<PAGE>
SECURITIES AND EXCHANGE COMMISSION
WASHINGTON, D.C. 20549
SCHEDULE 13D
UNDER THE SECURITIES EXCHANGE ACT OF 1934
(AMENDMENT NO. 3)(1)
GENOME THERAPEUTICS CORPORATION
-------------------------------
(Name of Issuer)
Common Stock
------------
(Title of Class of Securities)
372430 10 8
-----------
(CUSIP Number)
Hope Flack
BVF Partners L.P.
227 West Monroe Drive, Suite 4800
Chicago, Illinois 60606
(312) 263-7777
--------------------------------------------
(Name, Address and Telephone Number of Person
Authorized to Receive Notices and Communications)
December 23, 1998
-----------------
(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 which is the subject of this Schedule 13D, and is filing
this schedule because of Rule 13d-1(b)(3) or (4), check the following box / /.
Check the following box if a fee is being paid with the statement / /. (A
fee is not required only if the reporting person: (1) has a previous statement
on file reporting beneficial ownership of more than five percent of the class of
securities described in Item 1; and (2) has filed no amendment subsequent
thereto reporting beneficial ownership of five percent or less of such class.)
(See Rule 13d-7.)
NOTE: Six copies of this statement, including all exhibits, should be
filed with the Commission. SEE Rule 13d-1(a) for other parties to whom
copies are to be sent.
(Continued on following pages)
(Page 1 of 7 Pages)
- ------------------
(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).
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CUSIP NO. 372430 10 8 13D Page 2 of 7 Pages
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- -------------------------------------------------------------------------------
1 NAME OF REPORTING PERSONS
S.S. OR I.R.S. IDENTIFICATION NOS. OF ABOVE PERSONS
BIOTECHNOLOGY VALUE FUND, L.P.
- -------------------------------------------------------------------------------
2 CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*
(a) /X/ (b) / /
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3 SEC USE ONLY
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4 SOURCE OF FUNDS*
WC
- -------------------------------------------------------------------------------
5 CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDING IS
REQUIRED PURSUANT TO ITEMS 2(d) OR 2(e) / /
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6 CITIZENSHIP OR PLACE OF ORGANIZATION
DELAWARE
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NUMBER 7 SOLE VOTING POWER
OF -0-
SHARES --------------------------------------------
BENEFICIALLY 8 SHARED VOTING POWER
OWNED BY 824,763
REPORTING --------------------------------------------
PERSON 9 SOLE DISPOSITIVE POWER
WITH -0-
--------------------------------------------
10 SHARED DISPOSITIVE POWER
824,763
- -------------------------------------------------------------------------------
11 AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH
REPORTING PERSON
824,763
- -------------------------------------------------------------------------------
12 CHECK BOX IF THE AGGREGATE AMOUNT IN ROW 11 EXCLUDES
CERTAIN SHARES* / /
- -------------------------------------------------------------------------------
13 PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 11
4.5%
- -------------------------------------------------------------------------------
14 TYPE OF REPORTING PERSON*
PN
- -------------------------------------------------------------------------------
* SEE INSTRUCTIONS BEFORE FILLING OUT!
<PAGE>
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CUSIP NO. 372430 10 8 13D Page 3 of 7 Pages
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1 NAME OF REPORTING PERSONS
S.S. OR I.R.S. IDENTIFICATION NOS. OF ABOVE PERSONS
BVF PARTNERS L.P.
- -------------------------------------------------------------------------------
2 CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*
(a) /X/ (b) / /
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3 SEC USE ONLY
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4 SOURCE OF FUNDS*
WC
- -------------------------------------------------------------------------------
5 CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDING IS
REQUIRED PURSUANT TO ITEMS 2(d) OR 2(e) / /
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6 CITIZENSHIP OR PLACE OF ORGANIZATION
DELAWARE
- -------------------------------------------------------------------------------
NUMBER 7 SOLE VOTING POWER
OF -0-
SHARES --------------------------------------------
BENEFICIALLY 8 SHARED VOTING POWER
OWNED BY 1,552,089
REPORTING --------------------------------------------
PERSON 9 SOLE DISPOSITIVE POWER
WITH -0-
--------------------------------------------
10 SHARED DISPOSITIVE POWER
1,552,089
- -------------------------------------------------------------------------------
11 AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH
REPORTING PERSON
1,552,089
- -------------------------------------------------------------------------------
12 CHECK BOX IF THE AGGREGATE AMOUNT IN ROW 11 EXCLUDES
CERTAIN SHARES* / /
- -------------------------------------------------------------------------------
13 PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 11
8.5%
- -------------------------------------------------------------------------------
14 TYPE OF REPORTING PERSON*
PN
- -------------------------------------------------------------------------------
* SEE INSTRUCTIONS BEFORE FILLING OUT!
<PAGE>
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CUSIP NO. 372430 10 8 13D Page 4 of 7 Pages
- --------------------- -----------------
- -------------------------------------------------------------------------------
1 NAME OF REPORTING PERSONS
S.S. OR I.R.S. IDENTIFICATION NOS. OF ABOVE PERSONS
BVF INC.
- -------------------------------------------------------------------------------
2 CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*
(a) /X/ (b) / /
- -------------------------------------------------------------------------------
3 SEC USE ONLY
- -------------------------------------------------------------------------------
4 SOURCE OF FUNDS*
WC
- -------------------------------------------------------------------------------
5 CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDING IS
REQUIRED PURSUANT TO ITEMS 2(d) OR 2(e) / /
- -------------------------------------------------------------------------------
6 CITIZENSHIP OR PLACE OF ORGANIZATION
DELAWARE
- -------------------------------------------------------------------------------
NUMBER 7 SOLE VOTING POWER
OF -0-
SHARES --------------------------------------------
BENEFICIALLY 8 SHARED VOTING POWER
OWNED BY 1,769,285
REPORTING --------------------------------------------
PERSON 9 SOLE DISPOSITIVE POWER
WITH -0-
--------------------------------------------
10 SHARED DISPOSITIVE POWER
1,769,285
- -------------------------------------------------------------------------------
11 AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH
REPORTING PERSON
1,769,285
- -------------------------------------------------------------------------------
12 CHECK BOX IF THE AGGREGATE AMOUNT IN ROW 11 EXCLUDES
CERTAIN SHARES* / /
- -------------------------------------------------------------------------------
13 PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 11
9.6%
- -------------------------------------------------------------------------------
14 TYPE OF REPORTING PERSON*
IA, CO
- -------------------------------------------------------------------------------
* SEE INSTRUCTIONS BEFORE FILLING OUT!
<PAGE>
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CUSIP NO. 372430 10 8 13D Page 5 of 7 Pages
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This Amendment No. 3 (this "Amendment") relates to the Statement on
Schedule 13D, dated March 20, 1995, and filed with the Securities and Exchange
Commission (the "SEC") on March 28, 1995, as amended by Amendment No. 1, dated
July 21, 1995 and Amendment No.2, dated February 22, 1996 filed with the SEC on
behalf of Biotechnology Value Fund, L.P., a Delaware limited partnership
("BVF"), BVF Partners L.P., a Delaware limited partnership ("BVF Partners"), and
BVF Inc., a Delaware corporation ("BVF Inc."), with respect to the common stock,
par value $0.10 (the "Stock"), of Genome Therapeutics Corporation ("Genome").
ITEM 3. SOURCE AND AMOUNT OF FUNDS OR OTHER CONSIDERATION.
Since January 20, 1999, Partners, in its capacity as general partner of
BVF, has purchased on behalf of such limited partnership an aggregate number
of 369,400 shares of the Stock for an aggregate consideration of
$1,159,790.94, utilizing funds provided by BVF from its working capital
pursuant to the terms of its limited partnership agreement with Partners. In
addition, Partners, in its capacity as investment manager with respect to
certain other accounts, has purchased on behalf of such accounts an aggregate
number of 349,300 shares of the Stock for an aggregate consideration of
$1,101,610.55, utilizing funds under management by Partners pursuant to
investment management agreements between Partners and such accounts. The
managed accounts on whose behalf BVF Partners owns shares of the Stock are
Investment 10 L.L.C., an Illinois limited liability company ("ILL10"),
Palamundo, L.D.C., a limited duration company organized under the laws of the
Cayman Islands ("Palamundo"), ZPG Securities, L.L.C., a New York limited
liability company ("ZPG"), and Biotechnology Value Fund, Ltd., a Cayman
Islands Corporation ("BVF Ltd."). The managed accounts on whose behalf BVF
Inc. owns shares of the Stock are Biotech 1 Investment L.L.C., an Illinois
limited liability company ("Biotech 1"), and Biotech 2 Investment L.L.C., an
Illinois limited liability company ("Biotech 2"). ILL10, ZPG, Palamundo, BVF
Ltd., Biotech 1 and Biotech 2 are collectively referred to herein as the
"Accounts." The Accounts specialize in holding biotechnology stocks for
investment purposes and the business address of each is Grosvenor Capital
Management, L.P., 227 West Monroe Drive, Suite 4800, Chicago, Illinois 60606.
ITEM 5. INTEREST IN SECURITIES OF THE ISSUER.
(a) BVF beneficially owns 824,763 shares of the Stock, BVF Partners
beneficially owns 1,552,089 shares of the Stock and BVF Inc. beneficially
owns 1,769,285 shares of the Stock, approximately 4.5%, 8.5% and 9.6%,
respectively, of the aggregate number of shares outstanding as of January 11,
1999 (as reported in Genome's most recent quarterly statement on Form 10-Q).
(b) BVF shares voting and dispositive power over the 824,763 shares of
the Stock it beneficially owns with BVF Partners. BVF Partners shares voting
and dispositive power over the 1,552,089 shares of the Stock it beneficially
owns with, in addition to BVF, BVF Inc. and the managed account on whose behalf
BVF Partners, as investment manager, purchased such shares. BVF Inc. shares
voting and dispositive power over the 1,769,285 shares of the Stock it
beneficially owns with BVF, BVF Partners and the managed accounts on whose
behalf BVF Inc., as investment manager, purchased such shares.
<PAGE>
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CUSIP NO. 372430 10 8 13D Page 6 of 7 Pages
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(c) Exhibit B attached hereto contains information as to all transactions
in the Stock by the Reporting Persons during the last 60 days. All such
transactions were made for cash in open market, over-the-counter transactions.
Except as provided below, no other transactions in the Stock have been effected
by the Reporting Persons during the last 60 days. On January 26, 1999, Partners
transferred 11,275 shares of Stock that it owned on behalf of Palamundo to BVF
and transferred 9,225 shares of Stock that it owned on behalf of Palamundo to
BVF, Ltd. Additionally, on February 11, 1999, Partners transferred 8,000 shares
of Stock that it owned on behalf of ILL10 to BVF and transferred 6,000 shares of
Stock that it owned on behalf of ILL10 to BVF, Ltd. The aggregate number of
shares of the Stock beneficially owned by Partners and BVF Inc. was not affected
by these transfers.
(d) The Accounts are entitled to receive dividends and any sale proceeds
with respect to the Stock in proportion to their respective ownership interests
therein.
Item 7 is hereby amended to read in its entirety as follows:
ITEM 7. MATERIAL TO BE FILED AS EXHIBITS.
Exhibit A - Agreement Regarding Joint Filing
Exhibit B - Transactions in the Stock by the Reporting Persons during the
last 60 days.
<PAGE>
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CUSIP NO. 372430 10 8 13D Page 7 of 7 Pages
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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: March 24, 1999
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
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
<PAGE>
EXHIBIT A
AGREEMENT REGARDING JOINT FILING
The undersigned, Biotechnology Value Fund, L.P., a Delaware limited
partnership, and BVF Partners L.P., a Delaware limited partnership, and BVF
Inc., a Delaware corporation, hereby agree and acknowledge that the Amendment
containing the information required by Schedule 13D, to which this Agreement is
attached as an exhibit, is filed on behalf of each of them. The undersigned
further agree that any further amendments or supplements thereto shall also be
filed on behalf of each of them.
Dated: March 24, 1999
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
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
<PAGE>
EXHIBIT B
TRANSACTIONS IN THE STOCK BY THE REPORTING PERSONS
DURING THE PAST SIXTY DAYS
<TABLE>
<CAPTION>
- --------------------------------------------------------------------------------------------------
Trade Date By For the Account of Quantity Price per Share Type of Trade Broker
---------- -- ------------------ -------- --------------- ------------- ------
<S> <C> <C> <C> <C> <C> <C>
02/25/99 Partners ILL10 2,000 $3.2500 Purchase INET
- --------------------------------------------------------------------------------------------------
02/26/99 Partners BVF 6,000 $3.2500 Purchase INET
- --------------------------------------------------------------------------------------------------
02/26/99 Partners ILL10 3,500 $3.2500 Purchase INET
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02/26/99 Partners BVF Ltd. 10,000 $3.2500 Purchase INET
- --------------------------------------------------------------------------------------------------
03/01/99 Partners BVF 6,000 $3.3059 Purchase INET
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03/01/99 Partners ILL10 2,900 $3.3059 Purchase INET
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03/01/99 Partners ZPG 2,000 $3.3059 Purchase INET
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03/01/99 Partners BVF Ltd. 22,000 $3.3059 Purchase INET
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03/02/99 Partners BVF 3,000 $3.3125 Purchase INET
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03/02/99 Partners BVF Ltd. 2,000 $3.3125 Purchase INET
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03/03/99 Partners BVF 6,000 $3.2500 Purchase INET
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03/03/99 Partners ILL10 1,500 $3.2500 Purchase INET
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03/04/99 Partners BVF 4,000 $3.1875 Purchase INET
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03/04/99 Partners BVF Ltd. 4,000 $3.1875 Purchase INET
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03/05/99 Partners BVF 4,600 $3.1250 Purchase INET
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03/15/99 Partners BVF 2,000 $3.0625 Purchase INET
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03/16/99 Partners BVF 225,000 $3.1250 Purchase JONE
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03/16/99 Partners ILL10 5,000 $3.1250 Purchase JONE
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03/16/99 Partners BVF Ltd. 190,000 $3.1250 Purchase JONE
- --------------------------------------------------------------------------------------------------
03/16/99 Partners BVF 31,800 $3.1048 Purchase INET
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</TABLE>
<PAGE>
<TABLE>
<CAPTION>
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Trade Date By For the Account of Quantity Price per Share Type of Trade Broker
---------- -- ------------------ -------- --------------- ------------- ------
<S> <C> <C> <C> <C> <C> <C>
- --------------------------------------------------------------------------------------------------
03/16/99 Partners BVF Ltd. 25,000 $3.1048 Purchase INET
- --------------------------------------------------------------------------------------------------
03/17/99 Partners BVF 27,000 $3.1250 Purchase INET
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03/17/99 Partners BVF Ltd. 23,000 $3.1250 Purchase INET
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03/19/99 Partners BVF 9,000 $3.1136 Purchase INET
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03/19/99 Partners ILL10 5,400 $3.1136 Purchase INET
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03/19/99 Partners BVF Ltd. 9,000 $3.1136 Purchase INET
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03/22/99 Partners BVF 45,000 $3.1250 Purchase INET
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03/22/99 Partners ILL10 5,000 $3.1250 Purchase INET
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03/22/99 Partners BVF Ltd. 37,000 $3.1250 Purchase INET
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</TABLE>
INET = Instinet
JONE = Jones & Associates
