ISIS PHARMACEUTICALS INC
10-Q/A, 2000-08-29
PHARMACEUTICAL PREPARATIONS
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<PAGE>

                       SECURITIES AND EXCHANGE COMMISSION
                              WASHINGTON, DC 20549

                                   FORM 10-Q/A
                                (Amendment No. 1)

(MARK ONE)

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

For the quarterly period ended June 30, 2000

                                       OR

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

For the transition period from ______to _______
Commission file number   0-19125

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

          Delaware                                    33-0336973
(State or other jurisdiction of            (I.R.S. Employer Identification No.)
 incorporation or organization)

                        2292 Faraday Avenue, Carlsbad, CA
                 92008 (Address of principal executive offices,
                               including zip code)

                                 (760) 931-9200
              (Registrant's telephone number, including area code)

              (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.

     (1)Yes  [X]        No  [ ](2)           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.

  COMMON STOCK $.001 PAR VALUE                         38,448,777 SHARES
  ----------------------------                         -----------------
           (Class)                               (Outstanding at July 31, 2000)
<PAGE>
                           ISIS PHARMACEUTICALS, INC.
                                    FORM 10-Q
                                      INDEX

<TABLE>
<CAPTION>
                                                                                              Page
                                                                                              ----
<S>                                                                                           <C>
PART I              FINANCIAL INFORMATION

ITEM 1:             Financial Statements
                    Condensed Balance Sheets as of June 30, 2000 and December 31, 1999          3
                    Condensed Statements of Operations for the three and six months
                    ended June 30, 2000 and 1999                                                4
                    Condensed Statements of Cash Flows for the six months
                    ended June 30, 2000 and 1999                                                5
                    Notes to Financial Statements                                               6

ITEM 2:             Management's Discussion and Analysis of Financial Condition
                    and Results of Operations                                                   *
                    Results of Operations                                                       *
                    Liquidity and Capital Resources                                             *
                    Quantitative and Qualitative Disclosures About Market Risk                  *

PART II             OTHER INFORMATION

ITEM 1:             Legal Proceedings                                                           *

ITEM 2:             Changes in Securities                                                       *

ITEM 3:             Default upon Senior Securities                                              *

ITEM 4:             Submission of Matters to a Vote of Security Holders                         *

ITEM 5:             Other Information                                                           *

ITEM 6:             Exhibits and Reports on Form 8-K                                           14

SIGNATURES
</TABLE>

* N/A

Explanatory Note: This amendment to form 10-Q is filed solely to amend
Part I, Item 1, Note 3 to Financial Statements, and Part II Item 6(a),
Exhibits.

                                      2
<PAGE>

                           ISIS PHARMACEUTICALS, INC.
                            CONDENSED BALANCE SHEETS
                                 (In Thousands)

                                     ASSETS

<TABLE>
<CAPTION>
                                                                                       June 30,      December 31,
                                                                                        2000             1999
                                                                                    ------------     ------------
                                                                                    (Unaudited)         (Note)
<S>                                                                                 <C>              <C>
Current assets:
  Cash and cash equivalents                                                               62,043           35,296
  Short-term investments                                                                  58,291           17,543
  Contract revenue receivable                                                              4,644            5,429
  Prepaid expenses and other current assets                                                1,210              929
                                                                                    ------------     ------------
           Total current assets                                                          126,188           59,197

Property, plant and equipment, net                                                        22,596           23,945
Patent costs, net                                                                         11,886           11,250
Deposits and other assets                                                                  1,587            1,724
Investment in joint ventures                                                              14,767            6,991
                                                                                    ------------     ------------
                      Total assets                                                       177,024          103,107
                                                                                    ============     ============

                      LIABILITIES AND STOCKHOLDERS' EQUITY

Current liabilities:
  Accounts payable                                                                         1,134            3,148
  Accrued payroll and related expenses                                                     2,344            1,215
  Accrued liabilities                                                                      3,210            2,563
  Deferred contract  revenues                                                              2,351            4,166
  Current portion of long term debt and capital lease obligations                          3,723            3,892
                                                                                    ------------     ------------
           Total current liabilities                                                      12,762           14,984

Long-term debt and capital lease obligations, less current portion                        94,504           87,254

Stockholders' equity:
  Series A Convertible Exchangeable 5% Preferred stock, $.001 par value;
     15,000,000 shares authorized, 120,150 shares issued
     and outstanding at June 30, 2000 and December 31, 1999, respectively                 12,623           12,315
  Accretion of Series A Preferred stock dividends                                            122              120
  Series B Convertible Exchangeable 5% Preferred stock, $.001 par
     value; 16,620 shares authorized, 12,015 shares and no shares issued and
     outstanding at June 30, 2000 and December 31, 1999,
     respectively                                                                         12,015             --
  Accretion of Series B Preferred stock dividends                                            277             --
  Common stock, $.001 par value; 50,000,000 shares authorized, 38,375,438 shares
     and 31,613,000 shares issued and outstanding
     at June 30, 2000 and December 31, 1999, respectively                                     38               32
  Additional paid-in capital                                                             334,687          245,192
  Unrealized gain (loss) on investments                                                      (26)             (29)
  Accumulated deficit                                                                   (289,978)        (256,761)
                                                                                    ------------     ------------
           Total stockholders' equity                                                     69,758              869
                                                                                    ------------     ------------
                      Total liabilities and stockholders' equity                         177,024          103,107
                                                                                    ============     ============
</TABLE>

Note: The balance sheet at December 31, 1999 has been derived from the audited
financial statements at that date.

                             See accompanying notes.

                                       3

<PAGE>

                           ISIS PHARMACEUTICALS, INC.
                       CONDENSED STATEMENTS OF OPERATIONS
                      (In Thousands, Except Per Share Data)

<TABLE>
<CAPTION>
                                                        Three months ended,           Six months ended,
                                                             June 30,                      June 30,
                                                          2000          1999           2000         1999
                                                     -------------------------    -------------------------
<S>                                                  <C>               <C>        <C>             <C>
Revenue:
     Research and development revenues under
        collaborative agreements                         $4,224        $5,815         $7,110       $12,391
     Research and development revenues
        from joint ventures                               2,761         1,393          3,929         1,393
                                                     -------------------------    -------------------------
Total Revenue                                             6,985         7,208         11,039        13,784

Expenses:
  Research and development                               12,746        16,443         25,985        30,759
  General and administrative                              2,414         2,762          4,238         5,577
  Restructuring activities                                    -             -          1,608             -
                                                     -------------------------    -------------------------
Total Operating Expenses                                 15,160        19,205         31,831        36,336
                                                     -------------------------    -------------------------

(Loss) from operations                                   (8,175)      (11,997)       (20,792)      (22,552)

Equity in loss of joint ventures                         (4,594)       (2,277)        (8,089)       (2,277)
Interest income                                           1,596           551          2,488         1,207
Interest expense                                         (3,129)       (2,800)        (6,236)       (5,505)
                                                     -------------------------    -------------------------
Net loss                                                (14,302)      (16,523)       (32,629)      (29,127)
                                                     -------------------------    -------------------------
Accretion of dividends on preferred stock                  (306)         (117)          (587)         (117)
                                                     -------------------------    -------------------------
Net loss applicable to common stock                     (14,608)      (16,640)       (33,216)      (29,244)
                                                     =========================    =========================
Basic and diluted net loss per share                     ($0.40)       ($0.59)        ($0.95)       ($1.06)
                                                     =========================    =========================
Shares used in computing basic and diluted
    net loss per share                                   36,979        28,047         35,021        27,615
                                                     =========================    =========================
</TABLE>

                             See accompanying notes.

                                      4
<PAGE>

                           ISIS PHARMACEUTICALS, INC.
                       CONDENSED STATEMENTS OF CASH FLOWS
                                 (In Thousands)
                                   (Unaudited)

<TABLE>
<CAPTION>
                                                                                        Six Months Ended
                                                                                             June 30,
                                                                                         2000        1999
                                                                                  -------------    -------------
<S>                                                                               <C>              <C>
Cash used in operations                                                                (19,385)        (28,351)

Investing activities:
   Short-term investments                                                              (40,745)         22,632
   Property and equipment                                                                 (924)           (894)
   Other assets                                                                           (876)         (1,423)
   Investment in joint venture                                                         (15,865)        (12,015)
                                                                                  ------------------------------
            Net cash used for investing activities                                     (58,410)          8,300
                                                                                  ------------------------------
Financing activities:
    Net proceeds from issuance of equity securities                                    102,103          28,144
    Proceeds from long-term borrowings                                                   3,850               -
    Principal payments on debt and capital lease obligations                            (1,411)         (1,338)
                                                                                  ------------------------------
            Net cash provided from financing activities                                104,542          26,806
                                                                                  ------------------------------

Net increase (decrease) in cash and cash equivalents                                    26,747           6,755

Cash and cash equivalents at beginning of period                                        35,296          27,618
                                                                                  ------------------------------
Cash and cash equivalents at end of period                                              62,043          34,373
                                                                                  ==============================
SUPPLEMENTAL DISCLOSURES OF CASH FLOW INFORMATION:
    Interest paid                                                                          530           1,654

SUPPLEMENTAL DISCLOSURES OF NON-CASH INVESTING AND FINANCING ACTIVITIES:
     Additions to long-term debt obligations for acquisitions of property,
     plant and equipment                                                                     -           2,071
     Conversion of preferred stock dividends into preferred stock                          308               -
</TABLE>

                             See accompanying notes.

                                      5

<PAGE>

                           ISIS PHARMACEUTICALS, INC.

                          NOTES TO FINANCIAL STATEMENTS

1.  BASIS OF PRESENTATION

     The unaudited interim financial statements for the six month periods ended
June 30, 2000 and 1999 have been prepared on the same basis as the Company's
audited financial statements for the year ended December 31, 1999. The financial
statements include all adjustments (consisting only of normal recurring
adjustments) which the Company considers necessary for a fair presentation of
the financial position at such dates and the operating results and cash flows
for those periods. Results for the interim periods are not necessarily
indicative of the results for the entire year. For more complete financial
information, these financial statements, and notes thereto, should be read in
conjunction with the audited financial statements for the year ended December
31, 1999 included in the Company's Annual Report on Form 10-K filed with the
Securities and Exchange Commission.

2.  STRATEGIC ALLIANCES

     ORASENSE

     On April 20, 1999, Isis Pharmaceuticals, Inc., a Delaware corporation
("Isis" or the "Company") and Elan Corporation, plc ("Elan") formed a joint
venture to develop technology for the formulation of oral oligonucleotide
drugs. The joint venture, Orasense Ltd. ("Orasense"), a Bermuda limited
company, is initially owned 80.1% by the Company and 19.9% by Elan. Isis and
Elan each contributed rights to certain oral drug delivery technology to the
joint venture. In addition, Isis contributed rights to ISIS 104838, an
antisense oligonucleotide to inhibit TNF-(alpha), which will be the first
candidate for oral formulation by Orasense. Isis and Elan will provide
development and manufacturing services to Orasense and will be entitled to a
portion of milestone payments and royalties received by Orasense for
development of orally formulated oligonucleotide drugs. If Isis enters into
an agreement with Orasense for oral formulation of any Isis oligonucleotide
drug, Isis will pay Orasense royalties and a portion of certain third party
milestone payments with respect to the drug.

     While Isis owns 80.1% of the outstanding common stock of Orasense, Elan and
its subsidiaries have retained significant minority investor rights that are
considered "participating rights" as defined in EITF 96-16. Therefore, Isis does
not consolidate the financial statements of Orasense, but instead accounts for
its investment in Orasense under the equity method of accounting. During the six
month period ended June 30, 2000, Isis recognized $2,490,566 in contract
revenues for research and development activities performed for Orasense Ltd.
This amount is included as research and development revenues from joint ventures
for the related periods.

     The results of operations of Orasense Ltd. for the six month period ended
June 30, 2000 is as follows (in thousands):

<TABLE>
<CAPTION>
                                                SIX MONTHS ENDED
                                                 JUNE 30, 2000
                                                ----------------
<S>                                             <C>
     Revenue                                     $     --
     Research and Development expense            $    6,151
     Net Loss                                    $    6,151
</TABLE>

     HEPASENSE

     On January 14, 2000, Isis and Elan Corporation formed a new joint venture
to develop an antisense drug, ISIS 14803, to treat patients chronically infected
with the Hepatitis C virus (HCV). The new joint venture is called HepaSense and
plans to develop and commercialize this novel therapeutic for HCV while
investigating delivery of the therapeutic with Elan's proprietary
MEDIPAD-Registered Trademark- Drug Delivery System, a disposable subcutaneous
infusion device. ISIS 14803 began Phase I clinical trials in early 2000. Isis
and Elan have each licensed technology to HepaSense.

     In conjunction with the formation of HepaSense, Elan International
Services, Ltd. ("EIS") purchased 12,015 shares of Isis' Series B Preferred stock
for $12,015,000. In April 2000, EIS purchased an additional 298,000 shares of
Isis' common stock for $7,500,000. EIS will purchase an additional $7.5 million
of common stock at a premium to Isis' market price upon completion of a mutually
agreed milestone.

     After June 30, 2002, the preferred stock (including accrued dividends) will
be convertible at EIS' option, into shares of Isis' common stock at 125% of the
60-trading day average closing price of Isis' common stock ending two business
days prior to June 30,

                                      6
<PAGE>
2002 (as adjusted for stock splits, stock dividends and the like). In the
event of a liquidation of Isis or certain transactions involving a change of
control of Isis, the agreement provides for automatic conversion of the
preferred stock on terms similar to those set forth above.

     Isis is not obligated to issue shares representing more than 19.99% of its
then outstanding Common Stock upon conversion of the Preferred Stock if it would
result in a violation of the rules of any securities market or exchange upon
which the Common Stock is traded.

     At any time until June 30, 2002, the holders of preferred stock may
exchange their preferred stock with Isis for preferred shares of HepaSense, Ltd.
held by Isis that represent 60.2% of the total outstanding preferred stock of
HepaSense. The exchange right will terminate if the Isis Series B Convertible
Preferred stock is converted into Isis' common stock, unless such conversion
occurs as a result of a liquidation or certain transactions involving a change
of control of Isis.

     Isis contributed $12,015,000 to HepaSense as the purchase price for 6,001
shares of common stock of HepaSense and 3,612 shares of HepaSense preferred
stock. Until July 14, 2002, EIS will, at Isis' request, purchase convertible
debt of Isis in an amount equal to Isis' share of budgeted funding for
HepaSense. The convertible debt will have a term of six years, bear interest at
the rate of 12% and be convertible into Isis' common stock at a premium. Isis
may prepay the convertible debt in cash or Isis' common stock. Isis will use the
proceeds of the sale of the convertible debt to provide additional development
funding to HepaSense.

     While Isis owns 80.1% of the outstanding common stock of HepaSense, Elan
and its subsidiaries have retained significant minority investor rights that are
considered "participating rights" as defined in EITF 96-16. Therefore, Isis does
not consolidate the financial statements of HepaSense, but instead accounts for
its investment in HepaSense under the equity method of accounting. During the
six month period ended June 30, 2000, Isis recognized $1,439,126 in contract
revenues for research and development activities performed for HepaSense Ltd.
This amount is included as research and development revenues from joint ventures
for the related periods.

     The results of operations of HepaSense Ltd. for the six month period ended
June 30, 2000 is as follows (in thousands):
<TABLE>
<CAPTION>                                       SIX MONTHS ENDED
                                                  JUNE 30, 2000
                                                ----------------
     <S>                                        <C>
     Revenue                                     $     --
     Research and Development expense            $    3,939
                                                 ----------
     Net Loss                                    $    3,939
                                                 ==========
</TABLE>

     AGOURON

    In June 2000, Ibis Therapeutics ("Ibis"), a division of Isis
Pharmaceuticals, Inc. and Agouron Pharmaceuticals, Inc., a Pfizer Company,
entered into a collaboration for the discovery and development of small molecule
drugs against certain RNA targets in an undisclosed therapeutic area. Using
Ibis' proprietary technology and Agouron's expertise in small molecule drug
discovery, the collaboration will focus on discovering drugs that bind to RNA.
Agouron will fund collaborative research, pay an upfront technology access fee
and make milestone payments totaling $37 million for the first product. In
addition, Agouron will develop and commercialize drugs discovered by the
collaboration and will pay Isis royalties on the sales of drugs.

3.  FINANCING

     Over the six months ended June 30, 2000, Isis sold 2,939,460 shares of
its common stock to institutional investors at negotiated prices of $10.45
per share to $27.25 per share. In addition, over the six months ended June
30, 2000 the company sold 1,997,879 shares of its common stock to Ridgeway
Investment Limited at prices ranging from an average of $7.57 per share to
$14.45 per share under the terms of the Common Stock Purchase Agreement filed
as an exhibit to the prospectus dated December 6, 1999. The per share average
purchase prices reflect the average trading prices of the common stock over a
period of time less a discount from 4.5% to 5.875%.

                                      7
<PAGE>
ITEM 6.        EXHIBITS AND REPORTS ON FORM 8-K

     a. Exhibits

            3.1  Amended and Restated Certificate of Incorporation.(1)

            3.2  Bylaws.(1)

            3.3  Certificate of Designation of the Series A Convertible
                 Preferred Stock.(2)

            3.4  Certificate of Designation of the Series B Convertible
                 Preferred Stock.(3)

            4.1  Reference is made to Exhibits 3.1, 3.2, 3.3 and 3.4.

            4.2  Specimen Common Stock Certificate.(1)

            4.3  Specimen Series A Preferred Stock Certificate.

            4.4  Specimen Series B Preferred Stock Certificate.

            4.5  Purchase Agreement for 14% Senior Subordinated Discount
                 Notes due November 1, 2001 and Warrants for Common Stock
                 dated October 24, 1997 (with certain confidential
                 information deleted).(4)

            4.6  First Supplement to Purchase Agreement for 14% Senior
                 Subordinated Discount Notes due November 1, 2001 and Warrants
                 for Common Stock dated May 1, 1998 (with certain confidential
                 information deleted).(5)

            4.7  Registration Rights Agreement dated April 20, 1999 among
                 Registrant, Elan International Services, Ltd., and Orasense,
                 Ltd.(6)

            4.8  Registration Rights Agreement dated January 14, 2000 among
                 Registrant, Elan International Services, Ltd., and Hapasense,
                 Ltd.(7)

            4.9  Voting Rights Agreement among the Registrant, Novartis and
                 Dr. Cooke, dated November 9, 1990.(1)

           10.33 Agreement between Registrant and Agouron Pharmaceuticals dated
                 June 9, 2000 (with certain confidential information deleted).*

           27.1  Financial Data Schedules*
-----------
(1)  Filed as an exhibit to the Registrant's Registration Statement on Form
S-1 (No. 33-39640) or amendments thereto and incorporated herein by reference.

(2)  Filed as an exhibit to the Registrant's Registration Statement on Form
S-3 (No. 333-71911) or amendments thereto and incorporated herein by
reference.

(3)  Filed as an exhibit to the Registrant's 8-K dated as of January 8, 2000
and incorporated herein by reference.

(4)  Filed as an exhibit to the Registrant's Annual Report on Form 10-K for the
year ended December 31, 1997, and incorporated herein by reference.

(5)  Filed as an exhibit to the Registrant's Quarterly Report on Form 10-Q
for the quarter ended June 30, 1998 and incorporated herein by reference.

(6)  Filed as an exhibit to the Registrant's report on Form 8-K dated April
20, 1999 and incorporated herein by reference.

(7)  Filed as an exhibit to the Registrant's report on Form 8-K dated January
28, 2000 and incorporated herein by reference.

*  Previously filed.

     b. Reports on Form 8-K

         Not applicable

                                      8
<PAGE>

                           ISIS PHARMACEUTICALS, INC.

                                   SIGNATURES

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.

                                                 ISIS PHARMACEUTICALS, INC.
                                                        (Registrant)


Date:   August 29, 2000                  By:  /S/ B. LYNNE PARSHALL
        ---------------                   -------------------------------
                                           B. Lynne Parshall
                                           Executive Vice President and
                                           Chief Financial Officer
                                           (Duly Authorized Officer and
                                           Principal Financial and
                                           Accounting Officer)


                                      9


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