AGOURON PHARMACEUTICALS INC
S-3, 1997-06-23
PHARMACEUTICAL PREPARATIONS
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      As filed with the Securities and Exchange Commission on June 23, 1997
                                            Registration No. 333-

================================================================================

                       SECURITIES AND EXCHANGE COMMISSION
                             Washington, D.C. 20549
                             -----------------------

                                    FORM S-3
                             REGISTRATION STATEMENT
                                      UNDER
                           THE SECURITIES ACT OF 1933

                          Agouron Pharmaceuticals, Inc.
             (Exact name of registrant as specified in its charter)



                California                              33-0061928
       (State or other jurisdiction                   (I.R.S. Employer
    of incorporation or organization)                Identification No.)
                           -----------------------

            10350 North Torrey Pines Road, La Jolla, California 92037
                                 (619) 622-8000
   (Address, including zip code, and telephone number, including area code, of
                   registrant's principal executive offices)






                                  Peter Johnson
                      President and Chief Executive Officer
                          AGOURON PHARMACEUTICALS, INC.
            10350 North Torrey Pines Road, La Jolla, California 92037
                                 (619) 622-8000
 (Name, address, including zip code, and telephone number, including area code,
                              of agent for service)

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

     Approximate date of commencement of proposed sale to the public:  From time
to time after the effective date of this Registration Statement as determined by
the Selling Stockholders.
     If the only  securities  being  registered  on this Form are being  offered
pursuant to dividend or interest  reinvestment plans, please check the following
box. / /
     If any of the securities being registered on this Form are to be offered on
a delayed or continuous  basis  pursuant to Rule 415 under the Securities Act of
1933, other than securities offered only in connection with dividend or interest
reinvestment plans, check the following box. /X/
     If this Form is filed to  register  additional  securities  for an offering
pursuant to Rule 462(b) under the Securities Act, please check the following box
and list  the  Securities  Act  registration  statement  number  of the  earlier
effective registration statement for the same offering. / /
     If this Form is a  post-effective  amendment  filed pursuant to Rule 462(c)
under the  Securities  Act,  check the following box and list the Securities Act
registration  statement number of the earlier effective  registration  statement
for the same offering. / /
     If delivery of the  Prospectus is expected to be made pursuant to Rule 434,
please check the following box. / /
                                   CALCULATION OF REGISTRATION FEE
<TABLE>
<CAPTION>
=================================================================================================================================
                                                               Proposed maximum
                                                                 offering price
 Title of each class of securities to be       Amount to be       per share(1)        Proposed maximum          Amount of
               registered                       registered                           aggregate offering      registration fee
                                                                                          price(1)
- --------------------------------------------------------------------------------------------------------------------------------
<S>                                            <C>             <C>                   <C>                     <C>  
Common Stock, no par value..........             197,056            $85.375              $16,823,656             $5,098.08
================================================================================================================================
<FN>
(1)Calculated in accordance with Rule 457(c) under the Securities Act of 1933.
</FN>
</TABLE>

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

     The Registrant  hereby amends this  Registration  Statement on such date or
dates as may be necessary to delay its effective date until the Registrant shall
file a further  amendment  which  specifically  states  that  this  Registration
Statement shall  thereafter  become effective in accordance with Section 8(a) of
the  Securities  Act of 1933 or until the  Registration  Statement  shall become
effective on such date as the  Commission  acting  pursuant to said Section 8(a)
may determine.

================================================================================


<PAGE>


                   SUBJECT TO COMPLETION, DATED JUNE 23, 1997

                                [GRAPHIC OMITTED]

                                   PROSPECTUS

                                 197,056 Shares

                                  Common Stock

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

         This  Prospectus  relates  to the public  offering,  which is not being
underwritten,  of 197,056 shares (the  "Shares") of Common Stock,  no par value,
(the  "Common  Stock")  of  Agouron  Pharmaceuticals,  Inc.  ("Agouron"  or  the
"Company").  The Shares may be offered by certain  stockholders  of the  Company
(the "Selling  Stockholders")  from time to time in  transactions  on The Nasdaq
Stock Market,  in privately  negotiated  transactions  or a combination  of such
methods  of sale,  at  fixed  prices  that  may be  changed,  at  market  prices
prevailing  at the time of sale,  at prices  related to such  prevailing  market
prices or at  negotiated  prices.  The  Selling  Stockholders  may  affect  such
transactions  by  selling  the  Shares to or  through  broker-dealers,  and such
broker-dealers may receive compensation in the form of discounts, concessions or
commissions  from the Selling  Stockholders  or the purchasers of the Shares for
whom such  broker-dealers  may act as agent or to whom they sell as principal or
both (which  compensation  to a particular  broker-dealer  might be in excess of
customary commissions). See "Selling Stockholders" and "Plan of Distribution."

         The Shares were issued to the Selling  Stockholders in connection with,
and  as  partial   consideration  for,  the  merger  (the  "Merger")  of  Alanex
Corporation,  a  Delaware  corporation  ("Alanex"),   with  Agouron  Acquisition
Corporation, a Delaware corporation and a wholly owned subsidiary of Agouron, in
which Alanex was the surviving corporation. The Company is obligated to keep the
registration statement herein effective until the earlier to occur of the resale
of all of the Shares  described  above  pursuant to this  Prospectus  or May 23,
1998.

         None of the  proceeds  from  the  sale  of the  Shares  by the  Selling
Stockholders  will be  received by the  Company.  The Company has agreed to bear
certain  expenses  (other  than fees and  expenses,  if any, of counsel or other
advisors to the Selling Stockholders) in connection with the registration of the
Shares  being  offered by the  Selling  Stockholders.  The Company has agreed to
indemnify  the  Selling  Stockholders  against  certain  liabilities,  including
certain   liabilities  under  the  Securities  Act  of  1933,  as  amended  (the
"Securities Act"). See "Plan of Distribution."

         The Common  Stock of the Company is traded on The Nasdaq  Stock  Market
under the symbol "AGPH." The last reported  sales price of the Company's  Common
Stock on The Nasdaq Stock Market on June 16, 1997, was $85.50 per share.

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

  The shares offered hereby involve a high degree of risk. See "Risk Factors."

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

          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.


                The date of this Prospectus is June _____, 1997.


<PAGE>


         No person is authorized in connection  with any offering made hereby to
give any information or make any representation not contained or incorporated by
reference in this Prospectus,  and any information not contained or incorporated
herein must not be relied upon as having been  authorized  by the Company.  This
Prospectus  does not constitute an offer to sell, or a solicitation  of an offer
to buy,  by any  person in any  jurisdiction  in which it is  unlawful  for such
person  to make  such  offer  or  solicitation.  Neither  the  delivery  of this
Prospectus  at  any  time  nor  any  sale  made  hereunder   shall,   under  any
circumstances,  imply  that the  information  herein is  correct  as of any date
subsequent to the date hereof.

         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 the section  entitled "Risk
Factors," as well as those discussed elsewhere in this Prospectus.

                              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,  Suite
1300, 7 World Trade Center,  New York, New York 10048.  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  Commission  maintains a Website that  contains  reports,  proxy and
information  statements and other  information  regarding  registrants that file
electronically  with the  Commission.  The  Commission's  Website  is located at
http://www.sec.com.  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

         The following documents previously filed with the Commission, except as
superseded or modified  herein,  are hereby  incorporated by reference into this
Prospectus:

                  1.  The Company's Annual Report on Form 10-K for the fiscal 
          year ended June 30, 1996.

                  2.  The  Company's  Quarterly  Reports  on Form  10-Q  for the
         quarters  ended  September  30,  1996,  December 31, 1996 and March 31,
         1997.

                  3.  The Company's Current Reports on Form 8-K filed May 5, 
          1997 and June 3, 1997.

                  4. 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).

                  5.  The Company's registration statement on Form S-3 
         (Registration No. 333-06493) filed with the Commission on June 21,
         1996.

         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>

                                   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's first product,  VIRACEPT(R) (nelfinavir mesylate),
is an orally  administered  inhibitor  of the enzyme HIV  protease.  The Company
received  clearance to market Viracept in the United States by the Food and Drug
Administration  ("FDA")  in  March  1997  under  the  provisions  of  the  FDA's
accelerated  approval process. The Company is conducting ongoing clinical trials
of Viracept and phase  II/III  clinical  trials of a second  drug,  THYMITAQ(TM)
(formerly  AG337),  for treatment of malignant solid tumors.  Additionally,  the
Company has  initiated  phase I clinical  testing of its  anti-cancer  compounds
AG3340 and AG2034. 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.

         Agouron has developed 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, 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 New Drug  Application  ("NDA") to FDA for
Thymitaq in calendar 1999.  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  in  phase I  clinical  trials  in the  United  States.  Under
provisions of this letter of intent,  Agouron has received  initial license fees
and is to receive  additional  development  milestone payments from Roche. Roche
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.

         In May 1997,  the Company  completed  the  acquisition,  pursuant to an
Agreement  and  Plan  of  Reorganization,  of  Alanex  Corporation,  a  Delaware
corporation ("Alanex").  Alanex, located in San Diego, California, is engaged in
the discovery of drug leads through the high-speed screening of diverse chemical
libraries  designed by  computational  methods and  generated  by  combinatorial
chemistry. Alanex utilizes proprietary software to design either broad or highly
targeted combinatorial libraries of molecules that can readily be synthesized in
large numbers.  To date,  Alanex has  identified  preclinical  drug  development
candidates in four of its programs for the treatment of pain, diabetes,  obesity
and anxiety. Alanex has entered into collaboration agreements with Astra Pharma,
Inc.,  Novo Nordisk A/S, Roche  Bioscience,  a division of Syntex (U.S.A.) Inc.,
Aurora Biosciences Corporation and ICOS Corporation.

         The Company was  incorporated  in  California  in 1984.  The  Company's
executive  offices  are  located at 10350 North  Torrey  Pines  Road,  La Jolla,
California 92037 and its telephone number is (619) 622-3000.

                                  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.

Uncertainty of Product Development and Market Acceptance; 
Technological Uncertainty

         The Company has completed the development and commercialization of only
one  product,  Viracept,  and does not  expect to have any  additional  products
commercially  available  until  fiscal  1999,  if at all.  While the Company has
received  regulatory  approval to begin human clinical testing for certain other
of its compounds,  these and other  compounds  currently  being developed by the
 
                                      3
<PAGE>

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  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. 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  additional
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.  Further,  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
Viracept,  an HIV protease  inhibitor,  currently  the  Company's  only product.
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.

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 and phase I, II or III  clinical  testing of its
compounds  AG3340,  AG2034,  Viracept  and  Thymitaq in Europe,  Asia and/or 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  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 could 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,  Thymitaq,  AG3340 and AG2034,
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,  human clinical
trials, or the commercial use 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 obtain  regulatory  approval or that any
such approval by FDA or any other regulatory  authority will be made in a timely
manner, or at all.
                                       4
<PAGE>

History of Operating Losses

         The Company has had net operating  losses since its  inception  and, at
March  31,  1997,  had an  accumulated  deficit  of  $115,047,000.  The  Company
anticipates  that net operating  losses will continue on a quarterly  basis into
fiscal 1998 and until such time as product sales generate  sufficient revenue to
offset expenses and generate sufficient cash flow to fund continuing operations.
In March 1997,  the Company  received FDA approval of, and began the  commercial
sale of, Viracept,  its first proprietary product to reach the market. While the
Company   anticipates   that  commercial   sales  of  Viracept  will  contribute
significantly  toward profitable operating results in the near future, there can
be no assurance that  commercial  sales of Viracept alone will be able to either
generate or maintain  profitable  operating  results on a consistent  basis.  In
addition, ongoing operating results will be impacted by the timing and amount of
the Company's  research,  development and clinical trial programs,  the level of
its selling and marketing efforts,  the efficiency and cost of its manufacturing
activities,  the nature of its business development activities and on the timing
and receipt of fees from existing and future collaborative relationships.  There
can be no assurance that the Company will ever achieve significant product sales
or profitable operations.

Additional Financing Requirements and Access to Capital

         The  Company  has  expended  more than  $260,000,000  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,  maintain and
expand its  manufacturing  and sales and  marketing  capabilities  and otherwise
commercialize any of its approved products.  Additional funds may be required to
support  the  foregoing  activities  and for working  capital and other  general
corporate needs.

         The Company  believes  that its  current  capital  resources,  existing
contractual commitments and the anticipated contribution from ongoing commercial
sales of  Viracept  will be  sufficient  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.   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 could have a
material adverse effect on the Company.

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.

         Additionally,  under the  provisions of a binding letter of intent with
Roche and agreements  entered into thereunder,  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 research program focused on cell
cycle control.  Roche is obligated to make certain payments to the Company under
the provisions of the agreements. In the event 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.

                                       5
<PAGE>

Manufacturing Capability

         The Company does not have the facilities to manufacture  its product or
product  candidates in commercial  quantities  under current good  manufacturing
practices  ("GMP")  prescribed  by  FDA.  The  Company  currently  fulfills  its
commercial    manufacturing    requirements   through   contract   manufacturing
relationships.  To be successful,  the Company's product and any future products
must  be  manufactured  in  sufficient   commercial  quantities  under  GMP,  at
acceptable costs and in a timely manner.  As a result,  the Company is currently
dependent on a number of contract  manufacturers for the commercial  manufacture
of Viracept,  its only  commercial  product.  No assurance can be given that the
Company will be able to continue to arrange for contract  manufacturing  or that
adequate  supplies of raw materials will be available.  In the event the Company
is unable to continue to obtain contract  manufacturing on acceptable terms, its
ability to commercialize or timely deliver sufficient quantities of its products
at acceptable cost may be adversely affected.

Unproved Sales and Marketing Capabilities

         While the Company has recently  developed a sales and  marketing  force
for the sales and  marketing of Viracept in the United  States,  it has no prior
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 future 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 maintain  or expand its 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 obtaining
patents and maintaining the  confidentiality of its 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  having  pharmaceutical  utilities.  The  Company is also  expected to
provide technical  services relating to the discovery,  research and development
of synthetic  chemical  compounds.  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.  Moreover,  there can be no assurance that any patents issued to the
Company,  or for  which  the  Company  has a  license,  will not be  challenged,
invalidated or circumvented  or that the rights granted  thereunder will provide
competitive  advantages  to the  Company.  Litigation,  which  could  result  in
substantial  cost to the  Company,  may be  necessary  to enforce the  Company's
patent and  license  rights or to  determine  the scope and  validity of others'
proprietary  rights.  If  competitors  of the  Company  prepare  and file patent
applications  in the United  States that claim  technology  also  claimed by the
Company,  the Company may have to  participate  in  interference  proceedings to
determine who is entitled to a patent, which could result in substantial cost to
the  Company,  even if the  outcome is  favorable  to 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.

         Much of the  know-how  of  importance  to the  Company  is based on the
unpatentable  skills,  knowledge and  experience of its scientific and technical
personnel.  To help  protect its  unpatented  rights,  the Company  requires all
employees,  relevant  consultants and advisors,  and collaborators to enter into
confidentiality  agreements  with it. 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's   competitors  may
independently develop substantially  equivalent technology or otherwise discover
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
have not  infringed or will not infringe  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.

Alanex Technology and Integration of Operations

         Alanex's approach to the discovery of drug leads through the high-speed
screening of diverse chemical  libraries  designed by computational  methods and
generated by combinatorial  chemistry is new and unproven.  Alanex's  integrated
approach to drug  discovery has never  resulted in the discovery of any compound
that  has been  commercialized.  There  can be no  assurance  that  its  product
development efforts will result in the successful  development of lead compounds
in the future,  that such compounds can be commercialized,  or that they will be
safe and efficacious.

                                       6
<PAGE>

         Alanex's strategy for the development and commercialization of its drug
technology   involves  the  formation  of   collaborations,   principally   with
pharmaceutical and biotechnology  companies. To date, revenue received by Alanex
has been principally from its collaborations and technology alliances. There can
be  no  assurance  that  the  Company  will  be  able  to  negotiate  additional
collaboration  agreements in the future on acceptable  terms, if at all, or that
such current or future  collaborations  will be  successful.  To the extent that
Alanex is unable to establish such  agreements,  the Company will be required to
expend  its  capital to fund the  research  and  development  of  Alanex's  drug
discovery process.

         If the  Company is to realize the  anticipated  benefits of the Merger,
the  operations  of Alanex  and the  Company  must be  integrated  and  combined
efficiently. The process of integrating management and administrative resources,
facilities,  management  information  systems and other  aspects of  operations,
while  managing a larger  entity,  will present a  significant  challenge to the
management  of  the  combined  Company.  There  can  be no  assurance  that  the
integration  process will be successful or that the anticipated  benefits of the
business  combination  will be fully  realized.  The  dedication  of  management
resources to such integration may detract attention from the day-to-day business
of the combined Company. The difficulties of integration may be increased by the
problems of combining different  corporate  cultures.  There can be no assurance
that  there  will  not  be  unforeseen   sustained  costs  associated  with  the
integration  process or that there will not be other material adverse effects of
these integration efforts.

Technological Change and Intense Competition

         The pharmaceutical and biotechnology  industries are subject to intense
competition  and  rapid   technological   change.   The  Company  believes  that
industry-wide interest in the application of protein structure-based drug design
and related  technology  will  continue  and may  accelerate  as the  technology
becomes more widely understood.  Competitors of the Company in the United States
and abroad are numerous and include, among others, pharmaceutical, biotechnology
and chemical  companies,  universities  and other  research  organizations.  For
example, HIV protease inhibitors developed by Abbott Laboratories, Inc., Merck &
Co., Inc. and Roche are currently being marketed. There can be no assurance that
these and other  competitors  will not have  products  or succeed in  developing
technologies  and products that are more  effective  than any which have been or
are  being  developed  by the  Company  or  which  would  render  the  Company's
technology and products obsolete and noncompetitive.

         Many of the Company's  competitors have substantially greater financial
and technical resources and production and marketing capabilities and experience
than  the  Company.  In  addition,   many  of  the  Company's  competitors  have
significantly  greater  experience  than the Company in  conducting  preclinical
testing  and  human  clinical  trials  of  new  pharmaceutical  products  and in
obtaining FDA and other regulatory approvals of products.  Accordingly,  certain
of the Company's  competitors may succeed in obtaining  regulatory  approval for
products more rapidly or effectively  than the Company.  Further,  in conducting
commercial  sales of its  products,  the  Company  will also be  competing  with
respect to manufacturing efficiency and sales and marketing capabilities,  areas
in which it currently has little experience.

Government Regulation

         Preclinical  studies,  clinical trials and the production and marketing
of the Company's  products and its ongoing  research and development  activities
and  commercial  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.

         Regulatory  approval of a drug 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.

                                       7
<PAGE>

Uncertainty of Third-Party Reimbursement and Product Pricing

         The  Company's  ability to  commercialize  products  successfully  will
depend  in  part on the  availability  of  reimbursement  of the  costs  of such
products  and  related   treatments   at  acceptable   levels  from   government
authorities,  private health  insurers and other  organizations,  such as health
maintenance organizations ("HMOs"). There can be no assurance that reimbursement
in the United  States or foreign  countries  will be available for the Company's
products  or,  if  available,  will  not be  decreased  in the  future,  or that
reimbursement  amounts  will not  reduce the  demand  for,  or the price of, the
Company's products, thereby adversely affecting the Company's business.

         Third-party payors are increasingly  challenging the prices charged for
medical products and services. Also, the trend toward managed health care in the
United States and the concurrent  growth of  organizations,  such as HMOs, which
can control or significantly  influence the purchase of health care services and
products,  as well as  legislative  proposals  to reform  health  care or reduce
government  insurance  programs,  may result in lower prices for  pharmaceutical
products.   The  cost  containment  measures  that  health  care  providers  are
instituting and the effect of any health care reform could materially  adversely
affect the Company's ability to sell its products if successfully  developed and
approved. Moreover, the Company is unable to predict what additional legislation
or  regulation,  if any,  relating  to the health care  industry or  third-party
coverage  and  reimbursement  may be enacted in the future or what  effect  such
legislation or regulation would have on the Company's business.

Product Liability; Limited Insurance Coverage

         The testing, marketing and sale of human health care products entail an
inherent risk of allegations of product  liability and there can be no assurance
that product  liability  claims will not be asserted  against the  Company,  its
collaborators  or its licensees.  The Company  currently has limited  amounts of
product liability  insurance for clinical trials and commercial sales. There can
be no  assurance  that the Company  will be able to 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.

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,  introductions of commercial products,  availability
and sales of 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.

                                       8
<PAGE>

                              SELLING STOCKHOLDERS

         The Selling Stockholders  represented in their purchase agreements that
they were acquiring the Shares for  investment and with no present  intention of
distributing   the  Shares.   In  recognition  of  the  fact  that  the  Selling
Stockholders,  even though  purchasing  the Shares without a view to distribute,
may wish to be legally permitted to sell the Shares when each deems appropriate,
the Company has filed with the Commission a Registration  Statement on Form S-3,
which this  Prospectus  forms a part,  with respect to, among other things,  the
resale  of  the  Shares  from  time  to  time  at   prevailing   prices  in  the
over-the-counter market or in  privately-negotiated  transactions and has agreed
to  prepare  and  file  such  amendments  and  supplements  to the  Registration
Statement as may be necessary to keep the Registration Statement effective until
the earlier to occur of the resale of all of the Shares described above pursuant
to this Prospectus or May 23, 1998.

         The  following  table sets forth the name of the Selling  Stockholders,
the number of Shares  beneficially  owned by each Selling  Stockholder as of May
23,  1997,  and the  number of  Shares  which may be  offered  pursuant  to this
Prospectus.  This information is based upon information  provided to the Company
by the Selling  Stockholders.  Because the Selling  Stockholders  may offer all,
some or none of their shares of Common Stock,  no definitive  estimate as to the
number of shares  thereof  that will be held by the Selling  Stockholders  after
such offering can be provided.

<TABLE>
<CAPTION>
        Name of Selling            Shares Beneficially Owned Prior       Number of Shares Being        Shares Beneficially Owned 
        Stockholders(1)                     to Offering                          Offered                   After Offering(1)(3)
- ----------------------------       -------------------------------       ----------------------        -----------------------------
                                      Number           Percent(2)                Number                   Number          Percent(2)
                                      ------           ---------                 ------                   ------          ----------
<S>                                <C>                 <C>               <C>                     <C>                 <C> 
Debar ERA, Inc.                       309,770            2.1%                     77,443                  232,327             1.6%
Jon & Caroline Jessen Family          145,774            1.0%                     36,444                  109,330               *
1990 Trust
Marvin Brown(4)                        98,888              *                      24,722                   74,166               *
Alexander Polinsky                     98,888              *                      24,722                   74,166               *
Howard Gwynn                            5,933              *                       2,908                    3,025               *
Arnold Hagler                          20,719              *                      10,153                   10,566               *
Christopher Wright                     11,770              *                       5,768                    6,002               *
Laura Delmas                            2,825              *                       1,385                    1,440               *
Martin Strnat                             565              *                         277                      288               *
Heling Liu                                436              *                         214                      222               *
Rathna Basava                             391              *                         192                      199               *
Galina Krokhina                         2,260              *                       1,108                    1,152               *
Atsuo Kuki                              1,412              *                         692                      720               *
Dorothy Haskell                           485              *                         238                      247               *
Amy Wells                                 125              *                          62                       63               *
Martha Obermeier                          941              *                         462                      479               *
Talia Hagler                              941              *                         462                      479               *
R. Tamar Hagler                           941              *                         462                      479               *
Eitan Hagler                              941              *                         462                      479               *
Yoav Hagler                               941              *                         462                      479               *
Susan Hagler                              941              *                         462                      479               *
Lauri Sampson                             815              *                         400                      415               *
Howard Sampson                            376              *                         185                      191               *
Robert Feinstein                        9,417              *                       4,615                    4,802               *
Michelle Youngers                       1,506              *                         738                      768               *
Dale Dhanoa                             4,117              *                       2,018                    2,099               *
                                  ===========       ===========              ===========              ===========       =========
       Total                          722,118            5.0%                    197,056                  525,062             3.6%

     *--Less than 1%
- ---------------------------
<FN>
(1)Unless otherwise  indicated,  the persons named in the table have sole voting
   and investment power with respect to all shares  beneficially  owned by them,
   subject to community property laws where applicable.
(2)Applicable  percentage  of  ownership  is based on  approximately  14,500,000
   shares of Common Stock  outstanding on May 29, 1997,  adjusted as required by
   rules promulgated by the Commission.
(3)Assumes the sale of all shares offered hereby.
(4)Dr. Brown is the president of Alanex Corporation and a vice president of the
   Company.
</FN>
</TABLE>
                                       9
<PAGE>

                              PLAN OF DISTRIBUTION

         The Company has been advised that the Selling Stockholders or pledgees,
donees,   transferees  of  or  other  successors  in  interest  to  the  Selling
Stockholders  may sell  Shares from time to time in  transactions  on The Nasdaq
Stock Market,  in privately  negotiated  transactions  or a combination  of such
methods  of sale,  at fixed  prices  which  may be  changed,  at  market  prices
prevailing  at the time of sale,  at prices  related to such  prevailing  market
prices or at  negotiated  prices.  The  Selling  Stockholders  may  effect  such
transactions  by  selling  the  Shares to or  through  broker-dealers,  and such
broker-dealers may receive compensation in the form of discounts, concessions or
commissions  from the Selling  Stockholders  or the purchasers of the Shares for
whom such broker-dealers may act as agent or to whom they sell as principal,  or
both (which  compensation  to a particular  broker-dealer  might be in excess of
customary commissions.)

         At any  time a  particular  offer of  Shares  is  made,  to the  extent
required, a supplemental Prospectus will be distributed which will set forth the
number of shares  offered and the terms of the  offering  including  the name or
names of any  underwriters,  dealers or agents,  the purchase  price paid by any
underwriter  for  the  Shares  purchased  from  the  Selling  Stockholders,  any
discounts,  commission,  and  other  items  constituting  compensation  from the
Selling  Stockholders and any discounts,  concessions or commissions  allowed or
reallowed or paid to dealers.

         The Selling  Stockholders and any  broker-dealers who act in connection
with the sale of Shares  hereunder  may be deemed to be  "underwriters"  as that
term is defined in the Securities Act, and any commissions  received by them and
profit  on any  resale  of  the  Shares  as  principal  might  be  deemed  to be
underwriting discounts and commissions under the Securities Act.

         Any or all of the  sales or other  transactions  involving  the  Shares
described above, whether effected by the Selling Stockholders, any broker-dealer
or others, may be made pursuant to this Prospectus. In addition, any Shares that
qualify  for sale  pursuant to Rule 144 under the Act may be sold under Rule 144
rather than pursuant to this Prospectus.

         In order to comply  with the  securities  laws of  certain  states,  if
applicable, the Shares may be sold in such jurisdictions only through registered
or licensed  brokers or dealers.  In addition,  in certain states the Shares may
not be sold  unless  they  have  been  registered  or  qualified  for sale or an
exemption from  registration or  qualification  requirements is available and is
complied with.

         Under  applicable  rules and  regulations  under the Exchange  Act, any
person engaged in the distribution of the Shares may not  simultaneously  engage
in market making activities with respect to Agouron Common Stock for a period of
two business days prior to the  commencement of such  distribution.  In addition
and without limiting the foregoing,  the Selling Stockholders will be subject to
applicable  provisions  of the  Exchange  Act  and  the  rules  and  regulations
thereunder,  which  provisions  may limit the timing of  purchases  and sales of
shares of the Shares by the Selling Stockholders.

         All  costs   associated  with  registering  the  Shares  being  offered
hereunder  with  the  Securities  and  Exchange  Commission  will be paid by the
Company.

         The Company and the Selling Stockholders may agree to indemnify certain
persons  including  broker-dealers  or others,  against  certain  liabilities in
connection  with any  offering of the Shares,  including  liabilities  under the
securities Act.

                                  LEGAL MATTERS

         The validity of the issuance of the Shares will be passed upon for the
Company by Gary E. Friedman, Esq., Vice President, General Counsel of the 
Company.  Additionally, Mr. Friedman is a Director and Secretary of the Company.
Mr. Friedman beneficially holds Common Stock of the Company and holds stock 
options under the Company's stock option plans.  He may receive additional
options under such plans in the future.

                                     EXPERTS

         The  financial  statements as of June 30, 1996 and 1995 and for each of
the  three  years  in the  period  ended  June  30,  1996  incorporated  in this
Prospectus  by  reference  to the Annual  Report on Form 10-K for the year ended
June 30, 1996 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.

                                       10
<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
          The Company.................................    3
          Risk Factors................................    3
          Selling Stockholders........................    9
          Plan of Distribution........................   10
          Legal Matters...............................   10
          Experts.....................................   10


                                 197,056 Shares


                                [GRAPHIC OMITTED]


                                  Common Stock


                                   PROSPECTUS


                                June _____, 1997

================================================================================


<PAGE>



                                     PART II

                     INFORMATION NOT REQUIRED IN PROSPECTUS

Item 14.  Other Expenses of Issuance and Distribution

         The following  table sets forth the expenses,  other than  underwriting
discounts and commissions, payable by the Company in connection with the sale of
the Common Stock being registered.  All amounts shown are estimates,  except the
registration fee and the NASD filing fee.
<TABLE>
<CAPTION>
<S>                                                                       <C>
Securities and Exchange Commission Registration Fee...................... $  5,098.08 
Accounting Fees and Expenses.............................................    2,000.00
Miscellaneous............................................................    5,000.00
                                                                          -----------
                                                                          $ 12,098.08
                                                                          ===========
</TABLE>

Item 15.  Indemnification of Directors and Officers

         Section  317  of  the  California  General  Corporation  Law  generally
provides  indemnification  to officers  and  directors  of the  Company  against
expenses,  judgments,  fines  and  amounts  paid  in  settlement  under  certain
conditions and subject to certain limitations.

         Article VII of the articles of  incorporation  of the Company  provides
that  liability of the  directors of the Company for monetary  damages  shall be
eliminated to the fullest extent  permissible  under  California  law.  Further,
Article VIII of the articles of incorporation  authorizes the Company to provide
indemnification  of agents (as defined in Section 317) for breach of duty to the
Company and its shareholders through bylaw provisions or through agreements with
such agents, or both, in excess of the  indemnification  otherwise  permitted by
Section 317, subject to the limits on such excess  indemnification  set forth in
Section 317.

         Section  3.15 of the bylaws of the  Company  authorizes  the Company to
indemnify any person who was or is a party, or is threatened to be made a party,
to any  proceeding  (other  than  actions  by or in the right of the  Company to
procure a judgment  in its  favor) by reason of the fact that such  person is or
was an agent of the Company, against expenses, judgments, fines, settlements and
other  amounts  actually  and  reasonably   incurred  in  connection  with  such
proceeding  if such  person  acted in good  faith  and in a manner  such  person
reasonably  believed to be in the best  interests of the  Company.  Section 3.15
also authorizes the Company to indemnify any person who was or is a party, or is
threatened to be made a party, to any threatened, pending or completed action by
or in the right of the  Company to procure a judgment  in its favor by reason of
the fact that such  person is or was an agent of the  Company  against  expenses
actually and reasonably  incurred by such person in connection  with the defense
or settlement of such action if such person acted in good faith.

         Any  indemnification  under  Section  3.15 is to be made by the Company
only if authorized in the specific case upon determination that  indemnification
of the  agent is  proper  in the  circumstances  because  the  agent has met the
applicable  standard of conduct  required by Paragraphs  3.15.2 or 3.15.3 of the
bylaws.

         Pursuant to authorization  provided under the articles of incorporation
and the bylaws,  the Company has entered into  indemnification  agreements  with
each of its  present  directors.  The  Company  has also  entered  into  similar
agreements  with  certain  of the  Company's  officers  who are  not  directors.
Generally,  the  indemnification  agreements  attempt  to  provide  the  maximum
protection  permitted by California  law as it may be amended from time to time.
Moreover,   the  indemnification   agreements  provide  for  certain  additional
indemnification.  Under such additional indemnification provisions,  however, an
individual  will not  receive  indemnification  for  judgments,  settlements  or
expenses if he or she is found  liable to the Company  (except to the extent the
court  determines he or she is fairly and  reasonably  entitled to indemnity for
expenses) for  settlements  not approved by the Company or for  settlements  and
expenses if the  settlement  is not approved by the court.  The  indemnification
agreements  provide  for the  Company to advance to the  individual  any and all
reasonable   expenses   (including   legal  fees  and   expenses)   incurred  in
investigating  or defending  any such action,  suit or  proceeding.  In order to
receive an advance of expenses, the individual must submit to the Company copies
of invoices presented to him or her for such expenses. Also, the individual must
repay  such  advances  upon a  final  judicial  decision  that  he or she is not
entitled to indemnification.

         Section  3.15 of the  bylaws  also  provides  that,  in the  event of a
determination by the Board of Directors of the Company to purchase insurance for
certain of its agents,  the Company  shall  purchase and  maintain  insurance on
behalf of any such agent against  liability  asserted against or incurred by the
agent in such capacity or arising out of the agent's status,  whether or not the
Company would have the power to indemnify the agent against such liability under
the provisions of Section 3.15.

         The Company has in effect  directors and officers  liability  insurance
policies which insure directors and officers of the Company. The policies expire
on October 13, 1997.  Although  the Company  intends to renew the policies on or
before their  expiration  date, there can be no assurance that the policies will
be renewed on terms acceptable to the Company. Under the policies, the directors
and  officers of the Company are insured  against  loss arising from claims made
against  them  due to  wrongful  acts  while  

                                      II-1
<PAGE>

acting  in  their  individual  and collective capacities as directors and 
officers,  subject to certain exclusions. In  addition,  the  policies  insure 
the  Company  against  losses for which its directors and officers are entitled
to  indemnification,  subject to a retention of $250,000 payable by the Company.
The policies are "claims made" policies and provide  coverage  only for losses  
arising out of claims first made against the Company and reported to the insurer
during the policy period.

Item 16.  Exhibits

          EXHIBIT
          NUMBER

            5.1                  Opinion of Gary E. Friedman, Esq.

            23.1                 Consent of Independent Accountants.

            23.2                 Consent of Gary E. Friedman, Esq. 
                                 (contained in Exhibit 5.1).

            24.1                 Power of Attorney (contained on signature page
                                 of the Registration Statement).


Item 17.  Undertakings

         Insofar as indemnification for liabilities arising under the Securities
Act  may  be  permitted  to  directors,  officers  or  persons  controlling  the
registrant,  pursuant  to the  foregoing  provisions,  the  registrant  has been
advised  that in the opinion of the  Securities  and  Exchange  Commission  such
indemnification  is against public policy as expressed in the Securities Act and
is,  therefore,  unenforceable.  In the event  that a claim for  indemnification
against such  liabilities  (other than the payment by the registrant of expenses
incurred or paid by a director,  officer or controlling person of the registrant
in the successful defense of any action, suit or proceeding) is asserted by such
director,  officer or controlling person in connection with the securities being
registered, the registrant will, unless in the opinion of counsel the matter has
been  settled  by  controlling  precedent,  submit  to a  court  of  appropriate
jurisdiction the question whether such  indemnification  by it is against public
policy as  expressed  in the  Securities  Act and will be  governed by the final
adjudication of such issue.

         The undersigned registrant hereby undertakes that:

         (1) For purposes of determining any liability under the Securities Act,
the  information  omitted  from  the  form of  prospectus  filed as part of this
registration  statement  in reliance  upon Rule 430A and  contained in a form of
prospectus  filed by the registrant  pursuant to Rule 424(b)(1) or (4) or 497(h)
under  the  Securities  Act  shall  be  deemed  to be part of this  registration
statement as of the time it was declared effective.

         (2) For the purpose of determining  any liability  under the Securities
Act, each  post-effective  amendment that contains a form of prospectus shall be
deemed to be a new  registration  statement  relating to the securities  offered
therein,  and the offering of such securities at that time shall be deemed to be
the initial bona fide offering thereof.

         The  undersigned  registrant  hereby  undertakes  that, for purposes of
determining  any  liability  under  the  Securities  Act,  each  filing  of  the
registrant's  Annual  Report  pursuant to Section  13(a) or Section 15(d) of the
Exchange Act (and, where  applicable,  each filing of an employee benefit plan's
Annual  Report   pursuant  to  Section  15(d)  of  the  Exchange  Act)  that  is
incorporated by reference in the registration  statement shall be deemed to be a
new registration  statement relating to the securities offered therein,  and the
offering of such  securities at that time shall be deemed to be the initial bona
fide offering thereof.

                                   SIGNATURES

         Pursuant  to the  requirements  of the  Securities  Act  of  1933,  the
registrant certifies that it has reasonable grounds to believe that it meets all
of the requirements for filing on Form S-3 and has duly caused this amendment to
registration statement to be signed on its behalf by the undersigned,  thereunto
duly authorized,  in the City of San Diego, State of California, on the 23rd day
of June, 1997.

                          AGOURON PHARMACEUTICALS, INC.

                          By:/s/ Gary E. Friedman, Esq.
                             --------------------------
                             Gary E. Friedman, Esq.
                             Vice President, General Counsel, and Secretary

                                      II-2
<PAGE>

                                POWER OF ATTORNEY

     KNOW ALL MEN BY THESE PRESENTS,  that each person whose  signature  appears
below  constitutes  and  appoints  Peter  Johnson,  Steven S. Cowell and Gary E.
Friedman,  or any of  them,  his or her true and  lawful  attorneys-in-fact  and
agents, with full power of substitution and  resubstitution,  for him or her and
in his or her name,  place and stead, in any and all capacities,  to sign any or
all  amendments  to  this  registration  statement,   including   post-effective
amendments, and to file the same, with all exhibits thereto, and other documents
in connection  therewith with the Securities and Exchange  Commission,  granting
unto said  attorneys-in-fact  and  agents  full  power and  authority  to do and
perform each and every act and thing  requisite  and necessary to be done in and
about the premises,  as fully and to all intents and purposes as he or she might
or  could  do  in  person,   hereby  ratifying  and  confirming  all  that  said
attorneys-in-fact  and agents, or their substitute or substitutes,  may lawfully
do or cause to be done by virtue hereof.

     Pursuant  to  the   requirements  of  the  Securities  Act  of  1933,  this
Registration  Statement  has been signed below by the  following  persons in the
capacities and on the dates indicated.
<TABLE>
<CAPTION>

            Signature                                       Title                                  Date

<S>                                                  <C>                                       <C> 
     /s/ Peter Johnson                               President, Chief Executive                June 23, 1997
- ------------------------------------------           Officer and Director
Peter Johnson                                        

     /s/ Steven S. Cowell                            Vice President, Finance and               June 23, 1997
- ------------------------------------------           Chief Financial Officer
Steven S. Cowell                                     

     /s/ Gary  E. Friedman                           Vice President, General Counsel,          June 23, 1997
- ------------------------------------------           Secretary and Director
Gary E. Friedman                                     

     /s/ John N. Abelson                             Director                                  June 23, 1997
- ------------------------------------------
John N. Abelson

     /s/ Patricia M. Cloherty                        Director                                  June 23, 1997
- ------------------------------------------
Patricia M. Cloherty

     /s/ A.E. Cohen                                  Director                                  June 23, 1997
- ------------------------------------------
A.E. Cohen

     /s/ Michael E. Herman                           Director                                  June 23, 1997
- ------------------------------------------
Michael E. Herman

     /s/ Irving S. Johnson                           Director                                  June 23, 1997
- ------------------------------------------
Irving S. Johnson

     /s/ Antonie T. Knoppers                         Director                                  June 23, 1997
- ------------------------------------------
Antonie T. Knoppers

     /s/ Melvin I. Simon                             Director                                  June 23, 1997
- ------------------------------------------
Melvin I. Simon
</TABLE>
                                      II-3
<PAGE>


                                  EXHIBIT INDEX

         5.1                  Opinion of Gary E. Friedman, Esq.

         23.1                 Consent of Independent Accountants.

         23.2                 Consent of Gary E. Friedman, Esq. 
                              (contained in Exhibit 5.1).

         24.1                 Power of Attorney (contained on signature page of
                              the Registration Statement).


                                      II-4



                                                                     EXHIBIT 5.1
                              (AGOURON LETTERHEAD)


June 23, 1997





AGOURON PHARMACEUTICALS, INC.
10350 North Torrey Pines Road
La Jolla, California  92037

Gentlemen:

In connection with your registration on Form S-3 (the "Registration  Statement")
under the Securities Act of 1933, as amended,  of 197,056 shares of Common Stock
of Agouron  Pharmaceuticals,  Inc.  (the  "Company"),  I advise you that,  in my
opinion, when such shares have been issued and sold in the manner referred to in
the Registration Statement, such shares will be duly authorized, validly issued,
fully paid and non-assessable shares of the Company's Common Stock.

I hereby consent to the filing of this opinion as an exhibit to the Registration
Statement.

Sincerely,


/s/ Gary E. Friedman

Gary E. Friedman, Esq.
Vice President and General Counsel

GEF:hhf
                                     


                                                                    EXHIBIT 23.1



                       CONSENT OF INDEPENDENT ACCOUNTANTS



We hereby consent to the incorporation by reference in the Prospectus 
constituting part of this Registration Statement on Form S-3 of our report dated
August 7, 1996 appearing on page F-1 of Agouron Pharmaceuticals, Inc.'s Annual 
Report on Form 10-K for the year ended June 30, 1996.  We also consent to the 
reference to us under the heading "Experts" in such Prospectus.




PRICE WATERHOUSE LLP

San Diego, California
June 23, 1997


                                   


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