AGOURON PHARMACEUTICALS INC
424B1, 1996-07-26
PHARMACEUTICAL PREPARATIONS
Previous: CMS ENERGY CORP, 424B5, 1996-07-26
Next: SMITH BARNEY ARIZONA MUNICIPALS FUNDS INC, 485APOS, 1996-07-26



<PAGE>
                                                    FILED PURSUANT TO RULE
                                                    424(b)(1)
                                                    REG. STATEMENT NO. 333-06493
                                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  July 25, 1996, the closing  sale price of the Common
Stock as reported by  Nasdaq was $31.81  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.........................       $30.00              $1.65             $28.35
Total.............................     $75,000,000        $4,125,000         $70,875,000
Total Assuming Full Exercise of        $86,250,000        $4,743,750         $81,506,250
 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 July 31, 1996.
                              -------------------
 
PAINEWEBBER INCORPORATED                                      ALEX. BROWN & SONS
                                                                 INCORPORATED
 
                              -------------------
<PAGE>
                 THE DATE OF THIS PROSPECTUS IS JULY 26, 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 (the  "Exchange  Act"), and,  in  accordance
therewith,  files  reports,  proxy  statements and  other  information  with the
Securities and  Exchange  Commission  (the "Commission").  Such  reports,  proxy
statements  and  other information  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 as amended  by Form 8-K/A filed July 12, 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 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 other  anti-HIV  drugs  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...............  13,231,700 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  working  capital and
                                    other corporate purposes. See "Use of Proceeds."
Nasdaq Stock Market Symbol........  AGPH
</TABLE>
 
- ------------------------
(1) Based on the shares outstanding at June 30, 1996. Excludes (i) approximately
    3,414,400 shares  of Common  Stock  issuable upon  the exercise  of  options
    outstanding  at June  30, 1996 under  the Company's stock  option plans (ii)
    218,801 shares of Common Stock available for future grants under such  plans
    and (iii) 156,414 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    $  175,181
Working capital.......................................................................      72,116       142,641
Total assets..........................................................................     113,191       183,716
Long-term liabilities.................................................................       1,863         1,863
Stockholders' equity (2)..............................................................      76,196       146,721
</TABLE>
 
- ------------------------
 
(1)  As adjusted to give effect to the  sale of 2,500,000 shares of Common Stock
    in this offering at the  public offering price of  $30.00 per share and  net
    proceeds of approximately $70,525,000.
 
(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 of its drugs and/or to the processes
for  manufacturing   its   drugs.   Any   such   changes   in   formulation   or
 
                                       5
<PAGE>
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, 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.
 
                                       6
<PAGE>
    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. Definitive terms of this collaboration must be
negotiated by the  parties. In the  event Roche  and the Company  are unable  to
reach  agreement on definitive  terms of this  collaboration or Roche terminates
its rights under a development program or  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."
 
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.
 
                                       7
<PAGE>
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.
 
    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
 
                                       8
<PAGE>
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.
 
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.
 
                                       9
<PAGE>
    Third-party  payors  are  increasingly challenging  the  prices  charged for
medical products and services. Also, the trend toward managed health care in the
United States and the  concurrent growth of organizations,  such as HMOs,  which
can  control or significantly influence the purchase of health care services and
products, as  well as  legislative proposals  to reform  health care  or  reduce
government  insurance programs,  may result  in lower  prices for pharmaceutical
products.  The  cost  containment  measures  that  health  care  providers   are
instituting  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  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.
 
                                       10
<PAGE>
                                USE OF PROCEEDS
 
    The net proceeds to be received by Agouron from the sale of the Common Stock
offered hereby,  after  deducting  underwriting discounts  and  commissions  and
estimated offering expenses, are estimated to be $70,525,000 ($81,156,250 if the
Underwriters' over-allotment option is exercised in full) at the public offering
price of $30.00 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,
$10,000,000;  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  and
capital  equipment and facilities, including scientific equipment and computers.
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.  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.
 
                                 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     227,904
  Accumulated deficit..........................................................     (81,183)    (81,183)
                                                                                 ----------  -----------
      Total stockholders' equity...............................................      76,196     146,721
                                                                                 ----------  -----------
          Total capitalization.................................................  $   78,059   $ 148,584
                                                                                 ----------  -----------
                                                                                 ----------  -----------
</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), 172,789 shares available for purchase under the Company's Employee
    Stock  Purchase  Plan  and  45,000 shares  reserved  for  issuance  under an
    outstanding warrant (subsequently exercised in June 1996).
 
                                       11
<PAGE>
                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 ended June 30..............................................         47          32
</TABLE>
 
    On July 25, 1996, the last sale price of the Common Stock as reported by The
Nasdaq Stock  Market  was  $31.81  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.
 
                                    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  the
public  offering price  of $30.00  per share), the  pro forma  net tangible book
value of the  Company as  of March  31, 1996  would have  been $146,721,000,  or
$11.18  per share.  This represents an  immediate increase in  net tangible book
value of $4.01 per share to  existing shareholders and an immediate dilution  of
$18.82 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>
Public offering price........................................             $   30.00
  Net tangible book value before offering....................  $    7.17
  Increase attributable to new investors.....................       4.01
                                                               ---------
Pro forma net tangible book value after offering.............                 11.18
                                                                          ---------
Dilution of net tangible book value to new investors.........             $   18.82
                                                                          ---------
                                                                          ---------
</TABLE>
 
                                       12
<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.
 
                                       13
<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
 
                                       14
<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
 
                                       15
<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.
 
                                       16
<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  NDA to 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 other  anti-HIV
drugs  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  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 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,
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.
 
                                       17
<PAGE>
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.
 
  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
 
                                       18
<PAGE>
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 possible co-promotion rights and the payment of royalties to Agouron.
See "Research and Development Agreement -- Roche."
 
  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
 
                                       19
<PAGE>
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  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.
 
                                       20
<PAGE>
    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 for three years
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. 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
 
                                       21
<PAGE>
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, in a two-day combination with stavudine (d4T)  or
in a three-drug combination with zidovudine (AZT) and iamivudine (3TC), 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."
 
                                       22
<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
 
                                       23
<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.
 
                                       24
<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.
 
                                       25
<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   has  received  initial   license  fees   of
$15,000,000  and, under the  provisions of the  binding letter of  intent, is to
receive 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 possible 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.
Roche  also  has  agreed  to  grant  Agouron  the  right  in  North  America  to
commercialize a Roche anti-cancer  product to be designated  in the future.  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
 
                                       26
<PAGE>
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.
 
    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
 
                                       27
<PAGE>
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  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."
 
                                       28
<PAGE>
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
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 June 30, 1996, the Company had 374 employees, 96 of whom hold Ph.D. or
M.D.  degrees.  Three hundred  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  104,000  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 36,000  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.
 
                                       29
<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......................................     53      Vice President, Operations
 
John N. Abelson, Ph.D. (1)...........................     57      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.
 
    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.
 
                                       30
<PAGE>
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
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
 
                                       31
<PAGE>
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.
 
                                       32
<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 June 30, 1996, there were approximately 10,731,700 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  30, 1996, options  to purchase  a total of  3,414,400 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.
 
                                       33
<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...............................    925,000
Alex. Brown & Sons Incorporated........................    925,000
Hambrecht & Quist LLC..................................    100,000
Montgomery Securities..................................    100,000
Smith Barney Inc.......................................    100,000
Hanifen, Imhoff Inc....................................     50,000
Ladenburg, Thalmann & Co., Inc.........................     50,000
Pennsylvania Merchant Group, Ltd.......................     50,000
Punk, Ziegel & Knoell..................................     50,000
Rodman & Renshaw, Inc..................................     50,000
Unterberg Harris.......................................     50,000
H. C. Wainwright Co., Inc..............................     50,000
                                                         ---------
    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 $.95 per share; and that the Underwriters and such
dealers may reallow a discount not in excess of $.10 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.
 
                                       34
<PAGE>
    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  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.
 
                                       35
<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 has received an initial license fee of  $15
million  for Thymitaq and AG3340.  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..........................................................    11
Price Range of Common Stock and Dividend Policy.........................    12
Dilution................................................................    12
Selected Financial Data.................................................    13
Management's Discussion and Analysis of Financial Condition and Results
 of Operations..........................................................    14
Business................................................................    17
Management..............................................................    30
Description of Securities...............................................    33
Underwriting............................................................    34
Legal Matters...........................................................    35
Experts.................................................................    35
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
 
                             ---------------------
 
                                 JULY 26, 1996
 
- --------------------------------------------------------------------------------
- --------------------------------------------------------------------------------


© 2022 IncJournal is not affiliated with or endorsed by the U.S. Securities and Exchange Commission