10-K405/A 1 a2044162z10-k405a.txt 10-K405/A UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-K/A ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 FOR THE FISCAL YEAR ENDED DECEMBER 31, 2000 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 (IRS Employer Identification No.) incorporation or organization) 2292 FARADAY AVE., CARLSBAD, CA 92008 (Address of principal executive offices, including zip code) 760-931-9200 (Registrant's telephone number, including area code) Securities registered pursuant to Section 12(b) of the Act: None Securities registered pursuant to Section 12(g) of the Act: COMMON STOCK, $.001 PAR VALUE 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 and 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 by check mark if disclosure of delinquent filers pursuant to Item 405 of Regulation S-K is not contained herein, and will not be contained to the best of Registrant's knowledge, in definitive proxy or information statements incorporated by reference in Part III of this Form 10-K or any amendment to this Form 10-K. Yes X No . The approximate aggregate market value of the voting common stock held by non-affiliates of the Registrant, based upon the last sale price of the common stock reported on the National Association of Securities Dealers Automated Quotation National Market System was $299,046,755 as of January 12, 2001. * The number of shares of voting common stock outstanding as of January 12, 2001 was 40,119,564. DOCUMENTS INCORPORATED BY REFERENCE (To the extent indicated herein) Registrant's definitive Proxy Statement filed on or about February 28, 2001 with the Securities and Exchange Commission in connection with Registrant's annual meeting of stockholders to be held on April 6, 2001 is incorporated by reference into Part III of this Report. ------------------------ *Excludes 10,584,082 shares of common stock held by directors and officers and by stockholders whose beneficial ownership is known by the registrant to exceed 10% of the common stock outstanding at January 12, 2001. Exclusion of shares held by any person should not be construed to indicate that such person possesses the power, direct or indirect, to direct or cause the direction of the management or policies of the Registrant, or that such person is controlled by or under common control with the Registrant. 1 EXPLANATORY NOTE This Amendment to the Annual Report on Form 10-K for Isis Pharmaceuticals, Inc. is being filed solely to amend Item 14(a)(3) and Item 14(c) by adding Exhibit 10.25. PART IV ITEM 14. EXHIBITS, FINANCIAL STATEMENT SCHEDULES, AND REPORTS ON FORM 8-K (a)(1) INDEX TO FINANCIAL STATEMENTS The financial statements required by this item are submitted in a separate section beginning on page F-1 of this Report. (a)(2) INDEX TO FINANCIAL STATEMENT SCHEDULES These schedules are omitted because they are not required, or are not applicable, or the required information is shown in the financial statements or notes thereto. (a)(3) INDEX TO EXHIBITS See Index to Exhibits on pages 32 through 33. (b) REPORTS ON FORM 8-K On December 12, 2000, the registrant filed a report on Form 8-K relating to the adoption of a stockholder rights plan. (c) EXHIBITS The exhibits required by this Item are listed under Item 14(a)(3). (d) FINANCIAL STATEMENT SCHEDULES The financial statement schedules required by this Item are listed under Item 14(a)(2). 2 SIGNATURES Pursuant to the requirements of Section 14 or 15(d) of the Securities Exchange Act of 1934, the Registrant has duly caused this report on Form 10-K/A to be signed on its behalf by the undersigned, thereunto duly authorized on the 2nd day of April, 2001. ISIS PHARMACEUTICALS, INC. By: /s/ B. LYNNE PARSHALL ---------------------- B. Lynne Parshall Executive Vice President, Chief Financial Officer and Director Pursuant to the requirements of the Securities Exchange Act of 1934, this report has been signed below by the following persons on behalf of the Registrant and in the capacities and on the dates indicated.
SIGNATURES TITLE DATE ---------- ----- ---- STANLEY T. CROOKE, M.D., PH.D.* --------------------------------- Stanley T. Crooke, M.D., Ph.D. Chairman of the Board, Chief Executive Officer and Director (Principal executive officer) April 2, 2001 /s/ B. LYNNE PARSHALL --------------------------- B. Lynne Parshall Executive Vice President, Chief Financial Officer and Director (Principal financial and accounting officer) April 2, 2001 CHRISTOPHER F. O. GABRIELI* ----------------------------- Christopher F. O. Gabrieli Director Arpil 2, 2001 WILLIAM R. MILLER* ----------------------- William R. Miller Director April 2, 2001 /s/ FRED T. MUTO ----------------------- Fred T. Muto Director April 2, 2001 MARK B. SKALETSKY* ----------------------- Mark B. Skaletsky Director April 2, 2001 JOSEPH H. WENDER* ------------------------- Joseph H. Wender Director April 2, 2001 *By: /s/ B. LYNNE PARSHALL --------------------- B. Lynne Parshall Attorney-in-Fact
3 INDEX TO EXHIBITS Exhibit NUMBER DESCRIPTION OF DOCUMENT ------ ----------------------- 1.1 - Form of Common Stock Purchase Agreement between the Registrant and Ridgeway Investment Limited. (16) 3.1 - Amended and Restated Certificate of Incorporation filed June 19, 1991. (1) 3.2 - Bylaws. (1) 3.3 - Certificate of Designation of the Series A Convertible Preferred Stock. (11) 3.4 - Certificate of Designation of the Series B Convertible Preferred Stock. (14) 3.5 - Certificate of Designation of the Series C Junior Participating Preferred Stock. (17) 4.1 - Reference is made to Exhibits 3.1 through 3.5. 4.2 - Specimen Stock Certificate. (1) 4.3 - Specimen Series A Preferred Stock Certificate. (18) 4.4 - Specimen Series B Preferred Stock Certificate. (18) 4.5 - Form of Right Certificate. (17) 10.1 - Form of Indemnification Agreement entered into between the Registrant and its Directors and Officers with related schedule. (1) 10.2 * - Registrant's 1989 Stock Option Plan, as amended. (6) 10.3 * - Registrant's 1992 Non-Employee Directors Stock Option Plan, as amended. (4) 10.4 * - Form of Performance-Based Supplemental Stock Option Agreement dated January 6, 2000 under the 1989 Stock Option Plan entered into between the Registrant and certain of its officers together with related schedule. (19) 10.5 * - Registrant's Employee Stock Purchase Plan. (10) 10.6 * - Form of Employee Assignment of Patent Rights. (1) 10.7 * - Registrant's 2000 Broad-Based Equity Incentive Stock Option Plan. (10) 10.8 * - Severance Agreement dated January 11, 2000 entered into between the Registrant and its executive officers, together with related schedule. (10) 10.9 - Stock Purchase Agreement between the Registrant and Boehringer Ingelheim International GmbH, dated as of July 18, 1995 (with certain confidential information deleted). (2) 10.10 - Collaborative Agreement between the Registrant and Boehringer Ingelheim International GmbH, dated as of July 18, 1995 (with certain confidential information deleted). (3) 10.11 - Agreement between the Registrant and CIBA Vision Corporation (now Novartis Ophthalmics) dated July 10, 1997 (with certain confidential information deleted). (5) 10.12 - Amendment No. 2 to the Agreement between the Registrant and CIBA Vision Corporation, dated September 14, 1998 (with certain confidential information deleted). (8) 10.13 - Imperial Bank Note Secured by Deed of Trust dated March 24, 1997 in the amount of $6,000,000, together with the related Deed of Trust and Assignment of Rents dated March 24, 1997. (5) 10.14 - Imperial Bank Note Secured by Deed of Trust dated March 24, 1997 in the amount of $3,706,620, together with the related Deed of Trust and Assignment of Rents dated March 24, 1997. (5) 10.15 - Purchase Agreement between the Registrant and Reliance Insurance Company for 14% Senior Subordinated Discount Notes due November 1, 2007 and Warrants for Common Stock dated October 24, 1997 (with certain confidential information deleted). (6) 10.16 - First Supplement to Purchase Agreement between the Registrant and Reliance Insurance Company for 14% Senior Subordinated Discount Notes due November 1, 2007 and Warrants for Common Stock dated May 1, 1998 (with certain confidential information deleted). (7) 10.17 - Asset Purchase Agreement between the Registrant and Gen-Probe Incorporated dated December 19, 1997 (with certain confidential information deleted). (6) 10.18 - Research Collaboration and License Agreement between Merck & Co., Inc. and the Registrant dated June 1, 1998 (with certain confidential information deleted). (7) 10.19 - Patent Rights Purchase Agreement between the Registrant and Gilead Sciences, Inc., dated December 18, 1998 (with certain confidential information deleted). (9) 10.20 - Subscription, Joint Development and Operating Agreement, dated April 20, 1999 by and among the Registrant, Elan Corporation, plc, Elan International Services, Ltd. And Orasense, Ltd. (with certain 4 confidential information deleted); together with the related Securities Purchase Agreement, Convertible Promissory Note, Warrant to Purchase Shares of Common Stock, Registration Rights Agreements and License Agreements. (12) 10.21 - Agreement dated August 31, 1999 between Boehringer Ingelheim International GmbH and the Registrant; together with related Amendment to the Stock Purchase Agreement. (13) 10.22 - Subscription, Joint Development and Operating Agreement, dated January 14, 2000 by and among the Registrant, Elan Corporation, plc, Elan International Services, Ltd. and HepaSense, Ltd. (with certain confidential information deleted); together with the related Securities Purchase Agreement, Convertible Promissory Note, Warrant to Purchase Shares of Common Stock, Registration Rights Agreements and License Agreements. (14) 10.23 - Agreement between the Registrant and Agouron Pharmaceuticals, dated June 9, 2000 (with certain confidential information deleted). (15) 10.24 - Rights Agreement dated as of December 8, 2000 between the Registrant and American Stock Transfer & Trust Company. (17) 10.25 - Agreement between the Registrant and Coley Pharmaceutical Group, Inc., f/k/a CpG ImmunoPharmaceuticals, Inc., dated September 27, 2000. 23.1 - Consent of Ernst & Young LLP, Independent Auditors. (19) 24.1 - Power of Attorney. (19) 99.1 - Form of Confidentiality Agreement. (11) ------------------ (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 Report on Form 8-K dated July 18, 1995 and incorporated herein by reference. (3) Filed as an exhibit to the Registrant's Quarterly Report on Form 10-Q for the quarter ended September 30, 1995 and incorporated herein by reference. (4) Filed as an exhibit to the Registrant's Quarterly Report on Form 10-Q for the quarter ended September 30, 1996 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, 1997 and incorporated herein by reference. (6) 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. (7) 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. (8) Filed as an exhibit to the Registrant's Quarterly Report on Form 10-Q for the quarter ended September 30, 1998 and incorporated herein by reference. (9) Filed as an exhibit to the Registrant's Annual Report on Form 10-K for the year ended December 31, 1998 and incorporated herein by reference. (10) Filed as an exhibit to the Registrant's Annual Report on Form 10-K for the year ended December 31, 1999 and incorporated herein by reference. (11) 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. (12) Filed as an exhibit to the Registrant's Report on Form 8-K dated April 20, 1999 and incorporated herein by reference. (13) Filed as an exhibit to the Registrant's Report on Form 8-K dated August 31, 1999 and incorporated herein by reference. (14) Filed as an exhibit to the Registrant's Report on Form 8-K dated January 28, 2000 and incorporated herein by reference. (15) Filed as an exhibit to the Registrant's Report on Form 10-Q for the quarter ended June 30, 2000 and incorporated herein by reference. (16) Filed as an exhibit to the Registrant's Registration Statement on Form S-3 (No. 333-90811) or amendment thereto and incorporated by reference. (17) Filed as an exhibit to Registrant's Report on Form 8-K dated December 8, 2000 and incorporated herein by reference. 5 (18) Filed as an exhibit to the Registrant's Report on Form 10-Q/A for the quarter ended June 30, 2000 and incorporated herein by reference. (19) Filed as an exhibit to Registrant's Annual Report on Form 10-K for the year ended December 31, 2000 and incorporated herein by reference. * Indicates management compensatory plans and arrangements as required to be filed as exhibits to this Report pursuant to Item 14(c). 6