AGOURON PHARMACEUTICALS INC
10-Q, 1998-10-20
PHARMACEUTICAL PREPARATIONS
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                                  UNITED STATES
                       SECURITIES AND EXCHANGE COMMISSION
                             Washington, D.C. 20549

                                    FORM 10-Q

             QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE
                         SECURITIES EXCHANGE ACT OF 1934

                For the quarterly period ended September 30, 1998


                         Commission File Number 0-15609

                          AGOURON PHARMACEUTICALS, INC.
             (Exact name of registrant as specified in its charter)

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

10350 North Torrey Pines Road, La Jolla, California                92037-1020
         (Address of principal executive offices)                  (Zip Code)

                                  (619) 622-3000
                  Registrant's telephone number, including area code)

                                      NONE
              (Former name, former address and former fiscal year,
                          if changed since last report)

Indicate by check mark whether the registrant (1) has filed all reports required
to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during
the  preceding 12 months (or for such  shorter  period that the  registrant  was
required  to file  such  reports),  and  (2) has  been  subject  to such  filing
requirements for the past 90 days:

                                  Yes X No ___

Indicate the number of shares  outstanding  of each of the  issuer's  classes of
common stock,  as of the latest  practicable  date: As of October 15, 1998,  the
registrant had 31,283,000 shares of Common Stock, no par value, outstanding.


<PAGE>


                          AGOURON PHARMACEUTICALS, INC.

                                      INDEX

                                                                        Page No.

Part I.   Financial Information

Item 1.   Financial Statements

          Consolidated Balance Sheet -                                       3
              September 30, 1998 and June 30, 1998

          Consolidated Statement of Income -                                 4
              Three Months Ended September 30, 1998 and 1997

          Consolidated Statement of Cash Flows -                             5
              Three Months Ended September 30, 1998 and 1997

          Notes to Consolidated Financial Statements                         6

Item 2.   Management's Discussion and Analysis of Financial                  9
              Condition and Results of Operations


Part II.  Other Information

Item 1.   Legal Proceedings                                                 13

Item 2.   Changes in Securities                                             13

Item 3.   Defaults Upon Senior Securities                                   13

Item 4.   Submission of Matters to a Vote of Security Holders               13

Item 5.   Other Information                                                 13

Item 6.   Exhibits and Reports on Form 8-K                                  13

          Signature                                                         14


                                    2
<PAGE>


PART I.           FINANCIAL INFORMATION

Item 1.           Financial Statements

                          AGOURON PHARMACEUTICALS, INC.
                           CONSOLIDATED BALANCE SHEET
                             (Dollars in thousands)

<TABLE>
<CAPTION>
                                                                       September 30,               June 30,
                                                                                1998                   1998
ASSETS                                                                   (unaudited)
- ------                                                                   -----------            -----------
<S>                                                                   <C>                    <C>

Current assets:
     Cash and cash equivalents                                        $       16,713         $      19,098
     Short-term investments                                                   45,227                68,025
     Accounts receivable, net                                                 51,755                51,341
     Inventories                                                             106,638               103,706
     Current deferred tax assets                                                 564                   564
     Other current assets                                                      3,868                 5,247
                                                                      --------------         -------------

     Total current assets                                                    224,765               247,981

Property and equipment,  net of accumulated
     depreciation and amortization of $27,187 and $24,321                     45,670                47,212
Deferred tax assets                                                           64,999                64,644
Purchased intangibles                                                          3,350                 3,500
                                                                      --------------         -------------

                                                                      $      338,784         $     363,337
                                                                      ==============         =============
LIABILITIES AND STOCKHOLDERS' EQUITY

Current liabilities:
     Accounts payable                                                 $       25,854         $      44,393
     Accrued liabilities                                                      36,747                35,356
     Deferred revenue and advances                                            21,191                23,563
     Current deferred tax liabilities                                          1,621                 1,139
     Loan payable and current portion of long-term debt                          819                15,802
                                                                      --------------         -------------

     Total current liabilities                                                86,232               120,253
                                                                      --------------         -------------

Long-term liabilities:
     Long-term debt, less current portion                                      6,242                 5,892
     Accrued rent                                                                938                 1,023
                                                                      --------------         -------------

     Total long-term liabilities                                               7,180                 6,915
                                                                      --------------         -------------

Stockholders' equity:
     Common stock, no par value, 75,000,000 shares authorized,
       31,246,645 and 31,053,380 shares issued and outstanding               350,947               348,482
     Accumulated other comprehensive income                                      232                   384
     Accumulated deficit                                                    (105,807)             (112,697)
                                                                      --------------         -------------

     Total stockholders' equity                                              245,372               236,169
                                                                      --------------         -------------

                                                                      $      338,784         $     363,337
                                                                      ==============         =============
</TABLE>

See accompanying notes to consolidated financial statements.

                                      3
<PAGE>


                          AGOURON PHARMACEUTICALS, INC.
                        CONSOLIDATED STATEMENT OF INCOME
                                   (Unaudited)
                    (In thousands, except per share amounts)
<TABLE>
<CAPTION>

                                                          Three Months Ended    
                                                             September 30,     
                                                       ------------------------
<S>                                                    <C>           <C> 
                                                           1998           1997
                                                       ---------      ---------
Revenues:
   Product sales                                       $ 133,870      $  79,502
   Contracts                                               6,017         10,003
   License fees and royalties                              5,050          2,352
                                                       ---------      ---------

                                                         144,937         91,857
                                                       ---------      ---------

Operating expenses:
   Cost of product sales                                  57,045         34,073
   Research and development                               37,364         26,932
   Selling, general and administrative                    17,142         12,546
   Royalties                                              25,893         13,376
                                                       ---------       --------


                                                         137,444        86,927
                                                       ---------       --------

Operating income                                           7,493          4,930
                                                       ---------       --------
Other income (expense):
   Interest and other income                               1,036          1,281
   Interest expense                                         (423)          (161)
                                                       ---------       --------

                                                             613          1,120
                                                       ---------      ---------
Income before income taxes                                 8,106          6,050

Income tax provision                                       1,216          2,420
                                                       ---------      ---------

Net income                                             $   6,890      $   3,630
                                                       =========      =========

Earnings per share:
   Basic                                               $     .22      $     .12
                                                       =========      =========
   Diluted                                             $     .21      $     .11
                                                       =========      =========

Shares used in calculation of:
   Basic                                                  31,127         29,964
   Diluted                                                33,179         33,158


</TABLE>


See accompanying notes to consolidated financial statements.


                                    4
<PAGE>


                          AGOURON PHARMACEUTICALS, INC.
                      CONSOLIDATED STATEMENT OF CASH FLOWS
                                   (Unaudited)
                             (Dollars in thousands)

<TABLE>
<CAPTION>

                                                                                        Three Months Ended  
                                                                                  --------------------------
                                                                                          September 30,                  
                                                                                  --------------------------
                                                                                      1998            1997
<S>                                                                              <C>             <C>
                                                                                  -----------    ----------- 
Cash flows from operating activities:
     Cash received from product sales, contracts, licenses fees and royalties     $   142,151    $    81,701
     Cash paid to suppliers, employees and service providers                         (152,857)       (77,401)
     Interest received                                                                    991          1,281
     Interest paid                                                                       (423)          (161)
                                                                                  -----------    -----------

     Net cash provided (used) by operating activities                                 (10,138)         5,420
                                                                                  ------------   -----------

Cash flows from investing activities:
     Proceeds from maturities/sales of short-term investments                          29,529         21,818
     Purchases of short-term investments                                               (6,883)       (51,972)
     Purchases of property and equipment                                               (1,636)        (3,846)
                                                                                  -----------    -----------

     Net cash provided (used) by investing activities                                  21,010        (34,000)
                                                                                  -----------    -----------

Cash flows from financing activities:
     Net proceeds from issuance of common stock                                         1,376          6,211
     Proceeds from credit line                                                          8,000              0
     Principal payments on credit line, long-term debt and capital leases             (22,633)          (237)
                                                                                  -----------    -----------

     Net cash provided (used) by financing activities                                 (13,257)         5,974
                                                                                  -----------    -----------

Net increase (decrease) in cash and cash equivalents                                   (2,385)       (22,606)

Cash and cash equivalents at beginning of period                                       19,098         52,484
                                                                                  -----------    -----------

Cash and cash equivalents at end of period                                        $    16,713    $    29,878
                                                                                  ===========    ===========

Reconciliation   of  net  income  to  net  cash  provided  (used)  by  operating
  activities:
     Net income                                                                   $     6,890    $     3,630
     Depreciation and amortization                                                      3,328          1,893
     Provision for deferred income taxes                                                1,216          2,420
     Net (increase) decrease in accounts receivable
       and other current assets                                                           965        (11,151)
     Net (increase) decrease in inventories                                            (2,932)           889
     Net increase (decrease) in accounts payable, accrued liabilities,
       deferred revenue and advances, and other liabilities                           (19,605)         7,739
                                                                                  ------------   -----------

     Net cash provided (used) by operating activities                             $   (10,138)   $     5,420
                                                                                  ===========    ===========


</TABLE>

See accompanying notes to consolidated financial statements.

                                  5
<PAGE>


                          AGOURON PHARMACEUTICALS, INC.
                   NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
                              (September 30, 1998)


Note 1 - The Company and its significant accounting policies

The Company

Agouron  Pharmaceuticals,  Inc.  ("Agouron" or the  "Company") was organized and
incorporated in California in June 1984. Agouron is an integrated pharmaceutical
company committed to the discovery, development,  manufacturing and marketing of
innovative therapeutic products engineered to inactivate proteins which play key
roles in cancer, AIDS and other serious diseases.  The Company,  through its own
sales and marketing  organization,  is currently  marketing in the United States
its  first  drug,  VIRACEPT(R)   (nelfinavir  mesylate)  for  treatment  of  HIV
infection.  The Company is also conducting  pivotal phase II/III clinical trials
for AG3340 for treatment of lung and prostate cancer.  In addition,  Agouron has
initiated a phase II/III  pivotal  clinical  trial of  REMUNE(TM)  (AG1661),  an
immune-based  therapeutic  agent for  treatment of HIV  infection and AIDS being
co-developed by Agouron and The Immune Response  Corporation  ("IRC").  Further,
the Company has a number of programs in progress for discovery or development of
other new  drugs in the  fields  of  cancer,  viral  disease  and other  serious
diseases.  The  Company  is also  using  the  proprietary  core  drug  discovery
technology of Alanex Corporation  ("Alanex"),  a wholly-owned  subsidiary of the
Company,  to  accelerate  the steps  necessary to discover  small-molecule  drug
candidates,  from the initial  identification of compounds that exhibit activity
against  selected  biological  targets to the  progression of these compounds to
drug candidates for human clinical trials.

Principles of consolidation

The consolidated  financial  statements  include the accounts of the Company and
its  wholly-owned  subsidiaries.   All  significant  intercompany  accounts  and
transactions have been eliminated.

Financial statements and estimates

The  consolidated  balance sheet as of September  30, 1998 and the  consolidated
statements of income and cash flows for the three-month  periods ended September
30, 1998 and 1997 have been  prepared by the Company and have not been  audited.
Such financial statements, in the opinion of management, include all adjustments
necessary for their fair  presentation  in conformity  with  generally  accepted
accounting principles.  These financial statements should be read in conjunction
with the financial  statements and notes thereto  included in the Company's June
30,  1998  Annual  Report  on  Form  10-K.  Certain   information  and  footnote
disclosures  normally  included in financial  statements  prepared in accordance
with generally  accepted  accounting  principles  have been condensed or omitted
pursuant  to the  Securities  and  Exchange  Commission  rules and  regulations.
Interim results are not necessarily indicative of results for the full year.

                                 6
<PAGE>


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.

Inventories

The inventories consist of the following components:

                                                 September 30,          June 30,
                                                          1998              1998
                                                 -------------     -------------
  Raw materials and work in process              $      98,520     $      95,517
  Finished goods                                         8,118             8,189
                                                 -------------     -------------

                                                 $     106,638     $     103,706
                                                 =============     =============

Product sales

In March  1997,  the  Company  received  clearance  from the FDA to  market  its
anti-HIV drug VIRACEPT.  The Company has the exclusive  right to market VIRACEPT
in the United  States and Canada.  Accordingly,  the Company  ships  VIRACEPT to
wholesalers  throughout the United States and certain  provinces of Canada,  and
recognizes  sales  revenue upon  shipment.  Sales are reported net of discounts,
rebates, chargebacks and product returns.

Also included in product sales for the  three-month  periods ended September 30,
1998 and 1997 are  approximately  $26,683,000  and  $4,128,000 of sales (at cost
plus contractually determined mark-ups) to Roche of clinical and commercial drug
supplies to be used by Roche in its licensed  territory.  The Company receives a
royalty on Roche's subsequent commercial sales of such drug supplies.

License fees and royalties

License fees are  recognized  as revenue  when earned as generally  evidenced by
certain factors including: receipt of such fees, satisfaction of any performance
obligations  and the  non-refundable  nature of such fees.  In August 1998,  the
Company and JT granted Roche certain exclusive rights to VIRACEPT in Mexico. For
such  rights,  the Company  realized  as revenue a license fee of $125,000  from
Roche.

Royalty  revenues are recognized based on estimated and actual sales of licensed
products in licensed territories.

For the  three-month  periods ended September 30, 1998 and 1997, the Company has
accrued  and/or  received  royalties of  approximately  $4,925,000  and $352,000
resulting  from  estimated  and actual net sales of VIRACEPT by Roche within its
licensed territory.


                                   7
<PAGE>


Income tax provision

The Company  records a provision for current and deferred income taxes using the
liability method.

Earnings per share

Basic  earnings  per share is based upon the weighted  average  number of common
shares outstanding during a period. Diluted earnings per share is based upon the
weighted  average number of common shares  outstanding and dilutive common stock
equivalents  during a period.  Common stock  equivalents  are options  under the
Company's  stock  option  plans  which are  included in the  earnings  per share
computation  under the treasury  stock method and common  shares  expected to be
issued under the Company's employee stock purchase plan.

Common stock equivalents of approximately 2,052,000 and 3,194,000 shares for the
three-month  periods  ended  September  30, 1998 and 1997 were used to calculate
diluted  earnings per share.  There are no reconciling  items in calculating the
numerator  for  basic and  diluted  earnings  per  share for any of the  periods
presented.

Certain concentrations

A portion of the Company's research and development  expenditures are related to
programs  funded  in  part  by  corporate  partners.  The  termination  of  such
collaborative  research and development  programs could result in the absence of
any prospective  funding for such programs and the need to evaluate the level of
future program spending, if any.



Note 2 - Comprehensive income

As of July 1, 1998,  the  Company  adopted  Statement  of  Financial  Accounting
Standards  No.  130  ("FAS  130"),   "Reporting   Comprehensive  Income,"  which
establishes new rules for the reporting and display of comprehensive  income and
its components.  FAS 130 requires  unrealized  gains and losses on the Company's
available-for-sale  securities to be included in other comprehensive income. The
Company presents such information in its statement of stockholders' equity on an
annual basis and in a footnote in its quarterly reports. During the three months
ended September 30, 1998 and 1997, total comprehensive income was $6,738,000 and
$3,630,000, respectively.

                                    8

<PAGE>


Item 2.           Management's Discussion and Analysis of Financial Condition
                  and Results of Operations

When used in this discussion,  the words  "believes,"  "anticipates" and similar
expressions are intended to identify forward-looking statements. Such statements
are subject to certain risks and uncertainties  (including those associated with
continued  growth of VIRACEPT  sales,  the impact of  competitive  products  and
regulatory approvals) which could cause actual results to differ materially from
those projected.  See "Important Factors Regarding  Forward-Looking  Statements"
attached as Exhibit 99 to the Company's  Annual Report on Form 10-K for the year
ended June 30, 1998 and incorporated herein by reference.  Readers are cautioned
not to place undue reliance on these forward-looking statements which speak only
as of the date hereof.  The Company undertakes no obligation to publicly release
the result of any  revisions to these  forward-looking  statements  which may be
made to reflect events or circumstances  after the date hereof or to reflect the
occurrence of unanticipated events.

Overview

The  Company is  committed  to the  discovery,  development,  manufacturing  and
marketing of human  pharmaceuticals  targeting  cancer,  AIDS, and other serious
diseases.  Operations  to date have been  principally  funded from the Company's
equity-derived  working capital,  various  collaborative  arrangements and, most
recently, from the gross margin contribution of its first product, VIRACEPT. The
net income reported in the three-month periods ended September 30, 1998 and 1997
is  principally  due to the  commercialization  of VIRACEPT  while the Company's
prior net  operating  losses  reflect  primarily  the result of its  independent
research and substantial  investment in the clinical and commercial  development
of VIRACEPT and certain anti-cancer compounds.

In March 1997,  the Company  received  clearance from the United States Food and
Drug  Administration  to market VIRACEPT in the United States.  In January 1998,
March 1998 and August 1998, VIRACEPT was approved for marketing in Europe, Japan
and Canada,  respectively.  For the three-month periods ended September 30, 1998
and 1997, due principally to the increasing  product  contribution from VIRACEPT
sales,  license  fees and  royalties,  the  Company  realized  a net  income  of
$6,890,000 and $3,630,000.

Results of Operations

Product sales

Product sales for the three-month periods ended September 30, 1998 and 1997 were
approximately  $133,870,000  and  $79,502,000,  which  included  sales  in North
America of $107,187,000 and $75,374,000,  respectively.  The Company anticipates
that  VIRACEPT  sales  in  North  America  will   approximate   $430,000,000  to
$440,000,000 for fiscal 1999.

Contract revenues

Collaborative  research  and  development  agreements  with Japan  Tobacco  Inc.
("JT"),  Hoffman-La Roche Inc. and F. Hoffman-La Roche Ltd (collectively  "HLR")
accounted for
                                    9
<PAGE>


substantially all of the Company's contract revenues for the three-month periods
ended September 30, 1998 and 1997.  Total contract  revenues for the three-month
periods  decreased  approximately  40% due principally to termination of the HLR
collaboration in fiscal 1998. The Company anticipates that contract revenues for
fiscal 1999 will approximate $30,000,000 to $35,000,000.

License fees and royalties

Royalty revenues of  approximately  $4,925,000 and $352,000 have been recognized
in the three-month  periods ended September 30, 1998 and 1997 based on estimated
and actual  Roche  sales of  VIRACEPT  in its  licensed  territory.  The Company
anticipates  that  license  fees and  royalties  for fiscal 1999 will range from
$30,000,000 to $35,000,000.

Cost of product sales

The  aggregate  cost of  product  sales as a  percentage  of  product  sales was
approximately 43% for the three-month periods ended September 30, 1998 and 1997.
Gross margins on United States  commercial sales were  approximately 70% and 60%
for the three-months ended September 30, 1998 and 1997.

Research and development

Research and development  spending increased 39% from the prior year periods due
generally to costs  associated  with  increasing  average staff levels and staff
related  spending,   and  increasing   expenses  associated  with  the  clinical
development of certain of the Company's anti-cancer compounds.

Selling, general and administrative

Selling,  general and administrative  costs have increased by 37% from the prior
year periods due  principally to increasing  sales and marketing  activities and
the support of VIRACEPT phase IV marketing studies.

Royalties

The  Company's  obligation  to share  VIRACEPT  profits  with JT is reflected in
royalty  expense for the  three-month  periods ended September 30, 1998 and 1997
and represents approximately 24% and 18% of United States product sales.

Income tax provision

The income tax  provision  in the  current  quarter has been  computed  using an
effective,  combined  federal and state rate of 15%. The cash obligation of such
provision has been mostly offset by the  utilization of deductions  generated by
the exercise of stock options  and/or the  utilization  of deferred tax benefits
(comprised mostly of net operating loss carryforwards and research tax credits).

                                    10
<PAGE>


Year 2000

The Year 2000 issue results from computer programs and systems that were created
to accept only two digit dates. Such systems may not be able to distinguish 20th
century dates from 21st century dates. This could result in miscalculations  and
system  failures that could  inhibit the  Company's  ability to engage in normal
business activities.

The Company has established a Year 2000 project team that is currently reviewing
information  technology ("IT") systems and non-IT systems that could be affected
by this issue.  Additionally,  the Company has made initial  contact with all of
its significant  external business partners to determine the extent to which the
Company is vulnerable to their  failures and to ascertain  Year 2000  compliance
and risk. The Company estimates that the inventory and assessment of IT systems,
non-IT  systems,  and  material  third  parties  will be completed by the end of
calendar 1998. The Company expects to complete remediation efforts by the end of
fiscal 1999, and to complete the  validation  phase by the end of calendar 1999.
At this time the Company has not initiated the formulation of contingency plans.
The determination of the necessity for contingency plans will be made by the end
of fiscal 1999.

While the total cost to obtain Year 2000  compliance  is not known at this time,
the Company  believes such cost will not have a material effect on the Company's
business, financial position, or results of operation.  However, even though the
Company  expects to have obtained Year 2000  compliance  prior to the year 2000,
the inability of the Company or its business partners to remedy Year 2000 issues
could have a significant impact on the Company's  business,  financial position,
or results of operations.

Liquidity and Capital Resources

Prior to fiscal 1998, the Company has relied  principally  on equity  financings
and corporate  collaborations  to fund its operations and capital  expenditures.
Beginning in fiscal 1998,  the gross  margin from  commercial  sales of VIRACEPT
contributed significantly to the Company's overall working capital requirements.
Commercial sales of VIRACEPT for the  three-months  ended September 30, 1998 and
1997 resulted in gross margins of approximately $76,825,000 and $45,429,000.

At September  30,  1998,  the Company had net working  capital of  approximately
$138,533,000,  an  increase  of  $10,805,000  over  June  30,  1998  levels  due
principally to the Company's  pre-tax profit of $8,106,000.  Individual  working
capital components  significantly  impacted by the commercialization of VIRACEPT
include trade accounts  receivable (a decrease of  $1,829,000),  inventories (an
increase  of  $2,932,000),  accounts  payable (a decrease  of  $18,539,000)  and
accrued  liabilities  (an  increase  of  $1,391,000,  primarily  due to  accrued
royalties  payable  to  JT).  It  is  anticipated  that  these  working  capital
components and cash and short-term investments will continue to be significantly
impacted by VIRACEPT  sales.  At September 30, 1998, the Company had cash,  cash
equivalents and short-term investments of approximately $61,940,000. The Company
believes that its current capital resources,  existing  contractual  commitments
and  anticipated  VIRACEPT  product sales are sufficient to maintain its current
operations  through  fiscal 1999.  This belief is based 

                                     11
<PAGE>


on current research and clinical development plans,  anticipated working capital
requirementsassociated  with the expanding  commercialization  of VIRACEPT,  the
current  regulatory   environment,   historical   industry   experience  in  the
development of therapeutic drugs and general economic conditions.

The  Company  believes  that  additional  financing  may be required to meet the
planned operating needs after fiscal 1999 if significant and increasing positive
cash flows are not  generated  from  commercial  activities.  Such  needs  would
include the expenditure of substantial funds to continue and expand research and
development  activities,  conduct existing and planned  preclinical  studies and
human clinical trials and to support the increasing working capital requirements
of a  growing  commercial  infrastructure  including  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  securities.  If such  alternatives  are not
available,  the Company may be required to defer or restrict certain  commercial
activities,  delay  or  eliminate  expenditures  for  certain  of its  potential
products  under  development,  cancel  licenses from third parties or to license
third parties to commercialize  products or technologies  that the Company would
otherwise seek to develop or commercialize itself.

                                     12
<PAGE>


PART II. OTHER INFORMATION

Item 1.           Legal Proceedings:

                  The  Company is involved  in certain  legal or  administrative
                  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.

Item 2.           Changes in Securities:  None

Item 3.           Defaults Upon Senior Securities:  None

Item 4.           Submission of Matters to a Vote of Security Holders:  None

Item 5.           Other Information:  None

Item 6.           Exhibits and Reports on Form 8-K:
                  a.   Exhibits:

                      10.1* Amended and Restated 1996 Stock Option Plan

                      10.2* Amended and Restated Employee Stock Purchase Plan


                      10.3* Form of 1998 Employee Stock Option Plan.

                      27.   Financial   Data  Schedule  for  the  quarter  ended
                            September 30, 1998. 

                  b.   Reports on Form 8-K:  None








*    Incorporated by reference to Form S-4 dated August 13, 1998



                                        13


<PAGE>


                                    SIGNATURE

Pursuant  to the  requirements  of the  Securities  Exchange  Act of  1934,  the
registrant  has duly  caused  this  report  to be  signed  on its  behalf by the
undersigned thereunto duly authorized.


                                               AGOURON PHARMACEUTICALS, INC.




Date:  October 20, 1998                          /s/ Steven S. Cowell
                                               ----------------------------
                                               Steven S. Cowell
                                               Corporate Vice President, Finance
                                               Chief Financial Officer
                                               Chief Accounting Officer


                                   14
<PAGE>

<TABLE> <S> <C>
                                              
<ARTICLE>                                          5
<LEGEND>                                      
This schedule contains summary financial  information extracted from the balance
sheet and the  statement  of income  (loss) and is  qualified in its entirety by
reference to such financial statements.
</LEGEND>                                     

<MULTIPLIER>                                                 1,000
                                                    
<S>                                                  <C>
<PERIOD-TYPE>                                      3-mos
<FISCAL-YEAR-END>                                  Jun-30-1999
<PERIOD-END>                                       Sep-30-1998
<CASH>                                                      16,713
<SECURITIES>                                                45,227
<RECEIVABLES>                                               52,349
<ALLOWANCES>                                                   594
<INVENTORY>                                                106,638
<CURRENT-ASSETS>                                           224,765
<PP&E>                                                      72,857
<DEPRECIATION>                                              27,187
<TOTAL-ASSETS>                                             338,784
<CURRENT-LIABILITIES>                                       86,232
<BONDS>                                                          0
                                            0
                                                      0
<COMMON>                                                   350,947
<OTHER-SE>                                                (105,575)
<TOTAL-LIABILITY-AND-EQUITY>                               338,784
<SALES>                                                    133,870
<TOTAL-REVENUES>                                           144,937
<CGS>                                                       57,045
<TOTAL-COSTS>                                               68,829
<OTHER-EXPENSES>                                                 0
<LOSS-PROVISION>                                                 0
<INTEREST-EXPENSE>                                             423
<INCOME-PRETAX>                                              8,106
<INCOME-TAX>                                                 1,216
<INCOME-CONTINUING>                                          6,890
<DISCONTINUED>                                                   0
<EXTRAORDINARY>                                                  0
<CHANGES>                                                        0
<NET-INCOME>                                                 6,890
<EPS-PRIMARY>                                                 0.22
<EPS-DILUTED>                                                 0.21
        

</TABLE>


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