SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 SCHEDULE 13G (RULE 13d-102) INFORMATION TO BE INCLUDED IN STATEMENTS FILED PURSUANT TO RULES 13D-1(b) (c) AND (d) AND AMENDMENTS THERETO FILED PURSUANT TO 13d-2(b) (AMENDMENT NO. 2)1 GENOME THERAPEUTICS CORP. ------------------------- (Name of Issuer) COMMON STOCK ----------------------------- (Title of Class of Securities) 372430 10 8 ----------- (CUSIP Number) JUNE 11, 2001 ------------- (Date of Event Which Requires Filing of this Statement) Check the appropriate box to designate the rule pursuant to which this Schedule is filed: |_| Rule 13d-1(b) |X| Rule 13d-1(c) |_| Rule 13d-1(d) ------------------ (1) The remainder of this cover page shall be filled out for a reporting person's initial filing on this form with respect to the subject class of securities, and for any subsequent amendment containing information which would alter disclosures provided in a prior cover page. The information required on the remainder of this cover page shall not be deemed to be "filed" for the purpose of Section 18 of the Securities Exchange Act of 1934 or otherwise subject to the liabilities of that section of the Act but shall be subject to all other provisions of the Act (however, SEE the NOTES). ---------------------------- ---------------------------- CUISP NO. 372430 10 8 13G PAGE 2 OF 9 ---------------------------- ---------------------------- --------- ---------------------------------------------------------------------- 1 NAME OF REPORTING PERSON: BIOTECHNOLOGY VALUE FUND, L.P. I.R.S. IDENTIFICATION NO. OF ABOVE PERSON (ENTITIES ONLY): --------- ---------------------------------------------------------------------- 2 CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP* (a) |X| (b) |_| --------- ---------------------------------------------------------------------- 3 SEC USE ONLY --------- ---------------------------------------------------------------------- 4 CITIZENSHIP OR PLACE OF ORGANIZATION DELAWARE -------------------------- ----- ----------------------------------------------- NUMBER 5 SOLE VOTING POWER OF 0 SHARES ----- ----------------------------------------------- BENEFICIALLY 6 SHARED VOTING POWER OWNED BY EACH 263,000 REPORTING ----- ----------------------------------------------- PERSON 7 SOLE DISPOSITIVE POWER WITH 0 ----- ----------------------------------------------- 8 SHARED DISPOSITIVE POWER 263,000 --------- ---------------------------------------------------------------------- 9 AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON 263,000 --------- ---------------------------------------------------------------------- 10 CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES* |_| --------- ---------------------------------------------------------------------- 11 PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9 1.2% --------- ---------------------------------------------------------------------- 12 TYPE OF REPORTING PERSON* PN --------- ---------------------------------------------------------------------- * SEE INSTRUCTIONS BEFORE FILLING OUT! ---------------------------- ---------------------------- CUISP NO. 372430 10 8 13G PAGE 3 OF 9 ---------------------------- ---------------------------- --------- ---------------------------------------------------------------------- 1 NAME OF REPORTING PERSON: BIOTECHNOLOGY VALUE FUND II, L.P. I.R.S. IDENTIFICATION NO. OF ABOVE PERSON (ENTITIES ONLY): --------- ---------------------------------------------------------------------- 2 CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP* (a) |X| (b) |_| --------- ---------------------------------------------------------------------- 3 SEC USE ONLY --------- ---------------------------------------------------------------------- 4 CITIZENSHIP OR PLACE OF ORGANIZATION DELAWARE -------------------------- ----- ----------------------------------------------- NUMBER 5 SOLE VOTING POWER OF 0 SHARES ----- ----------------------------------------------- BENEFICIALLY 6 SHARED VOTING POWER OWNED BY EACH 118,124 REPORTING ----- ----------------------------------------------- PERSON 7 SOLE DISPOSITIVE POWER WITH 0 ----- ----------------------------------------------- 8 SHARED DISPOSITIVE POWER 118,124 --------- ---------------------------------------------------------------------- 9 AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON 118,124 --------- ---------------------------------------------------------------------- 10 CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES* |_| --------- ---------------------------------------------------------------------- 11 PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9 0.8% --------- ---------------------------------------------------------------------- 12 TYPE OF REPORTING PERSON* PN --------- ---------------------------------------------------------------------- * SEE INSTRUCTIONS BEFORE FILLING OUT! ---------------------------- ---------------------------- CUISP NO. 372430 10 8 13G PAGE 4 OF 9 ---------------------------- ---------------------------- --------- ---------------------------------------------------------------------- 1 NAME OF REPORTING PERSON: BVF INVESTMENTS, L.L.C. I.R.S. IDENTIFICATION NO. OF ABOVE PERSON (ENTITIES ONLY): --------- ---------------------------------------------------------------------- 2 CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP* (a) |X| (b) |_| --------- ---------------------------------------------------------------------- 3 SEC USE ONLY --------- ---------------------------------------------------------------------- 4 CITIZENSHIP OR PLACE OF ORGANIZATION DELAWARE -------------------------- ----- ----------------------------------------------- NUMBER 5 SOLE VOTING POWER OF 0 SHARES ----- ----------------------------------------------- BENEFICIALLY 6 SHARED VOTING POWER OWNED BY EACH 94,576 REPORTING ----- ----------------------------------------------- PERSON 7 SOLE DISPOSITIVE POWER WITH 0 ----- ----------------------------------------------- 8 SHARED DISPOSITIVE POWER 94,576 --------- ---------------------------------------------------------------------- 9 AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON 94,576 --------- ---------------------------------------------------------------------- 10 CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES* |_| --------- ---------------------------------------------------------------------- 11 PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9 0.4% --------- ---------------------------------------------------------------------- 12 TYPE OF REPORTING PERSON* OO --------- ---------------------------------------------------------------------- * SEE INSTRUCTIONS BEFORE FILLING OUT! ---------------------------- ---------------------------- CUISP NO. 372430 10 8 13G PAGE 5 OF 9 ---------------------------- ---------------------------- --------- ---------------------------------------------------------------------- 1 NAME OF REPORTING PERSON: BVF PARTNERS L.P. I.R.S. IDENTIFICATION NO. OF ABOVE PERSON (ENTITIES ONLY): --------- ---------------------------------------------------------------------- 2 CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP* (a) |X| (b) |_| --------- ---------------------------------------------------------------------- 3 SEC USE ONLY --------- ---------------------------------------------------------------------- 4 CITIZENSHIP OR PLACE OF ORGANIZATION DELAWARE -------------------------- ----- ----------------------------------------------- NUMBER 5 SOLE VOTING POWER OF 0 SHARES ----- ----------------------------------------------- BENEFICIALLY 6 SHARED VOTING POWER OWNED BY EACH 587,800 REPORTING ----- ----------------------------------------------- PERSON 7 SOLE DISPOSITIVE POWER WITH 0 ----- ----------------------------------------------- 8 SHARED DISPOSITIVE POWER 587,800 --------- ---------------------------------------------------------------------- 9 AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON 587,800 --------- ---------------------------------------------------------------------- 10 CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES* |_| --------- ---------------------------------------------------------------------- 11 PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9 2.6% --------- ---------------------------------------------------------------------- 12 TYPE OF REPORTING PERSON* PN --------- ---------------------------------------------------------------------- * SEE INSTRUCTIONS BEFORE FILLING OUT! ---------------------------- ---------------------------- CUISP NO. 372430 10 8 13G PAGE 6 OF 9 ---------------------------- ---------------------------- --------- ---------------------------------------------------------------------- 1 NAME OF REPORTING PERSON: BVF INC. I.R.S. IDENTIFICATION NO. OF ABOVE PERSON (ENTITIES ONLY): --------- ---------------------------------------------------------------------- 2 CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP* (a) |X| (b) |_| --------- ---------------------------------------------------------------------- 3 SEC USE ONLY --------- ---------------------------------------------------------------------- 4 CITIZENSHIP OR PLACE OF ORGANIZATION DELAWARE -------------------------- ----- ----------------------------------------------- NUMBER 5 SOLE VOTING POWER OF 0 SHARES ----- ----------------------------------------------- BENEFICIALLY 6 SHARED VOTING POWER OWNED BY EACH 587,800 REPORTING ----- ----------------------------------------------- PERSON 7 SOLE DISPOSITIVE POWER WITH 0 ----- ----------------------------------------------- 8 SHARED DISPOSITIVE POWER 587,800 --------- ---------------------------------------------------------------------- 9 AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON 587,800 --------- ---------------------------------------------------------------------- 10 CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES* |_| --------- ---------------------------------------------------------------------- 11 PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9 2.6% --------- ---------------------------------------------------------------------- 12 TYPE OF REPORTING PERSON* IA, CO --------- ---------------------------------------------------------------------- * SEE INSTRUCTIONS BEFORE FILLING OUT! ---------------------------- ---------------------------- CUISP NO. 372430 10 8 13G PAGE 7 OF 9 ---------------------------- ---------------------------- ITEM 1(a). NAME OF ISSUER: Genome Therapeutics Corp. ("Genome") ITEM 1(b). ADDRESS OF ISSUER'S PRINCIPAL EXECUTIVE OFFICES: 100 Beaver Street Waltham, Massachusetts 02154 ITEM 2(a). NAME OF PERSON FILING: This Amendment to Schedule 13G is being filed on behalf of the following persons* (the "Reporting Persons"): (i) Biotechnology Value Fund, L.P. ("BVF") (ii) Biotechnology Value Fund II, L.P. ("BVF2") (iii) BVF Investments, L.L.C. ("Investments") (iv) BVF Partners L.P. ("Partners") (v) BVF Inc. ("BVF Inc.") * Attached as Exhibit 1 is a copy of an agreement among the Reporting Persons filing (as specified hereinabove) that this Amendment to Schedule 13G is being filed on behalf of each of them. ITEM 2(b). ADDRESS OF PRINCIPAL BUSINESS OFFICE: The principal business office of the Reporting Persons comprising the group filing this Amendment to Schedule 13G is located at 227 West Monroe Street, Suite 4800, Chicago, Illinois, 60606. ITEM 2(c). CITIZENSHIP: BVF: a Delaware limited partnership BVF2: a Delaware limited partnership Investments: a Delaware limited liability company Partners: a Delaware limited partnership BVF Inc.: a Delaware corporation ITEM 2(d). TITLE OF CLASS OF SECURITIES: Common Stock, $0.10 par value. ITEM 2(e). CUSIP NUMBER: 372430 10 8 ---------------------------- ---------------------------- CUISP NO. 372430 10 8 13G PAGE 8 OF 9 ---------------------------- ---------------------------- ITEM 3. IF THIS STATEMENT IS FILED PURSUANT TO RULE 13d-1(b), OR 13d-2(b) OR (c) CHECK WHETHER THE PERSON FILING IS: ONE OF THE FOLLOWING Not applicable as this Amendment to Schedule 13G is filed pursuant to Rule 13d 1(c). ITEM 4. OWNERSHIP: The information in items 1 and 5 through 11 on the cover pages (pp. 2-6) on this Amendment to Schedule 13G is hereby incorporated by reference. ITEM 5. OWNERSHIP OF FIVE PERCENT OR LESS OF A CLASS: If this statement is being filed to report the fact that as of the date hereof the Reporting Persons have ceased to be the beneficial owner of more than five percent of the class of securities check the following. |X| ITEM 6. OWNERSHIP OF MORE THAN FIVE PERCENT ON BEHALF OF ANOTHER PERSON: BVF shares voting and dispositive power over the shares of the common stock it beneficially owns with Partners. BVF2 also shares voting and dispositive power over the shares of the common stock it beneficially owns with Partners. Investments also shares voting and dispositive power over the shares of the common stock it beneficially owns with Partners. Partners and BVF Inc. share voting and dispositive power over the shares of the common stock they beneficially own with, in addition to BVF, BVF2 and Investments, certain managed accounts on whose behalf Partners, as investment manager, purchased such shares. None of the managed accounts individually owns more than 5% of the common stock of Genome. ITEM 7. IDENTIFICATION AND CLASSIFICATION OF THE SUBSIDIARY WHICH ACQUIRED THE SECURITY BEING REPORTED ON BY THE PARENT HOLDING COMPANY: Not applicable. ITEM 8. IDENTIFICATION AND CLASSIFICATION OF MEMBERS OF A GROUP: Not applicable. ITEM 9. NOTICE OF DISSOLUTION OF GROUP: Not applicable. ---------------------------- ---------------------------- CUISP NO. 372430 10 8 13G PAGE 9 OF 9 ---------------------------- ---------------------------- ITEM 10. CERTIFICATION By signing below I certify that, to the best of my knowledge and belief, the securities referred to above were not acquired and are not held for the purpose of or with the effect of changing or influencing the control of the issuer of the securities and were not acquired and are not held in connection with or as a participant in any transaction having that purpose or effect. 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 15, 2001 BIOTECHNOLOGY VALUE FUND, L.P. By: BVF Partners L.P., its general partner By: BVF Inc., its general partner By: /s/ MARK N. LAMPERT ------------------------------------ Mark N. Lampert President BIOTECHNOLOGY VALUE FUND II, L.P. By: BVF Partners L.P., its general partner By: BVF Inc., its general partner By: /s/ MARK N. LAMPERT ------------------------------------ Mark N. Lampert President BVF INVESTMETNS L.L.C. By: BVF Partners L.P., its manager By: BVF Inc., its general partner By: /s/ MARK N. LAMPERT ------------------------------------ Mark N. Lampert President BVF PARTNERS L.P. By: BVF Inc., its general partner By: /s/ MARK N. LAMPERT ------------------------------------ Mark N. Lampert President BVF INC. By: /s/ MARK N. LAMPERT ------------------------------------ Mark N. Lampert President