 25,524 shares were issued at a price of $9.24 per  share
and  6,145 shares were issued at a price of $9.88 per share. During 1994, 10,073
shares were issued at a price of $8.2875 per share and 9,220 shares were  issued
at  a price of $9.35 per share. During 1993, 8,425 shares were issued at a price
of $8.2875 per share.
 
STOCK WARRANT
 
    As part of  certain financing  arrangements in  1986, the  Company issued  a
warrant  to purchase 45,000 shares of the  Company's common stock at a per share
price of $6.30. This warrant is currently exercisable and expires in July 1996.
 
NOTE 8 -- COMMITMENTS AND CONTINGENCIES
    Certain scientific  instrumentation and  computer  and other  equipment  are
subject  to leases which are classified as  capital leases. At June 30, 1994 and
1995 and March 31, 1996, $2,601,000 ($624,000, net), $2,364,000 ($227,000,  net)
and  $1,118,000  ($532,000,  net)  of such  leased  equipment  were  included in
property and equipment.
 
    Rental expenses (principally for leased facilities under long-term operating
lease commitments) were  $1,502,000, $1,973,000, $2,198,000  and $1,874,000  for
1993,  1994,  1995 and  the nine  months  ended March  31, 1996.  Future minimum
payments for capital and operating leases at June 30, 1995 are as follows:
 
<TABLE>
<CAPTION>
                                                                 CAPITAL
                                                                 LEASES      OPERATING LEASES
                                                              -------------  ----------------
<S>                                                           <C>            <C>
1996........................................................   $   350,000    $    2,579,000
1997........................................................        56,000         2,565,000
1998........................................................        37,000         2,244,000
1999........................................................         8,000         2,295,000
2000........................................................       --              2,411,000
Thereafter..................................................       --              2,291,000
                                                              -------------  ----------------
Total minimum lease payments................................       451,000    $   14,385,000
                                                                             ----------------
                                                                             ----------------
Less amount representing interest...........................       (34,000)
                                                              -------------
Obligation under capital leases.............................   $   417,000
                                                              -------------
                                                              -------------
</TABLE>
 
    The Company is involved in certain legal proceedings generally incidental to
its normal business activities. While the outcome of any such proceedings cannot
be accurately predicted, the Company does not believe the ultimate resolution of
any such existing matters should have a material adverse effect on its financial
position or results of operations.
 
                                      F-14
<PAGE>
                         AGOURON PHARMACEUTICALS, INC.
                   NOTES TO FINANCIAL STATEMENTS (CONTINUED)
 (THE FINANCIAL INFORMATION AS OF MARCH 31, 1996 AND FOR THE NINE MONTHS ENDED
                     MARCH 31, 1995 AND 1996 IS UNAUDITED.)
 
NOTE 9 -- SUBSEQUENT EVENT
    On August 24,  1995, the  Company received a  $24,000,000 milestone  payment
from  JT along with JT's commitment to continue with the clinical development of
Viracept. JT's actions were taken after their review and evaluation of a  number
of factors including certain results from two pilot phase II clinical studies of
Viracept.
 
SUPPLEMENTAL FINANCIAL INFORMATION (UNAUDITED)
 
ROCHE LETTER OF INTENT
 
    On  June  19, 1996,  the  Company and  F.  Hoffmann-La Roche  Ltd  of Basel,
Switzerland, and Hoffmann-La Roche Inc. of Nutley, New Jersey, signed a  binding
letter   of  intent  to  jointly  complete  the  worldwide  development  of  two
anti-cancer drugs currently being developed  by Agouron (Thymitaq, an  inhibitor
of  the enzyme thymidylate synthase, and  AG3340, an inhibitor of certain matrix
metalloprotease  enzymes)  and  to  collaborate  on  an  additional  early-stage
anti-cancer  drug discovery  program (initially  targeting cdk4,  a member  of a
family of  enzymes  (cyclin dependent  kinases)  that regulate  the  transitions
between  phases in the life cycles of all cells). In connection with the signing
of the letter of intent, the Company is to receive an initial license fee of $15
million for Thymitaq and AG3340 and an initial first year research payment of $3
million for cdk4.  Additional payments  of up to  $40 million  for Thymitaq  and
AG3340  and  $20  million  for  cdk4  will  accrue  to  the  Company  if certain
development milestones are satisfied in the future. Roche is to fund 80% of  the
future  development costs  of Thymitaq  and AG3340.  Roche is  to pay  an annual
research fee of  $3 million  in support  of cdk4  and 80%  of any  post-research
development   costs  of  cdk4.   In  North  America,   Agouron  and  Roche  will
cooperatively market  and share  the  profits from  the  sales of  any  approved
products  from the three programs. Outside of North America, Roche will lead the
commercialization of any products  and will pay Agouron  a royalty on net  sales
or, in certain circumstances, will share profits with Agouron.
 
                                      F-15
<PAGE>
- --------------------------------------------------------------------------------
- --------------------------------------------------------------------------------
 
    NO  PERSON  HAS BEEN  AUTHORIZED  TO GIVE  ANY  INFORMATION OR  TO  MAKE ANY
REPRESENTATIONS IN CONNECTION WITH THIS  OFFERING OTHER THAN THOSE CONTAINED  IN
THIS   PROSPECTUS  AND,   IF  GIVEN   OR  MADE,   SUCH  OTHER   INFORMATION  AND
REPRESENTATIONS MUST NOT BE RELIED UPON AS HAVING BEEN AUTHORIZED BY THE COMPANY
OR THE UNDERWRITERS. NEITHER THE DELIVERY  OF THIS PROSPECTUS NOR ANY SALE  MADE
HEREUNDER  SHALL, UNDER ANY CIRCUMSTANCES, CREATE ANY 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.
THIS PROSPECTUS DOES NOT  CONSTITUTE AN OFFER  TO SELL OR  A SOLICITATION OF  AN
OFFER  TO BUY ANY  SECURITIES OTHER THAN  THE REGISTERED SECURITIES  TO WHICH IT
RELATES. THIS PROSPECTUS DOES NOT CONSTITUTE AN OFFER TO SELL OR A  SOLICITATION
OF  AN OFFER TO BUY SUCH SECURITIES IN  ANY CIRCUMSTANCES IN WHICH SUCH OFFER OR
SOLICITATION IS UNLAWFUL.
 
                              -------------------
 
                               TABLE OF CONTENTS
 
                                                                           PAGE
                                                                           ----
Available Information...................................................     2
Incorporation of Certain Information By Reference.......................     2
Prospectus Summary......................................................     3
Risk Factors............................................................     5
Use of Proceeds.........................................................    11
Capitalization..........................................................    12
Price Range of Common Stock and Dividend Policy.........................    12
Dilution................................................................    13
Selected Financial Data.................................................    14
Management's Discussion and Analysis of Financial Condition and Results
 of Operations..........................................................    15
Business................................................................    18
Management..............................................................    31
Description of Securities...............................................    34
Underwriting............................................................    35
Legal Matters...........................................................    36
Experts.................................................................    36
Financial Statements....................................................   F-1
 
                                2,500,000 SHARES
 
                                     [LOGO]
 
                                  COMMON STOCK
 
                               -----------------
 
                              P R O S P E C T U S
 
                               -----------------
 
                            PAINEWEBBER INCORPORATED
 
                               ALEX. BROWN & SONS
                                  INCORPORATED
 
                             ---------------------
 
                                         1996
 
- --------------------------------------------------------------------------------
- --------------------------------------------------------------------------------
<PAGE>
                                    PART II
                     INFORMATION NOT REQUIRED IN PROSPECTUS
 
ITEM 14.  OTHER EXPENSES OF ISSUANCE AND DISTRIBUTION
 
    The  following  table  sets  forth  the  expenses,  other  than underwriting
discounts and commissions, payable by the Company in connection with the sale of
the Common Stock being registered. All  amounts shown are estimates, except  the
registration fee and the NASD filing fee.
 
<TABLE>
<S>                                                                         <C>
Securities and Exchange Commission Registration Fee.......................  $  38,912
NASD Filing Fee...........................................................     11,785
Transfer Agent's Fee and Expenses.........................................      *
Accounting Fees and Expenses..............................................      *
Legal Fees and Expenses...................................................      *
Blue Sky Fees and Expenses (including legal fees and expenses)............      *
Printing and Engraving....................................................      *
Miscellaneous.............................................................      *
                                                                            ---------
                                                                            $ 350,000
                                                                            ---------
                                                                            ---------
</TABLE>
 
- ------------------------
* To be supplied by amendment.
 
ITEM 15.  INDEMNIFICATION OF DIRECTORS AND OFFICERS
 
    Section  317 of  the California  General Corporation  Law generally provides
indemnification to  officers  and directors  of  the Company  against  expenses,
judgments,  fines and  amounts paid in  settlement under  certain conditions and
subject to certain limitations.
 
    Article VII of the  articles of incorporation of  the Company provides  that
liability  of  the  directors  of  the Company  for  monetary  damages  shall be
eliminated to  the fullest  extent permissible  under California  law.  Further,
Article  VIII of the articles of incorporation authorizes the Company to provide
indemnification of agents (as defined in Section 317) for breach of duty to  the
Company and its shareholders through bylaw provisions or through agreements with
such  agents, or both,  in excess of the  indemnification otherwise permitted by
Section 317, subject to the limits  on such excess indemnification set forth  in
Section 317.
 
    Section  3.15  of  the  bylaws  of the  Company  authorizes  the  Company to
indemnify any person who was or is a party, or is threatened to be made a party,
to any proceeding  (other than  actions by  or in the  right of  the Company  to
procure  a judgment in its favor)  by reason of the fact  that such person is or
was an agent of the Company, against expenses, judgments, fines, settlements and
other  amounts  actually  and  reasonably  incurred  in  connection  with   such
proceeding  if  such person  acted in  good faith  and in  a manner  such person
reasonably believed to  be in the  best interests of  the Company. Section  3.15
also authorizes the Company to indemnify any person who was or is a party, or is
threatened to be made a party, to any threatened, pending or completed action by
or  in the right of the Company to procure  a judgment in its favor by reason of
the fact that such  person is or  was an agent of  the Company against  expenses
actually  and reasonably incurred by such  person in connection with the defense
or settlement of such action if such person acted in good faith.
 
    Any indemnification under Section 3.15 is to be made by the Company only  if
authorized  in the specific case upon  determination that indemnification of the
agent is proper in  the circumstances because the  agent has met the  applicable
standard of conduct required by Paragraphs 3.15.2 or 3.15.3 of the bylaws.
 
    Pursuant  to authorization provided under  the articles of incorporation and
the bylaws, the Company has entered into indemnification agreements with each of
its present directors. The Company has also entered into similar agreements with
certain of  the  Company's  officers  who  are  not  directors.  Generally,  the
indemnification  agreements attempt to provide  the maximum protection permitted
by California  law  as it  may  be amended  from  time to  time.  Moreover,  the
indemnification agreements provide for certain additional indemnification. Under
such  additional  indemnification provisions,  however,  an individual  will not
receive indemnification for judgments, settlements or  expenses if he or she  is
found liable to the Company (except to the extent the court determines he or she
is fairly and reasonably entitled to indemnity for
 
                                      II-1
<PAGE>
expenses)  for settlements  not approved by  the Company or  for settlements and
expenses if the  settlement is not  approved by the  court. The  indemnification
agreements  provide for  the Company  to advance to  the individual  any and all
reasonable  expenses   (including  legal   fees   and  expenses)   incurred   in
investigating  or defending  any such  action, suit  or proceeding.  In order to
receive an advance of expenses, the individual must submit to the Company copies
of invoices presented to him or her for such expenses. Also, the individual must
repay such  advances upon  a  final judicial  decision that  he  or she  is  not
entitled to indemnification.
 
    Section  3.15  of  the  bylaws  also  provides  that,  in  the  event  of  a
determination by the Board of Directors of the Company to purchase insurance for
certain of its  agents, the  Company shall  purchase and  maintain insurance  on
behalf  of any such agent against liability  asserted against or incurred by the
agent in such capacity or arising out of the agent's status, whether or not  the
Company would have the power to indemnify the agent against such liability under
the provisions of Section 3.15.
 
    The  Company  has  in  effect  directors  and  officers  liability insurance
policies which insure directors and officers of the Company. The policies expire
on October 13, 1996 and provide a combined total limit of $5,000,000 per  policy
year.  Although the  Company intends  to renew the  policies on  or before their
expiration date, there can be no assurance that the policies will be renewed  on
terms  acceptable to the Company. Under the policies, the directors and officers
of the Company are  insured against loss arising  from claims made against  them
due  to wrongful acts while acting in their individual and collective capacities
as directors  and officers,  subject  to certain  exclusions. In  addition,  the
policies  insure the Company against losses for which its directors and officers
are entitled to indemnification, subject to  a retention of $250,000 payable  by
the  Company. The policies are "claims  made" policies and provide coverage only
for losses arising out of claims first made against the Company and reported  to
the insurer during the policy period.
 
ITEM 16.  EXHIBITS
 
    The  following is a list  of all exhibits filed  as part of the Registration
Statement:
 
<TABLE>
<CAPTION>
EXHIBIT
NUMBER    DESCRIPTION
- ------    ----------------------------------------------------------------------
<S>       <C>
 1.1      Form of Underwriting Agreement (Proof of June 21, 1996).
 
 4*       Restated Articles of Incorporation.
 
 5**      Opinion of Ferris, Britton & Proctor, A P.C., Regarding Legality.
 
23.1      Consent of Independent Accountants.
 
23.2**    Consent of Counsel for Company (contained in Exhibit 5).
 
24        Power of Attorney of Board of Directors (contained on signature page
           of this Registration Statement).
</TABLE>
 
- ------------------------
 * Incorporated by Reference to Form 10-Q for the Quarter ended December 31,
1992.
** To be filed by amendment.
 
ITEM 17.  UNDERTAKINGS
 
    Insofar as indemnification for liabilities arising under the Securities  Act
may  be permitted to directors, officers  or persons controlling the registrant,
pursuant to the foregoing  provisions, 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  Securities 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 counsel the matter has
been settled  by  controlling  precedent,  submit  to  a  court  of  appropriate
jurisdiction  the question whether such indemnification  by it is against public
policy as expressed  in the Securities  Act and  will be governed  by the  final
adjudication of such issue.
 
                                      II-2
<PAGE>
    THE UNDERSIGNED REGISTRANT HEREBY UNDERTAKES THAT:
 
    (1)  For purposes of determining any liability under the Securities Act, the
       information omitted from  the form of  prospectus filed as  part of  this
       registration statement in reliance upon Rule 430A and contained in a form
       of  prospectus filed by the registrant  pursuant to Rule 424(b)(1) or (4)
       or 497(h) under the  Securities Act shall  be deemed to  be part of  this
       registration statement as of the time it was declared effective.
 
    (2)  For the purpose of determining  any liability under the Securities Act,
       each post-effective amendment that contains a form of prospectus shall be
       deemed to  be a  new registration  statement relating  to the  securities
       offered  therein, and the offering of  such securities at that time shall
       be deemed to be the initial bona fide offering thereof.
 
    The  undersigned  registrant  hereby   undertakes  that,  for  purposes   of
determining  any  liability  under  the  Securities  Act,  each  filing  of  the
registrant's Annual Report  pursuant to Section  13(a) or Section  15(d) of  the
Exchange  Act (and, where applicable, each  filing of an employee benefit plan's
Annual  Report  pursuant  to  Section  15(d)  of  the  Exchange  Act)  that   is
incorporated  by reference in the registration statement 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-3
<PAGE>
                                   SIGNATURES
 
    Pursuant  to the requirements of the  Securities Act of 1933, the registrant
certifies that it has  reasonable grounds to  believe that it  meets all of  the
requirements  for  filing on  Form  S-3 and  has  duly caused  this registration
statement to  be  signed  on  its behalf  by  the  undersigned,  thereunto  duly
authorized,  in the City of  San Diego, State of California,  on the 19th day of
June, 1996.
 
                                          AGOURON PHARMACEUTICALS, INC.
 
                                          By:          /s/ PETER JOHNSON
 
                                             -----------------------------------
                                                       Peter Johnson,
                                                          PRESIDENT
 
                               POWER OF ATTORNEY
 
    KNOW ALL MEN  BY THESE PRESENTS,  that each person  whose signature  appears
below  constitutes  and appoints  Peter Johnson,  Steven S.  Cowell and  Gary E.
Friedman, or  any of  them, his  or her  true and  lawful attorneys-in-fact  and
agents,  with full power of substitution and  resubstitution, for him or her and
in his or her name, place and stead,  in any and all capacities, to sign any  or
all   amendments  to  this   registration  statement,  including  post-effective
amendments, and to file the same, with all exhibits thereto, and other documents
in connection therewith  with the Securities  and Exchange Commission,  granting
unto  said  attorneys-in-fact and  agents  full power  and  authority to  do and
perform each and every act and thing  requisite and necessary to be done in  and
about  the premises, as fully and to all intents and purposes as he or she might
or  could  do  in  person,  hereby  ratifying  and  confirming  all  that   said
attorneys-in-fact  and agents, or their  substitute or substitutes, may lawfully
do or cause to be done by virtue hereof.
 
    Pursuant  to  the  requirements  of   the  Securities  Act  of  1933,   this
Registration  Statement has  been signed below  by the following  persons in the
capacities and on the dates indicated.
 
<TABLE>
<C>                                                     <S>                                       <C>
                      SIGNATURE                                          TITLE                         DATE
- ------------------------------------------------------  ----------------------------------------  ---------------
 
                  /s/ PETER JOHNSON
     -------------------------------------------        President, Chief Executive Officer and     June 19, 1996
                    Peter Johnson                        Director
 
                 /s/ STEVEN S. COWELL
     -------------------------------------------        Vice President, Finance and Chief          June 19, 1996
                   Steven S. Cowell                      Financial Officer
 
                 /s/ GARY E. FRIEDMAN
     -------------------------------------------        Vice President, General Counsel,           June 19, 1996
                   Gary E. Friedman                      Secretary and Director
 
                 /s/ JOHN N. ABELSON
     -------------------------------------------        Director                                   June 19, 1996
                   John N. Abelson
 
               /s/ PATRICIA M. CLOHERTY
     -------------------------------------------        Director                                   June 19, 1996
                 Patricia M. Cloherty
</TABLE>
 
                                      II-4
<PAGE>
<TABLE>
<C>                                                     <S>                                       <C>
                      SIGNATURE                                          TITLE                         DATE
- ------------------------------------------------------  ----------------------------------------  ---------------
                    /s/ A.E. COHEN
     -------------------------------------------        Director                                   June 19, 1996
                      A.E. Cohen
 
                /s/ MICHAEL E. HERMAN
     -------------------------------------------        Director                                   June 19, 1996
                  Michael E. Herman
 
                /s/ IRVING S. JOHNSON
     -------------------------------------------        Director                                   June 19, 1996
                  Irving S. Johnson
 
               /s/ ANTONIE T. KNOPPERS
     -------------------------------------------        Director                                   June 19, 1996
                 Antonie T. Knoppers
 
                 /s/ MELVIN I. SIMON
     -------------------------------------------        Director                                   June 19, 1996
                   Melvin I. Simon
</TABLE>
 
                                      II-5
<PAGE>
                                 EXHIBIT INDEX
 
<TABLE>
<CAPTION>
EXHIBIT
NUMBER  DESCRIPTION                                                        PAGE
- ------  -----------------------------------------------------------------  ----
<S>     <C>                                                                <C>
 1.1    Form of Underwriting Agreement (Proof of June 21, 1996)..........
 4*     Restated Articles of Incorporation
 5**    Opinion of Ferris, Britton & Proctor, A P.C., Regarding Legality
23.1    Consent of Independent Accountants...............................
23.2**  Consent of Counsel for Company (contained in Exhibit 5)
24      Power of Attorney of Board of Directors (contained on signature
         page of this Registration Statement)............................
</TABLE>
 
- ------------------------
 * Incorporated  by Reference  to Form 10-Q  for the Quarter  ended December 31,
   1992.
** To be filed by amendment.

<PAGE>

                                                                     EXHIBIT 1.1
                                                          PROOF OF JUNE 21, 1996


                                2,500,000 Shares

                          AGOURON PHARMACEUTICALS, INC.

                                  Common Stock

                             UNDERWRITING AGREEMENT


                                                                July _____, 1996

PAINEWEBBER INCORPORATED
ALEX. BROWN & SONS INCORPORATED
  As Representatives of the
  several Underwriters
c/o PaineWebber Incorporated
  1285 Avenue of the Americas
  New York, New York  10019

Dear Sirs:

Agouron Pharmaceuticals, Inc., a California corporation (the "Company"),
proposes to sell an aggregate of 2,500,000 shares (the "Firm Shares") of the
Company's Common Stock, no par value (the "Common Stock"), to you and to the
several other Underwriters named in Schedule I hereto (collectively, the
"Underwriters"), for whom you are acting as representatives (the
"Representatives"), in connection with the offering and sale of such shares of
Common Stock. The Company has also agreed to grant to you and the other
Underwriters an option (the "Option") to purchase up to an additional 375,000
shares of Common Stock (the "Option Shares") on the terms and for the purposes
set forth in Section l(b). The Firm Shares and the Option Shares are referred to
collectively herein as the "Shares."

The initial public offering price per share for the Shares and the purchase
price per share for the Shares to be paid by the several Underwriters shall be
agreed upon by the Company and the Representatives, acting on behalf of the
several Underwriters, and such agreement shall be set forth in a separate
written instrument substantially in the form of Exhibit A hereto (the "Price
Determination Agreement"). The Price Determination Agreement may take the form
of an exchange of any standard form of written telecommunication among the
Company and the Representatives and shall specify such applicable information as
is indicated in Exhibit A hereto. The offering of the Shares will be governed by
this Agreement, as supplemented by the Price Determination Agreement. From and
after the date of the execution and

<PAGE>

                                                                               2

delivery of the Price Determination Agreement, this Agreement shall be deemed to
incorporate, and, unless the context otherwise indicates, all references
contained herein to "this Agreement" and to the phrases "herein" shall be deemed
to include the Price Determination Agreement.

1.   AGREEMENT TO SELL AND PURCHASE.

               (a)  On the basis of the respective representations, warranties
and agreements of the Company herein contained and subject to all the terms and
conditions of this Agreement, (i) the Company agrees to sell to the several
Underwriters and (ii) each of the Underwriters, severally and not jointly,
agrees to purchase from the Company at the purchase price per share for the Firm
Shares to be agreed upon by the Representatives and the Company in accordance
with Section l(c) or l(d) and set forth in the Price Determination Agreement,
the number of Firm Shares set forth opposite the name of such Underwriter in
Schedule I, plus such additional number of Firm Shares which such Underwriter
may become obligated to purchase pursuant to Section 8 hereof. If the Company
elects to rely on Rule 430A (as hereinafter defined), Schedule I may be attached
to the Price Determination Agreement.

               (b)  Subject to all the terms and conditions of this Agreement,
the Company grants the Option to the several Underwriters to purchase, severally
and not jointly, up to 375,000 Option Shares from the Company at the same price
per share as the Underwriters shall pay for the Firm Shares. The Option may be
exercised only to cover over-allotments in the sale of the Firm Shares by the
Underwriters and may be exercised in whole or in part at any time (but not more
than once) on or before the 45th day after the date of this Agreement (or, if
the Company has elected to rely on Rule 430A, on or before the 45th day after
the date of the Price Determination Agreement), upon written or telegraphic
notice (the "Option Shares Notice") by the Representatives to the Company no
later than 12:00 noon, New York City time, at least two and no more than five
business days before the date specified for closing in the Option Shares Notice
(the "Option Closing Date") setting forth the aggregate number of Option Shares
to be purchased and the time and date for such purchase. On the Option Closing
Date, the Company will issue and sell to the Underwriters the number of Option
Shares set forth in the Option Shares Notice, and each Underwriter will purchase
such percentage of the Option Shares as is equal to the percentage of Firm
Shares that such Underwriter is purchasing, as adjusted by the Representatives
in such manner as they deem advisable to avoid fractional shares.

               (c)  If the Company has elected not to rely on Rule 430A, the
initial public offering price per share for

<PAGE>

                                                                               3

the Firm Shares and the purchase price per share for the Firm Shares to be paid
by the several Underwriters shall be agreed upon and set forth in the Price
Determination Agreement, which shall be dated the date hereof, and an amendment
to the Registration Statement (as hereinafter defined) containing such per share
price information shall be filed before the Registration Statement becomes
effective.

               (d)  If the Company has elected to rely on Rule 430A, the initial
public offering price per share for the Firm Shares and the purchase price per
share for the Firm Shares to be paid by the several Underwriters shall be agreed
upon and set forth in the Price Determination Agreement. In the event such price
has not been agreed upon and the Price Determination Agreement has not been
executed by the close of business on the fourteenth business day following the
date on which the Registration Statement becomes effective, this Agreement shall
terminate forthwith, without liability of any party to any other party except
that Section 7 shall remain in effect.

2.   DELIVERY AND PAYMENT.

               (a)  Delivery of the Firm Shares shall be made to the
Representatives for the accounts of the Underwriters against payment of the
purchase price by credit to the account of the Company with the Depository Trust
Company. Such payment shall be made at 10:00 a.m., New York City time, on the
fourth business day following the date of this Agreement or, if the Company has
elected to rely on Rule 430A, the third business day after the date on which the
first bona fide offering of the Shares to the public is made by the Underwriters
or at such time on such other date as may be agreed upon by the Company and the
Representatives (such date is hereinafter referred to as the "Closing Date").

               (b)  To the extent the Option is exercised, delivery of the
Option Shares against payment by the Underwriters (in the manner specified
above) will take place at the time and date (which may be the Closing Date)
specified in the Option Shares Notice.

               (c)  The cost of original issue tax stamps, if any, in connection
with the issuance and delivery of the Firm Shares and Option Shares by the
Company to the respective Underwriters shall be borne by the Company. The
Company will pay and save each Underwriter and any subsequent holder of the
Shares harmless from any and all liabilities with respect to or resulting from
any failure or delay in paying Federal and state stamp and other transfer taxes,
if any, which may be payable or determined to be payable in connection with the
original issuance or sale to such Underwriter of the Firm Shares and Option
Shares.

<PAGE>

                                                                               4

3.   REPRESENTATIONS AND WARRANTIES OF THE COMPANY. The Company represents,
warrants and covenants to each Underwriter that:

               (a)  The Company meets the requirements for use of Form S-3 and a
registration statement (Registration No. 33-_______) on Form S-3 relating to the
Shares, including a preliminary prospectus and such amendments to such
registration statement as may have been required to the date of this Agreement,
has been prepared by the Company under the provisions of the Securities Act of
1933, as amended (the "Act"), and the rules and regulations (collectively
referred to as the "Rules and Regulations") of the Securities and Exchange
Commission (the "Commission") thereunder, and has been filed with the
Commission. The registration statement contains a form of preliminary prospectus
to be used in connection with the offering and sale of the Shares.  The term
"preliminary prospectus" as used herein means a preliminary prospectus as
contemplated by Rule 430 or Rule 430A ("Rule 430A") of the Rules and Regulations
included at any time as part of the registration statement. Copies of such
registration statement and amendments have been delivered to the Representatives
and copies of each related preliminary prospectus have been delivered to the
Representatives.  If such registration statement has not become effective, a
further amendment to such registration statement, including a form of final
prospectus, necessary to permit such registration statement to become effective
will be filed promptly by the Company with the Commission. If such registration
statement has become effective, a final prospectus containing information
permitted to be omitted at the time of effectiveness by Rule 430A will be filed
by the Company with the Commission in accordance with Rule 424(b) of the Rules
and Regulations promptly after execution and delivery of the Price Determination
Agreement. The term "Registration Statement" means the registration statement as
amended at the time it becomes or became effective (the "Effective Date"),
including financial statements and all exhibits and any information deemed to be
included by Rule 430A. The term "Prospectus" means a prospectus relating to the
Shares in the form it is first filed with the Commission pursuant to Rule 424(b)
of the Rules and Regulations or, if no such filing is required, the form of
final prospectus included in the Registration Statement at the Effective Date.
Any reference herein to the Registration Statement, any preliminary prospectus
or the Prospectus shall be deemed to refer to and include the documents
incorporated by reference therein pursuant to Item 12 of Form S-3 which were
filed under the Securities Exchange Act of 1934, as amended (the "Exchange
Act"), on or before the Effective Date or the date of such preliminary
prospectus or the Prospectus, as the case may be. Any reference herein to the
terms "amend,"

<PAGE>

                                                                               5

"amendment" or "supplement" with respect to the Registration Statement, any
preliminary prospectus or the Prospectus shall be deemed to refer to and include
the filing of any document under the Exchange Act after the Effective Date, or
the date of any preliminary prospectus or the Prospectus, as the case may be,
and deemed to be incorporated therein by reference.

               (b)  On the Effective Date, the date the Prospectus is first
filed with the Commission pursuant to Rule 424(b) (if required), at all times
subsequent to and including the Closing Date and, if later, the Option Closing
Date and when any post-effective amendment to the Registration Statement becomes
effective or any amendment or supplement to the Prospectus is filed with the
Commission, the Registration Statement and the Prospectus (as amended or as
supplemented if the Company shall have filed with the Commission any amendment
or supplement thereto), including the financial statements included or
incorporated by reference in the Prospectus, did or will comply with all
applicable provisions of the Act, the Exchange Act, the rules and regulations
thereunder (the "Exchange Act Rules and Regulations") and the Rules and
Regulations and will contain all statements required to be stated therein in
accordance with the Act, the Exchange Act, the Exchange Act Rules and
Regulations and the Rules and Regulations. On the Effective Date and when any
post-effective amendment to the Registration Statement becomes effective, no
part of the Registration Statement or any such amendment did or will contain any
untrue statement of a material fact or omit to state a material fact required to
be stated therein or necessary in order to make the statements therein not
misleading. At the Effective Date, the date the Prospectus or any amendment or
supplement to the Prospectus is filed with the Commission and at the Closing
Date and, if later, the Option Closing Date, the Prospectus did not or will not
contain any untrue statement of a material fact or omit to state a material fact
necessary to make the statements therein, in the light of the circumstances
under which they were made, not misleading. The foregoing representations and
warranties in this Section 3(b) do not apply to any statements or omissions made
in reliance on and in conformity with information relating to any Underwriter
furnished in writing to the Company by the Representatives specifically for
inclusion in the Registration Statement or Prospectus or any amendment or
supplement thereto. For all purposes of this Agreement, the amounts of the
selling concession and reallowance set forth in the Prospectus constitute the
only information relating to any Underwriter furnished in writing to the Company
by the Representatives specifically for inclusion in the preliminary prospectus,
the Registration Statement or the Prospectus. The Company has not distributed
any offering material in connection with the offering or sale of the Shares
other than the Registration Statement, the

<PAGE>

                                                                               6

preliminary prospectus, the Prospectus or any other materials, if any, permitted
by the Act.

               (c)  The documents which are incorporated by reference in the
preliminary prospectus and the Prospectus or from which information is so
incorporated by reference, when they become effective or were filed with the
Commission, as the case may be, complied in all material respects with the
requirements of the Act or the Exchange Act, as applicable, the Exchange Act
Rules and Regulations and the Rules and Regulations; and any documents so filed
and incorporated by reference subsequent to the Effective Date shall, when they
are filed with the Commission, conform in all material respects with the
requirements of the Act and the Exchange Act, as applicable, the Exchange Act
Rules and Regulations and the Rules and Regulations.

               (d)  The Company has no subsidiaries (as defined in the Rules and
Regulations). The Company is, and at the Closing Date will be, a corporation
duly organized, validly existing and in good standing under the laws of the
State of California. The Company has, and at the Closing Date will have, full
power and authority to conduct all the activities conducted by it, to own or
lease all the assets owned or leased by it and to conduct its business as
described in the Registration Statement and the Prospectus. The Company is, and
at the Closing Date will be, duly licensed or qualified to do business and in
good standing as a foreign corporation in all jurisdictions in which the nature
of the activities conducted by it or the character of the assets owned or leased
by it makes such licensing or qualification necessary. Except as disclosed in
the Registration Statement, the Company does not own, and at the Closing Date
will not own, directly or indirectly, any shares of stock or any other equity or
long-term debt securities of any corporation or have any equity interest in any
firm, partnership, joint venture, association or other entity. Complete and
correct copies of the articles of incorporation and of the by-laws of the
Company and all amendments thereto have been delivered to the Representatives or
their counsel, and no changes therein will be made subsequent to the date hereof
and prior to the Closing Date or, if later, the Option Closing Date.

               (e)  The outstanding shares of Common Stock have been, and the
Shares to be issued and sold by the Company upon such issuance will be, duly
authorized, validly issued, fully paid and nonassessable and will not be subject
to any preemptive or similar right (any such rights having been validly waived
with respect to the issuance and sale of the Shares). The description of the
Common Stock in the Registration Statement and the Prospectus is, and at the
Closing Date will be, complete and accurate in all respects. Except pursuant to
the Company's Stock Option Plans and

<PAGE>

                                                                               7

Employee Stock Purchase Plan or as otherwise set forth in the Prospectus, the
Company does not have outstanding, and at the Closing Date will not have
outstanding, any options to purchase, or any rights or warrants to subscribe
for, or any securities or obligations convertible into, or any contracts or
commitments to issue or sell, any shares of Common Stock, or any such warrants,
convertible securities or obligations.

               (f)  The financial statements and schedules included or
incorporated by reference in the Registration Statement or the Prospectus
present fairly the financial condition of the Company as of the respective dates
thereof and the results of operations and cash flows of the Company for the
respective periods covered thereby, all in conformity with generally accepted
accounting principles applied on a consistent basis throughout the entire period
involved, except as otherwise disclosed in the Prospectus. No other financial
statements or schedules of the Company are required by the Act, the Exchange Act
or the Rules and Regulations to be included in the Registration Statement or the
Prospectus. Price Waterhouse LLP (the "Accountants") who have reported on such
financial statements and schedules, are independent accountants with respect to
the Company as required by the Act and the Rules and Regulations. The statements
included in the Registration Statement with respect to the Accountants pursuant
to Rule 509 of Regulation S-K of the Rules and Regulations are true and correct
in all material respects.

               (g)  The Company maintains a system of internal accounting
controls sufficient to provide reasonable assurance that (i) transactions are
executed in accordance with management's general or specific authorization; (ii)
transactions are recorded as necessary to permit preparation of financial
statements in conformity with generally accepted accounting principles and to
maintain accountability for assets; (iii) access to assets is permitted only in
accordance with management's general or specific authorization; and (iv) the
recorded accountability for assets is compared with existing assets at
reasonable intervals and appropriate action is taken with respect to any
differences.

               (h)  Subsequent to the respective dates as of which information
is given in the Registration Statement and the Prospectus and prior to the
Closing Date, except as set forth in or contemplated by the Registration
Statement and the Prospectus, (i) there has not been and will not have been any
material change in the capitalization of the Company, or in the business,
properties, business prospects, condition (financial or otherwise) or results of
operations of the Company, arising for any reason whatsoever, (ii) the Company
has not incurred nor will it incur any material liabilities or obligations,
direct or contingent, nor has it entered into nor will it enter into any
material transactions other than

<PAGE>

                                                                               8

pursuant to this Agreement and the transactions referred to herein and (iii) the
Company has not and will not have paid or declared any dividends or other
distributions of any kind on any class of its capital stock.

               (i)  The Company is not an "investment company" or an "affiliated
person" of, or "promoter" or "principal underwriter" for, an "investment
company," as such terms are defined in the Investment Company Act of 1940, as
amended.

               (j)  Except as set forth in the Registration Statement and the
Prospectus, there are no actions, suits or proceedings pending or, to the
knowledge of the Company, threatened against or affecting the Company or any of
its officers in their capacity as such, before or by any Federal or state court,
commission, regulatory body, administrative agency or other governmental body,
domestic or foreign, wherein an unfavorable ruling, decision or finding might
materially and adversely affect the Company or its business, properties,
business prospects, condition (financial or otherwise) or results of operations.

               (k)  Except as expressly set forth in the Prospectus, the Company
has, and at the Closing Date will have, (i) all governmental licenses, permits,
consents, orders, approvals and other authorizations necessary to carry on its
business as contemplated in the Prospectus, (ii) complied in all material
respects with all laws, regulations and orders applicable to it or its business
and has not received notice or otherwise obtained knowledge that it is in
violation of any such law, regulation or order, and (iii) performed all its
material obligations required to be performed by it, and is not, and at the
Closing Date will not be, in default in any material respect, under any
indenture, mortgage, deed of trust, voting trust agreement, loan agreement,
bond, debenture, note agreement, lease, contract or other agreement or
instrument (collectively, a "Contract or Other Agreement") to which it is a
party or by which its property is bound or affected. To the best knowledge of
the Company, no other party under any Contract or Other Agreement to which it is
a party is in default in any material respect thereunder. The Company is not,
nor at the Closing Date will it be, in violation of any provision of its
articles of incorporation or by-laws.

               (l)  No consent, approval, authorization or order of, or any
filing or declaration with, any court or governmental agency or body is required
in connection with the authorization, issuance, transfer, sale or delivery of
the Shares by the Company, in connection with the execution, delivery and
performance of this Agreement by the Company or in connection with the taking by
the Company of any action contemplated hereby, except such as have been obtained
under

<PAGE>

                                                                               9

the Act or the Rules and Regulations and such as may be required under state
securities or Blue Sky laws or the by-laws and rules of the National Association
of Securities Dealers, Inc. (the "NASD") in connection with the purchase and
distribution by the Underwriters of the Shares to be sold by the Company.

               (m)  The Company has full corporate power and authority to enter
into this Agreement.  This Agreement has been duly authorized, executed and
delivered by the Company and constitutes a valid and binding agreement of the
Company and is enforceable against the Company in accordance with the terms
hereof. The performance of this Agreement, the consummation of the transactions
contemplated hereby and the application of the net proceeds from the offering
and sale of the Shares to be sold by the Company in the manner set forth in the
Prospectus under "Use of Proceeds" will not result in the creation or imposition
of any lien, charge or encumbrance upon any of the assets of the Company
pursuant to the terms or provisions of, or result in a breach or violation of
any of the terms or provisions of, or constitute a default under, or give any
other party a right to terminate any of its obligations under, or result in the
acceleration of any obligation under, the articles of incorporation or by-laws
of the Company, any Contract or Other Agreement to which the Company is a party
or by which the Company or any of its properties is bound or affected, or
violate or conflict with any judgment, ruling, decree, order, statute, rule or
regulation of any court or other governmental agency or body applicable to the
business or properties of the Company.

               (n)  The Company has good and marketable title to all properties
and assets described in the Prospectus as owned by it, free and clear of all
liens, charges, encumbrances or restrictions, except such as are described in
the Prospectus or are not material to the business of the Company. The Company
has valid, subsisting and enforceable leases for the properties described in the
Prospectus as leased by it, with such exceptions as are not material and do not
materially interfere with the use made and proposed to be made of such
properties by the Company.

               (o)  There is no document or contract of a character required to
be described in the Registration Statement or the Prospectus or to be filed as
an exhibit to the Registration Statement which is not described or filed as
required. All such contracts to which the Company is a party have been duly
authorized, executed and delivered by the Company, constitute valid and binding
agreements of the Company and are enforceable against the Company in accordance
with the terms thereof, except as such enforceability may be affected by
application of the bankruptcy laws or equitable remedies.

<PAGE>

                                                                              10

               (p)  No statement, representation, warranty or covenant made by
the Company in this Agreement or made in any certificate or document required by
this Agreement to be delivered to the Representatives was or will be, when made,
inaccurate, untrue or incorrect.

               (q)  Neither the Company nor any of its directors, officers or
controlling persons has taken, directly or indirectly, any action intended, or
which might reasonably be expected, to cause or result, under the Act or
otherwise, in, or which has constituted, stabilization or manipulation of the
price of any security of the Company to facilitate the sale or resale of the
Shares.

               (r)  No holder of securities of the Company has rights to the
registration of any securities of the Company because of the filing of the
Registration Statement.

               (s)  The Shares are eligible for listing on The Nasdaq National
Market.

               (t)  The Company is not involved in any material labor dispute
nor, to the knowledge of the Company, is any such dispute threatened.

               (u)  The Company owns, or possesses adequate rights to use, (i)
all patents, patent rights, trademarks, service marks, trade names and
copyrights described in the Prospectus as owned or used by it or that are
necessary for the material conduct of its business and activities as described
in the Prospectus and (ii) all inventions, trade secrets, know-how and
proprietary techniques, including processes and substances, described in the
Prospectus as owned or used by it or which are necessary for the material
conduct of its business and activities. The Company has not received any written
notice (or oral notice delivered to any executive officer of the Company who is
named in the Prospectus) of infringement of or conflict with asserted rights of
others with respect to any patents, patent rights, inventions, trade secrets,
know-how or proprietary techniques, including processes and substances,
trademarks, service marks, trade names or copyrights of others, which
infringement or conflict could reasonably be expected to have a material adverse
effect on the business, properties, business prospects, condition (financial or
otherwise) or results of operations of the Company.

               (v)  Except as disclosed in the Registration Statement or the
Prospectus, the Company maintains insurance of the types and in amounts
generally deemed adequate for its business and activities and consistent with
insurance coverage maintained by similar companies and businesses, all of which
insurance is in full force and effect.

<PAGE>

                                                                              11

               (w)  Neither the Company nor, to the Company's knowledge, any
employee or agent of the Company has made any payment of funds of the Company or
received or retained any funds in violation of any law, rule or regulation or of
a character required to be disclosed in the Prospectus.

               (x)  The Company has complied, and until the completion of the
distribution of the Shares will comply, with all of the provisions of
(including, without limitation, filing all forms required by) Section 517.075 of
the Florida Securities and Investor Protection Act and regulation 3E-900.001
issued thereunder with respect to the offering and sale of the Shares.

               (y)  The Company is not and has never been a United States real
property holding corporation" as defined in section 897(c)(2) of the Internal
Revenue Code of 1986, as amended (the "Code"), and the Treasury Department
regulations promulgated thereunder.

4.   AGREEMENTS OF THE COMPANY. The Company agrees with the several Underwriters
as follows:

               (a)  The Company will not, either prior to the Effective Date or
thereafter during such period as the Prospectus is required by law to be
delivered in connection with sales of the Shares by a Underwriter or dealer,
file any amendment or supplement to the Registration Statement or the
Prospectus, unless a copy thereof shall first have been submitted to the
Representatives within a reasonable period of time prior to the filing thereof
and the Representatives shall not have objected thereto in good faith.

               (b)  The Company will use its best efforts to cause the
Registration Statement to become effective, and will notify the Representatives
promptly, and will confirm such advice in writing, (1) when the Registration
Statement has become effective and when any post-effective amendment thereto
becomes effective, (2) of any request by the Commission for amendments or
supplements to the Registration Statement or the Prospectus or for additional
information, (3) of the issuance by the Commission of any stop order suspending
the effectiveness of the Registration Statement or the initiation of any
proceedings for that purpose or the threat thereof, (4) of the happening of any
event during the period mentioned in the second sentence of Section 4(e) that in
the judgment of the Company makes any statement made in the Registration
Statement or the Prospectus untrue or that requires the making of any changes in
the Registration Statement or the Prospectus in order to make the statements
therein, in light of the circumstances in which they are made, not misleading
and (5) of receipt by the Company or any representative or attorney of the
Company of any other

<PAGE>

                                                                              12

communication from the Commission relating to the Company, the Registration
Statement, any preliminary prospectus or the Prospectus. If at any time the
Commission shall issue any order suspending the effectiveness of the
Registration Statement, the Company will make every reasonable effort to obtain
the withdrawal of such order at the earliest possible moment. If the Company has
omitted any information from the Registration Statement pursuant to Rule 430A,
the Company will use its best efforts to comply with the provisions of, and make
all requisite filings with the Commission pursuant to, said Rule 430A and to
notify the Representatives promptly of all such filings.

               (c)  The Company will furnish to the Representatives, without
charge, two signed copies of the Registration Statement and of any post-
effective amendment thereto, including financial statements and schedules, and
all exhibits thereto (including any document filed under the Exchange Act and
deemed to be incorporated by reference into the Prospectus), and will furnish to
the Representatives, without charge, for transmittal to each of the other
Underwriters, a copy of the Registration Statement and any post-effective
amendment thereto, including financial statements and schedules but without
exhibits.

               (d)  The Company will comply with all the provisions of any
undertakings contained in the Registration Statement.

               (e)  On the Effective Date, and thereafter from time to time
during the periods of time set forth in the following sentence, the Company will
deliver  to each of the Underwriters, without charge, as many copies of the
Prospectus or any amendment or supplement thereto as the Representatives may
reasonably request. The Company consents to the use of the Prospectus or any
amendment or supplement thereto by the several Underwriters and by all dealers
to whom the Shares may be sold, both in connection with the offering or sale of
the Shares and for any period of time thereafter during which the Prospectus is
required by law to be delivered in connection therewith. If during such period
of time any event shall occur which in the judgment of the Company or counsel to
the Underwriters should be set forth in the Prospectus in order to make any
statement therein, in the light of the circumstances under which it was made,
not misleading, or if it is necessary to supplement or amend the Prospectus to
comply with law, the Company will forthwith prepare and duly file with the
Commission an appropriate supplement or amendment thereto, and will deliver to
each of the Underwriters, without charge, such number of copies of such
supplement or amendment to the Prospectus as the Representatives may reasonably
request. The Company shall not file any document under the Exchange Act before
the termination of the offering of the Shares by the Underwriters

<PAGE>

                                                                              13

if such document would be deemed to be incorporated by reference into the
Prospectus which is not approved by the Representatives after reasonable notice
thereof, which approval shall not unreasonably be withheld or delayed.

               (f)  Prior to any public offering of the Shares, the Company will
cooperate with the Representatives and counsel to the Underwriters in connection
with the registration or qualification of the Shares for offer and sale under
the securities or Blue Sky laws of such jurisdictions as the Representatives may
request, including, without limitation, the provinces and territories of Canada
and other jurisdictions outside of the United States; provided, that in no event
shall the Company be obligated to qualify to do business in any jurisdiction
where it is not now so qualified or to take any action which would subject it to
general service of process in any jurisdiction where it is not now so subject.

               (g)  During the period of five years commencing on the Effective
Date, the Company will furnish to the Representatives and each other Underwriter
who may so request copies of such financial statements and other periodic and
special reports as the Company may from time to time distribute generally
(without obligations of confidentiality) to the holders of any class of its
capital stock, and will furnish to the Representatives and each other
Underwriter who may so request a copy of each annual or other report it shall be
required to file with the Commission.

               (h)  The Company will make generally available to holders of its
securities as soon as may be practicable but in no event later than the last day
of the fifteenth full calendar month following the calendar quarter in which the
Effective Date falls, an earnings statement (which need not be audited but shall
be in reasonable detail) for a period of 12 months ended commencing after
Effective Date, and satisfying the provisions of Section 11(a) of the Act
(including Rule 158 of the Rules and Regulations).

               (i)  Whether or not the transactions contemplated by this
Agreement are consummated or this Agreement is terminated, the Company will pay,
or reimburse if paid by the Representatives, all costs and expenses incident to
the performance of the obligations of the Company under this Agreement,
including but not limited to costs and expenses of or relating to (1) the
preparation, printing and filing of the Registration Statement and exhibits to
it, each preliminary prospectus, Prospectus and any amendment or supplement to
the Registration Statement or Prospectus, (2) the preparation and delivery of
certificates representing the Shares, (3) the printing of this Agreement, any
Dealer Agreements and any Underwriters' Questionnaire, (4) furnishing (including
costs of shipping, mailing and courier)

<PAGE>

                                                                              14

such copies of the Registration Statement, the Prospectus and any preliminary
prospectus, and all amendments and supplements thereto, as may be requested for
use in connection with the offering and sale of the Shares by the Underwriters
or by dealers to whom Shares may be sold, (5) the listing of the Shares on The
Nasdaq National Market, (6) any filings required to be made by the Underwriters
with the NASD, and the fees, disbursements and other charges of counsel for the
Underwriters in connection therewith, (7) the registration or qualification of
the Shares for offer and sale under the securities or Blue Sky laws of such
jurisdictions designated pursuant to Section 5(f), including the fees,
disbursements and other charges of counsel (including counsel in Canadian
provinces and territories, if applicable) to the Underwriters in connection
therewith, and the preparation and printing of preliminary, supplemental and
final Blue Sky memoranda, (8) counsel to the Company, (9) the transfer agent for
the Shares and (10) the Accountants.

               (j)  If this Agreement shall be terminated by the Company
pursuant to any of the provisions hereof (otherwise than pursuant to Section 7
hereof) or if for any reason the Company shall be unable to perform its
obligations hereunder, the Company will reimburse the several Underwriters for
all out-of-pocket expenses (including the fees, disbursements and other charges
of counsel to the Underwriters) reasonably incurred by them in connection
herewith.

               (k)  The Company will not at any time, directly or indirectly,
take any action intended, or which might reasonably be expected, to cause or
result in, or which will constitute, stabilization of the price of the shares of
Common Stock to facilitate the sale or resale of any of the Shares.

               (l)  The Company will apply the net proceeds from the offering
and sale of the Shares to be sold by the Company in the manner set forth in the
Prospectus under "Use of Proceeds."

               (m)  During the period of 90 days commencing at the Closing Date,
the Company will not, without the prior written consent of the Representatives,
grant options to purchase shares of Common Stock at a price less than the public
offering price set forth on the cover page of the Prospectus, except options
granted pursuant to the Company's Stock Option Plans or Employee Stock Purchase
Plan at prices permitted under such plans.

               (n)  The Company will not, and will cause each of its executive
officers, directors and each beneficial owner of Common Stock named on Schedule
II hereto to enter into agreements with the Representatives to the effect that

<PAGE>

                                                                              15

they will not, for a period of 90 days (or such other time period as may be
agreed to the Representatives) after the commencement of the public offering of
the Shares, without the prior written consent of the Representatives, sell,
contract to sell or otherwise dispose of any shares of Common Stock or rights to
acquire such shares (other than pursuant to employee stock option plans,
employee stock purchase plans or in connection with other employee incentive
compensation arrangements).

               (o) The Company will (i) furnish to each Underwriter on the
Closing Date a certification, as contemplated by and in compliance with Treasury
Department regulations section 1.897-2(h), that, as of the Closing Date, the
Shares are not United States real property interests as defined in section
897(c)(1) of the Code, (ii) file such certification with the Internal Revenue
Service in the manner and within the time period specified in Treasury
Department regulations section 1.897-2(h) and (iii) promptly after such filing,
furnish to each Underwriter proof of such filing.

5.   CONDITIONS OF THE OBLIGATIONS OF THE UNDERWRITERS.  In addition to the
execution and delivery of the Price Determination Agreement, the obligations of
each Underwriter hereunder are subject to the following conditions:

               (a)  Notification that the Registration Statement has become
effective shall be received by the Representatives not later than 5:00 p.m., New
York City time, on the date of this Agreement or at such later date and time as
shall be consented to in writing by the Representatives and all filings required
by Rule 424 of the Rules and Regulations and Rule 430A shall have been made.

               (b)  (i) No stop order suspending the effectiveness of the
Registration Statement shall have been issued and no proceedings for that
purpose shall be pending or threatened by the Commission, (ii) no order
suspending the effectiveness of the Registration Statement or the qualification
or registration of the Shares under the securities or Blue Sky laws of any
jurisdiction shall be in effect and no proceeding for such purpose shall be
pending before or threatened or contemplated by the Commission or the
authorities of any such jurisdiction, (iii) any request for additional
information on the part of the staff of the Commission or any such authorities
shall have been complied with to the satisfaction of the staff of the Commission
or such authorities and (iv) after the date hereof no amendment or supplement to
the Registration Statement or the Prospectus shall have been filed unless a copy
thereof was first submitted to the Representatives and the Representatives do
not object thereto in good faith, and the Representatives shall have received
certificates, dated the Closing Date and

<PAGE>

                                                                              16

the Option Closing Date and signed by the Chief Executive Officer or the
Chairman of the Board of Directors of the Company and the Chief Financial
Officer of the Company (who may, as to proceedings threatened, rely upon the
best of their knowledge), to the effect of clauses (i), (ii) and (iii).

               (c)  Since the respective dates as of which information is given
in the Registration Statement and the Prospectus, (i) there shall not have been
a material adverse change in the general affairs, business, business prospects,
properties, management, condition (financial or otherwise) or results of
operations of the Company, whether or not arising from transactions in the
ordinary course of business, in each case other than as set forth in or
contemplated by the Registration Statement and the Prospectus and (ii) the
Company shall not have sustained any material loss or interference with its
business or properties from fire, explosion, flood or other casualty, whether or
not covered by insurance, or from any labor dispute or any court or legislative
or other governmental action, order or decree, which is not set forth in the
Registration Statement and the Prospectus, if in the judgment of the
Representatives any such development makes it impracticable or inadvisable to
consummate the sale and delivery of the Shares by the Underwriters at the
initial public offering price.

               (d)  Since the respective dates as of which information is given
in the Registration Statement and the Prospectus, there shall have been no
litigation or other proceeding instituted against the Company or any of its
officers or directors in their capacities as such, before or by any Federal,
state or local court, commission, regulatory body, administrative agency or
other governmental body, domestic or foreign, in which litigation or proceeding
an unfavorable ruling, decision or finding would materially and adversely affect
the business, properties, business prospects, condition (financial or otherwise)
or results of operations of the Company.

               (e)  Each of the representations and warranties of the Company
contained herein shall be true and correct in all material respects at the
Closing Date and, with respect to the Option Shares, at the Option Closing Date
as if made at the Closing Date and, with respect to the Option Shares, at the
Option Closing Date, and all covenants and agreements contained herein to be
performed on the part of the Company and all conditions contained herein to be
fulfilled or complied with by the Company at or prior to the Closing Date and,
with respect to the Option Shares, at or prior to the Option Closing Date, shall
have been duly performed, fulfilled or complied with.

<PAGE>

                                                                              17

               (f)  The Representatives shall have received opinions, each dated
the Closing Date and, with respect to the Option Shares, the Option Closing
Date, and satisfactory in form and substance to counsel for the Underwriters,
from Ferris, Britton & Proctor, a professional corporation, counsel to the
Company, and Gary E. Friedman, General Counsel of the Company, to the effect set
forth in Exhibit B.

               (g)  The Representatives shall have received an opinion, dated
the Closing Date and, with respect to the Option Shares, the Option Closing
Date, from Morrison & Foerster LLP, counsel to the Underwriters, with respect to
the Registration Statement, the Prospectus and this Agreement, which opinion
shall be satisfactory in all respects to the Representatives.

               (h)  Concurrently with the execution and delivery of this
Agreement or, if the Company elects to rely on Rule 43OA, on the date of the
Prospectus, the Accountants shall have furnished to the Representatives a
letter, dated the date of its delivery, addressed to the Representatives and in
form and substance satisfactory to the Representatives, confirming that they are
independent accountants with respect to the Company as required by the Act and
the Rules and Regulations and with respect to the financial and other
statistical and numerical information contained in the Registration Statement or
incorporated by reference therein. At the Closing Date and, as to the Option
Shares, the Option Closing Date, the Accountants shall have furnished to the
Representatives a letter, dated the date of its delivery, which shall confirm,
on the basis of a review in accordance with the procedures set forth in the
letter from the Accountants, that nothing has come to their attention during the
period from the date of the letter referred to in the prior sentence to a date
(specified in the letter) not more than five days prior to the Closing Date and
the Option Closing Date, as the case may be, which would require any change in
their letter dated the date hereof or, if the Company elects to rely on Rule
430A, on the date of the Prospectus, if it were required to be dated and
delivered at the Closing Date and the Option Closing Date.

               (i)  At the Closing Date and, as to the Option Shares, the Option
Closing Date, there shall be furnished to the Representatives an accurate
certificate, dated the date of its delivery, signed by each of the Chief
Executive Officer and the Chief Financial Officer of the Company, in form and
substance satisfactory to the Representatives, to the effect that:

                    (i)  Each signer of such certificate has carefully
     examined the Registration Statement and the Prospectus (including any
     documents filed under the Exchange Act and deemed to be incorporated by
     reference

<PAGE>

                                                                              18

     into the Prospectus) and (A) as of the date of such certificate, such
     documents are true and correct in all material respects and do not omit to
     state a material fact required to be stated therein or necessary in order
     to make the statements therein, in light of the circumstances under which
     they were made, not untrue or misleading and (B) since the Effective Date,
     no event has occurred as a result of which it is necessary to amend or
     supplement the Prospectus in order to make the statements therein, in light
     of the circumstances under which they were made, not untrue or misleading
     in any material respect and there has been no document required to be filed
     under the Exchange Act and the Exchange Act Rules and Regulations that upon
     such filing would be deemed to be incorporated by reference into the
     Prospectus that has not been so filed.

                    (ii) Each of the representations and warranties of the
     Company contained in this Agreement were, when originally made, and are,
     at the time such certificate is dated, true and correct in all material
     respects.

                    (iii) Each of the covenants required to be performed
     by the Company herein on or prior to the date of such certificate has
     been duly, timely and fully performed and each condition herein required
     to be satisfied or fulfilled on or prior to the date of such certificate
     has been duly, timely and fully satisfied or fulfilled.

               (j) on or prior to the Closing Date, the Representatives shall
have received the executed agreements referred to in Section 4(n).

               (k) The Shares shall be qualified for sale in such jurisdictions
as the Representatives may reasonably request, each such qualification shall be
in effect and not subject to any stop order or other proceeding on the Closing
Date or the Option Closing Date.

               (l) Prior to the Closing Date, the Shares shall have been
qualified for listing on The Nasdaq National Market.

               (m) The Company shall have furnished to the Representatives such
certificates, in addition to those specifically mentioned herein, as the
Representatives may have reasonably requested as to the accuracy and
completeness at the Closing Date and the Option Closing Date of any statement in
this Registration Statement or the Prospectus or any documents filed under the
Exchange Act and deemed to be incorporated by reference into the Prospectus, as
to the accuracy at the Closing Date and the Option Closing Date of

<PAGE>

                                                                              19

the representations and warranties of the Company herein, as to the performance
by the Company of its obligations hereunder, or as to the fulfillment of the
conditions concurrent and precedent to the obligations hereunder of the
Representatives.

6. INDEMNIFICATION.

               (a)  The Company will indemnify and hold harmless each
Underwriter, the directors, officers, employees and agents of each Underwriter
and each person, if any, who controls each Underwriter, within the meaning of
Section 15 of the Act or Section 20 of the Exchange Act, from and against any
and all losses, claims, liabilities, expenses and damages (including any and all
investigative, legal and other expenses reasonably incurred in connection with,
and any amount paid in settlement of, any action, suit or proceeding or any
claim asserted), to which they, or any of them, may become subject under the
Act, the Exchange Act or other Federal or state statutory law or regulation, at
common law or otherwise, insofar as such losses, claims, liabilities, expenses
or damages arise out of or are based on any untrue statement or alleged untrue
statement of a material fact contained in any preliminary prospectus, the
Registration Statement or the Prospectus or any amendment or supplement to the
Registration Statement or the Prospectus, or in any documents filed under the
Exchange Act and deemed to be incorporated by reference into the Prospectus, or
the omission or alleged omission to state in such document a material fact
required to be stated in it or necessary to make the statements in it (with
respect to statements in any preliminary prospectus, Prospectus or supplement
thereto, in light of the circumstances under which they were made) not
misleading, provided that the Company will not be liable to any Underwriter, the
directors, officers, employees and agents of such Underwriter, or any person
controlling such Underwriter, with respect to any untrue statement or omission
made in any preliminary prospectus which is corrected by the Prospectus if the
person asserting any such loss, claim, liability, expense or damage purchased
shares from such Underwriter but was not sent or given a copy of the Prospectus
at or prior to the written confirmation of such Shares to such person, and
provided further that the Company will not be liable to the extent that such
loss, claim, liability, expense or damage arises from the sale of the Shares in
the public offering to any person by a Underwriter and is based on an untrue
statement or omission or alleged untrue statement or omission made in reliance
on and in conformity with information relating to any Underwriter furnished in
writing to the Company by the Representatives on behalf of any Underwriter
expressly for inclusion in the Registration Statement, the preliminary
prospectus or the

<PAGE>

                                                                              20

Prospectus. This indemnity agreement will be in addition to any liability that
the Company might otherwise have.

               (b)  Each Underwriter will indemnify and hold harmless the
Company, each person, if any, who controls the Company within the meaning of
Section 15 of the Act or Section 20 of the Exchange Act, each director of the
Company and each officer of the Company who signs the Registration Statement to
the same extent as the foregoing indemnity from the Company to each Underwriter,
but only insofar as losses, claims, liabilities, expenses or damages arise out
of or are based on any untrue statement or omission or alleged untrue statement
or omission made in reliance on and in conformity with information relating to
any Underwriter furnished in writing to the Company by the Representatives on
behalf of such Underwriter expressly for use in the Registration Statement, the
preliminary prospectus or the Prospectus. This indemnity will be in addition to
any liability that each Underwriter might otherwise have.

               (c)  Any party that proposes to assert the right to be
indemnified under this Section 6 will, promptly after receipt of notice of
commencement of any action against such party in respect of which a claim is to
be made against an indemnifying party or parties under this Section 6, notify
each such indemnifying party of the commencement of such action, enclosing a
copy of all papers served, but the omission so to notify such indemnifying party
will not relieve it from any liability that it may have to any indemnified party
under the foregoing provisions of this Section 6 unless, and only to the extent
that, such omission results in the forfeiture of substantive rights or defenses
by the indemnifying party. If any such action is brought against any indemnified
party and it notifies the indemnifying party of its commencement, the
indemnifying party will be entitled to participate in and, to the extent that it
elects by delivering written notice to the indemnified party promptly after
receiving notice of the commencement of the action from the indemnified party,
jointly with any other indemnifying party similarly notified, to assume the
defense of the action, with counsel satisfactory to the indemnified party, and
after notice from the indemnifying party to the indemnified party of its
election to assume the defense, the indemnifying party will not be liable to the
indemnified party for any legal or other expenses except as provided below and
except for the reasonable costs of investigation subsequently incurred by the
indemnified party in connection with the defense. The indemnified party will
have the right to employ its own counsel in any such action, but the fees,
expenses and other charges of such counsel will be at the expense of such
indemnified party unless (1) the employment of counsel by the indemnified party
has been authorized in writing by the indemnifying party, (2) the indemnified
party has reasonably

<PAGE>

                                                                              21

concluded (based on advice of counsel) that there may be legal defenses
available to it or other indemnified parties that are different from or in
addition to those available to the indemnifying party, (3) a conflict or
potential conflict exists (based on advice of counsel to the indemnified party)
between the indemnified party and the indemnifying party (in which case the
indemnifying party will not have the right to direct the defense of such action
on behalf of the indemnified party) or (4) the indemnifying party has not in
fact employed counsel to assume the defense of such action within a reasonable
time after receiving notice of the commencement of the action, in each of which
cases the reasonable fees, disbursements and other charges of counsel will be at
the expense of the indemnifying party or parties. It is understood that the
indemnifying party or parties shall not, in connection with any proceeding or
related proceedings in the same jurisdiction, be liable for the reasonable fees,
disbursements and other charges of more than one separate firm admitted to
practice in such jurisdiction at any one time for all such indemnified party or
parties. All such fees, disbursements and other charges will be reimbursed by
the indemnifying party promptly as they are incurred. An indemnifying party will
not be liable for any settlement of any action or claim effected without its
written consent (which consent will not be unreasonably withheld).

               (d)  In order to provide for just and equitable contribution in
circumstances in which the indemnification provided for in the foregoing
paragraphs of this Section 6 is applicable in accordance with its terms but for
any reason is held to be unavailable from the Company or the Underwriters, the
Company and the Underwriters will contribute to the total losses, claims,
liabilities, expenses and damages (including any investigative, legal and other
expenses reasonably incurred in connection with, and any amount paid in
settlement of, any action, suit or proceeding or any claim asserted, but after
deducting any contribution received by the Company from persons other than the
Underwriters, such as persons who control the Company within the meaning of the
Act, officers of the Company who signed the Registration Statement and directors
of the Company, who also may be liable for contribution) to which the Company
and any one or more of the Underwriters may be subject in such proportion as
shall be appropriate to reflect the relative benefits received by the Company on
the one hand and the Underwriters on the other. The relative benefits received
by the Company on the one hand and the Underwriters on the other shall be deemed
to be in the same proportion as the total net proceeds from the offering (before
deducting expenses) received by the Company bear to the total underwriting
discounts and commissions received by the Underwriters, in each case as set
forth in the table on the cover page of the Prospectus. If, but only if, the
allocation provided by the foregoing sentence is not permitted by applicable
law, the

<PAGE>

                                                                              22

allocation of contribution shall be made in such proportion as is appropriate to
reflect not only the relative benefits referred to in the foregoing sentence but
also the relative fault of the Company, on the one hand, and the Underwriters,
on the other, with respect to the statements or omissions which resulted in such
loss, claim, liability, expense or damage, or action in respect thereof, as well
as any other relevant equitable considerations with respect to such offering.
Such relative fault shall be determined by reference to whether the untrue or
alleged untrue statement of a material fact or omission or alleged omission to
state a material fact relates to information supplied by the Company or the
Representatives on behalf of the Underwriters, the intent of the parties and
their relative knowledge, access to information and opportunity to correct or
prevent such statement or omission. The Company and the Underwriters agree that
it would not be just and equitable if contributions pursuant to this Section
6(d) were to be determined by pro rata allocation (even if the Underwriters were
treated as one entity for such purpose) or by any other method of allocation
which does not take into account the equitable considerations referred to
herein. The amount paid or payable by an indemnified party as a result of the
loss, claim, liability, expense or damage, or action in respect thereof,
referred to above in this Section 6(d) shall be deemed to include, for purpose
of this Section 6(d), any legal or other expenses reasonably incurred by such
indemnified party in connection with investigating or defending any such action
or claim. Notwithstanding the provisions of this Section 6(d), no Underwriter
shall be required to contribute any amount in excess of the underwriting
discounts received by it and no person found guilty of fraudulent
misrepresentation (within the meaning of Section 11(f) of the Act) will be
entitled to contribution from any person who was not guilty of such fraudulent
misrepresentation. The Underwriters' obligations to contribute as provided in
this Section 6(d) are several in proportion to their respective underwriting
obligations and not joint. For purposes of this Section 6(d), any person who
controls a party to this Agreement within the meaning of the Act will have the
same rights to contribution as that party, and each officer of the Company who
signed the Registration Statement will have the same rights to contribution as
the Company, subject in each case to the provisions hereof. Any party entitled
to contribution, promptly after receipt of notice of commencement of any action
against such party in respect of which a claim for contribution may be made
under this Section 6(d), will notify any such party or parties from whom
contribution may be sought, but the omission so to notify will not relieve the
party or parties from whom contribution may be sought from any other obligation
it or they may have under this Section 6(d). No party will be liable for
contribution with respect to any action or claim settled without its written
consent (which consent will not be unreasonably withheld).

<PAGE>

                                                                              23

               (e)  The indemnity and contribution agreements contained in this
Section 6 and the representations and warranties of the Company contained in
this Agreement shall remain operative and in full force and effect regardless of
(i) any investigation made by or on behalf of the Underwriters, (ii) acceptance
of any of the Shares and payment therefor or (iii) any termination of this
Agreement.

7.   TERMINATION.

                    The obligations of the several Underwriters under this
Agreement may be terminated at any time on or prior to the Closing Date (or,
with respect to the Option Shares, on or prior to the Option Closing Date), by
notice to the Company from the Representatives, without liability on the part of
any Underwriter to the Company, if, prior to delivery and payment for the Shares
(or the Option Shares, as the case may be), in the sole judgment of the
Representatives, (i) trading in any of the equity securities of the Company
shall have been suspended by the Commission, by an exchange that lists such
securities or by the Nasdaq National Market, (ii) trading in securities
generally on the New York Stock Exchange shall have been suspended or limited or
minimum or maximum prices shall have been generally established on such
exchange, or additional material governmental restrictions, not in force on the
date of this Agreement, shall have been imposed upon trading in securities
generally by such exchange or by order of the Commission or any court or other
governmental authority, (iii) a general banking moratorium shall have been
declared by either Federal or New York State authorities or (iv) any material
adverse change in the financial or securities markets in the United States or in
political, financial or economic conditions in the United States or any outbreak
or material escalation of hostilities or declaration by the United States of a
national emergency or war or other calamity or crisis shall have occurred, the
effect of any of which is such as to make it, in the sole judgment of the
Representatives, impracticable or inadvisable to market the Shares on the terms
and in the manner contemplated by the Prospectus.

8.   SUBSTITUTION OF UNDERWRITERS.

                    If any one or more of the Underwriters shall fail or refuse
to purchase any of the Firm Shares which it or they have agreed to purchase
hereunder, and the aggregate number of Firm Shares which such defaulting
Underwriter or Underwriters agreed but failed or refused to purchase is not more
than one-tenth of the aggregate number of Firm Shares, the other Underwriters
shall be obligated, severally, to purchase the Firm Shares which such defaulting
Underwriter or Underwriters agreed but failed or refused to

<PAGE>

                                                                              24

purchase, in the proportions which the number of Firm Shares which they have
respectively agreed to purchase pursuant to Section 1 bears to the aggregate
number of Firm Shares which all such nondefaulting Underwriters have so agreed
to purchase, or in such other proportions as the Representatives may specify;
provided that in no event shall the maximum number of Firm Shares which any
Underwriter has become obligated to purchase pursuant to Section 1 be increased
pursuant to this Section 8 by more than one-ninth of the number of Firm Shares
agreed to be purchased by such Underwriter without the prior written consent of
such Underwriter. If any Underwriter or Underwriters shall fail or refuse to
purchase any Firm Shares and the aggregate number of Firm Shares which such
defaulting Underwriter or Underwriters agreed but failed or refused to purchase
exceeds one-tenth of the aggregate number of the Firm Shares and arrangements
satisfactory to the Representatives and the Company for the purchase of such
Firm Shares are not made within 48 hours after such default, this Agreement will
terminate without liability on the part of any non-defaulting Underwriter or the
Company for the purchase or sale of any Shares under this Agreement. In any such
case either the Representatives or the Company shall have the right to postpone
the Closing Date, but in no event for longer than seven days, in order that the
required changes, if any, in the Registration Statement and in the Prospectus or
in any other documents or arrangements may be effected. Any action taken
pursuant to this Section 8 shall not relieve any defaulting Underwriter from
liability in respect of any default of such Underwriter under this Agreement.

9.   MISCELLANEOUS.

               (a)  Notice given pursuant to any of the provisions of this
Agreement shall be in writing and, unless otherwise specified, shall be mailed
or delivered (a) if to the Company, at the office of the Company, 10350 North
Torrey Pines Road, La Jolla, California 92037, Attention: President, or (b) if
to the Underwriters, to the Representatives at the offices of PaineWebber
Incorporated, 1285 Avenue of the Americas, New York, New York 10019, Attention:
Corporate Finance Department. Any such notice shall be effective only upon
receipt. Any notice under Section 6 or 7 may be made by telex, telephone or
other electronic means and shall be effective at the time such communication is
received if subsequently confirmed in writing within a reasonable period of
time.

               (b)  This Agreement has been and is made solely for the benefit
of the several Underwriters and the Company and of the controlling persons,
directors and officers referred to in Section 6, and their respective successors
and assigns and no other person shall acquire or

<PAGE>

                                                                              25

have any right under or by virtue of this Agreement. The term "successors and
assigns" as used in this Agreement shall not include a purchaser, as such
purchaser, of Shares from any of the several Underwriters.

               (c)  Any action required or permitted to be taken by the
Representatives under this Agreement may be taken by them jointly or by
PaineWebber Incorporated acting alone.

               (d)  THIS AGREEMENT SHALL BE GOVERNED BY AND CONSTRUED IN
ACCORDANCE WITH THE LAWS OF THE STATE OF NEW YORK WITHOUT REGARD TO THE CONFLICT
OF LAWS PRINCIPLES OF SUCH STATE.

               (e)  This Agreement may be signed in two or more counterparts
with the same effect as if the signatures thereto and hereto were upon the same
instrument.

               (f)  In case any provision in this Agreement shall be invalid,
illegal or unenforceable, the validity, legality and enforceability of the
remaining provisions shall not in any way be affected or impaired thereby.

               (g)  The Company and the Underwriters each hereby irrevocably
waive any right they may have to a trial by jury in respect of any claim based
upon or arising out of this Agreement or the transactions contemplated hereby.

               (h)  This Agreement may not be amended or otherwise modified or
any provision hereof waived except by an instrument in writing signed by the
Representatives and the Company.

               Please confirm that the foregoing correctly sets forth the
agreement among the Company and the several Underwriters.

                              Very truly yours,

                              AGOURON PHARMACEUTICALS, INC.


                              By:
                                   -------------------------
                                   Title:

<PAGE>

                                                                              26

Confirmed as of the date first
above mentioned:

PAINEWEBBER INCORPORATED
ALEX. BROWN & SONS INCORPORATED
Acting on behalf of themselves
and as the Representatives
of the other several Underwriters
named in Schedule I hereof.

BY:  PAINEWEBBER INCORPORATED

By:
     -------------------------
Title:

BY:  ALEX. BROWN & SONS INCORPORATED

By:
     -------------------------
Title:

<PAGE>

                                                                              27

                                   SCHEDULE I

                                  UNDERWRITERS

                                          Number of
                                         Firm Shares
Name of Underwriters                   to be Purchased
- --------------------                   ---------------
PaineWebber Incorporated
Alex. Brown & Sons Incorporated

                                       ---------------
Total                                       2,500,000
                                       ---------------
                                       ---------------

<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-3 of our report dated July 25, 1995, except 
as to Notes 1, 4 and 9, which are as of August 24, 1995, relating to the 
financial statements of Agouron 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."

PRICE WATERHOUSE LLP


San Diego, California
June 19, 1996


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