1 SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 SCHEDULE 13D (RULE 13d-101) INFORMATION TO BE INCLUDED IN STATEMENTS FILED PURSUANT TO RULE 13d-1(a) AND AMENDMENTS THERETO FILED PURSUANT TO RULE 13d-2(a) (AMENDMENT NO. 3) ISIS PHARMACEUTICALS, INC. ------------------------------------------------------------------ (Name of Issuer) COMMON STOCK, PAR VALUE $0.001 PER SHARE ------------------------------------------------------------------ (Title of Class of Securities) 464330 10 9 ------------------------------------------------------------------ (Cusip Number) HANS-PETER MUELLER BOEHRINGER INGELHEIM INTERNATIONAL GMBH BINGER STRASSE 173 D-55216 INGELHEIM AM RHEIN, GERMANY 011-49-61-32-77-2414 AND KLAUS H. JANDER, ESQ. CLIFFORD CHANCE ROGERS & WELLS LLP 200 PARK AVENUE NEW YORK, NY 10166 (212) 878-8000 ------------------------------------------------------------------ (Name, Address and Telephone Number of Person Authorized to Receive Notices and Communications) JUNE 5, 2000 ------------------------------------------------------------------ (Date of Event Which Requires Filing of This Statement) If the filing person has previously filed a statement on Schedule 13G to report the acquisition that is the subject of this Schedule 13D, and is filing this schedule because of Rule 13d-1(e), 13d-1(f) or 13d-1(g), check the following box / / Note. Schedules filed in paper format should include a signed original and five copies of the schedule, including all exhibits. See Rule 13d-7(b) for the other parties to whom copies are to be sent. (Continued on following pages) (Page 1 of 5 Pages)
2 - --------------------- ----------------- CUSIP NO. 464330 10 9 13D PAGE 2 OF 5 PAGES - --------------------- ----------------- - -------------------------------------------------------------------------------- 1. NAMES OF REPORTING PERSONS S.S. OR I.R.S. IDENTIFICATION NOS. OF ABOVE PERSONS (ENTITIES ONLY) Boehringer Ingelheim International GmbH - -------------------------------------------------------------------------------- 2. CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP (a) / / (b) / / - -------------------------------------------------------------------------------- 3. SEC USE ONLY - -------------------------------------------------------------------------------- 4. SOURCES OF FUNDS OO - -------------------------------------------------------------------------------- 5. CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDINGS IS REQUIRED PURSUANT TO ITEM 2(d) OR 2(e) / / - -------------------------------------------------------------------------------- 6. CITIZENSHIP OR PLACE OF ORGANIZATION Federal Republic of Germany - -------------------------------------------------------------------------------- 7. SOLE VOTING POWER 2,030,107 NUMBER OF ------------------------------------------------------------- UNITS 8. SHARED VOTING POWER BENEFICIALLY 0 OWNED BY ------------------------------------------------------------- EACH REPORTING 9. SOLE DISPOSITIVE POWER PERSON 2,030,107 WITH ------------------------------------------------------------- 10. SHARED DISPOSITIVE POWER 0 - -------------------------------------------------------------------------------- 11. AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON 2,030,107 - -------------------------------------------------------------------------------- 12. CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES CERTAIN SHARES / / - -------------------------------------------------------------------------------- 13. PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11) 5.5% - -------------------------------------------------------------------------------- 14. TYPE OF REPORTING PERSON CO - --------------------------------------------------------------------------------
3 SCHEDULE 13D FILED PURSUANT TO RULE 13d-1 OF THE GENERAL RULES AND REGULATIONS UNDER THE SECURITIES EXCHANGE ACT OF 1934, AS AMENDED This Amendment No. 3, which relates to shares of the common stock, par value $0.001 per share (the "Common Stock") of Isis Pharmaceuticals, Inc. (the "Issuer") and is being filed by Boehringer Ingelheim International GmbH ("Boehringer"), supplements and amends the statement on Schedule 13D, originally filed with the Commission on July 28, 1995, as amended by Amendment No. 1, filed with the Commission on December 23, 1996 and Amendment No. 2, filed with the Commission on September 2, 1999. ITEM 5. INTEREST IN THE SECURITIES OF THE ISSUER. Item 5 is hereby amended to read in its entirety as follows: (a) Beneficial Ownership: 2,030,107 Percentage Ownership: 5.5% (b) Sole Voting Power: 2,030,107 Shared Voting Power: -0- Sole Dispositive Power: 2,030,107 Shared Dispositive Power: -0- (c) Recent Transactions: The following table sets forth sales of shares of Common Stock by Boehringer since September 2, 1999. Such sales were effected on the open market over the Nasdaq Stock Market by a broker. APPROXIMATE PRICE AMOUNT OF PER SHARE DATE SHARES (exclusive of commissions) 3/23/00 10,000 $18.0688 3/29/00 20,000 $13.9263 3/30/00 20,000 $13.6075 4/3/00 20,000 $14.0000 4/5/00 20,000 $12.5125 4/5/00 20,000 $11.3388 4/6/00 40,000 $14.7729 4/7/00 21,600 $15.6079 4/11/00 3,800 $14.0000 4/12/00 20,000 $13.0000 5/2/00 20,000 $12.0775 5/3/00 20,000 $11.1016 5/4/00 9,600 $11.5078 5/5/00 20,000 $11.5000 5/15/00 20,000 $10.0109 5/16/00 20,000 $10.2538 5/18/00 20,000 $10.5141 5/19/00 6,600 $10.5000 5/22/00 1,900 $10.6140 6/2/00 20,000 $10.0863 6/5/00 9,000 $11.2688 6/5/00 20,000 $10.2500
4 (d) Right to Receive Dividends: Not Applicable (e) Ownership below 5%: Not Applicable
5 SIGNATURES After reasonable inquiry and to the best of my knowledge and belief, I certify that the information set forth in this statement is true, complete and correct. Dated: June 8, 2000 BOEHRINGER INGELHEIM INTERNATIONAL GmbH By: /s/ Mueller Name: Mr. Mueller Title: Authorized Signatory By: /s/ Joos Name: Mr. Joos Title: Authorized Signatory