SYNAPTIC PHARMACEUTICAL CORP
SC 13D/A, 1998-02-27
COMMERCIAL PHYSICAL & BIOLOGICAL RESEARCH
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<PAGE>
 
                       SECURITIES AND EXCHANGE COMMISSION
                            WASHINGTON, D.C.  20549
                              -------------------

                                  SCHEDULE 13D
                                 (RULE 13d-101)

                   UNDER THE SECURITIES EXCHANGE ACT OF 1934
                             (AMENDMENT NO. 2) /1/


                      SYNAPTIC PHARMACEUTICAL CORPORATION
                      -----------------------------------
                                (Name of Issuer)

                                  Common Stock
                                  ------------
                         (Title of Class of Securities)

                                  87156 R 109
                                  -----------
                                 (CUSIP Number)

                                   Hope Flack
                               BVF Partners L.P.
                       333 West Wacker Drive, Suite 1600
                            Chicago, Illinois  60606
                                 (312) 263-7777
                 --------------------------------------------
                 (Name, Address and Telephone Number of Person
               Authorized to Receive Notices and Communications)

                                January 26, 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 [ ].

          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).
<PAGE>
 
                                  SCHEDULE 13D

- -----------------------------                          -------------------------
CUSIP No.  87156 R 109                                 Page   2   of   7   Pages
- -----------------------------                          -------------------------

- --------------------------------------------------------------------------------
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) [_]

- --------------------------------------------------------------------------------
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
- --------------------------------------------------------------------------------
              7.  SOLE VOTING POWER
  NUMBER OF        -0-
   SHARES     ------------------------------------------------------------------
BENEFICIALLY  8.  SHARED VOTING POWER
  OWNED BY         515,592
 REPORTING    ------------------------------------------------------------------
  PERSON      9.  SOLE DISPOSITIVE POWER
   WITH            -0-
              ------------------------------------------------------------------
              10. SHARED DISPOSITIVE POWER
                   515,592
- --------------------------------------------------------------------------------
11. AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
     515,592
- --------------------------------------------------------------------------------
12. CHECK BOX IF THE AGGREGATE AMOUNT IN ROW 11 EXCLUDES CERTAIN SHARES* 
                                                                           [_]

- --------------------------------------------------------------------------------
13. PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 11
      4.9%
- --------------------------------------------------------------------------------
14. TYPE OF REPORTING PERSON*
      PN
- --------------------------------------------------------------------------------
                        *SEE INSTRUCTIONS BEFORE FILLING OUT!
<PAGE>
 
                                  SCHEDULE 13D

- -----------------------------                          -------------------------
CUSIP No.  87156 R 109                                 Page   3   of   7   Pages
- -----------------------------                          -------------------------

- --------------------------------------------------------------------------------
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) [_]

- --------------------------------------------------------------------------------
3. SEC USE ONLY

- --------------------------------------------------------------------------------
4. SOURCE OF FUNDS*
     OO
- --------------------------------------------------------------------------------
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
- --------------------------------------------------------------------------------
              7.  SOLE VOTING POWER
  NUMBER OF        -0-
   SHARES     ------------------------------------------------------------------
BENEFICIALLY  8.  SHARED VOTING POWER
  OWNED BY         1,022,192
 REPORTING    ------------------------------------------------------------------
  PERSON      9.  SOLE DISPOSITIVE POWER
   WITH            -0-
              ------------------------------------------------------------------
              10. SHARED DISPOSITIVE POWER
                   1,022,192
- --------------------------------------------------------------------------------
11. AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
      1,022,192
- --------------------------------------------------------------------------------
12. CHECK BOX IF THE AGGREGATE AMOUNT IN ROW 11 EXCLUDES CERTAIN SHARES* 
                                                                           [_]
      
- --------------------------------------------------------------------------------
13. PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 11
     9.7%
- --------------------------------------------------------------------------------
14. TYPE OF REPORTING PERSON*
     PN
- --------------------------------------------------------------------------------
                        *SEE INSTRUCTIONS BEFORE FILLING OUT!
<PAGE>
 
                                  SCHEDULE 13D

- -----------------------------                          -------------------------
CUSIP No.  87156 R 109                                 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, OO
- --------------------------------------------------------------------------------
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
- --------------------------------------------------------------------------------
              7.  SOLE VOTING POWER
  NUMBER OF        -0-
   SHARES     ------------------------------------------------------------------
BENEFICIALLY  8.  SHARED VOTING POWER
  OWNED BY         1,022,192
 REPORTING    ------------------------------------------------------------------
  PERSON      9.  SOLE DISPOSITIVE POWER
   WITH            -0-
              ------------------------------------------------------------------
              10. SHARED DISPOSITIVE POWER
                   1,022,192
- --------------------------------------------------------------------------------
11. AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
     1,022,192
- --------------------------------------------------------------------------------
12. CHECK BOX IF THE AGGREGATE AMOUNT IN ROW 11 EXCLUDES CERTAIN SHARES* 
                                                                           [_]

- --------------------------------------------------------------------------------
13. PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 11
     9.7%
- --------------------------------------------------------------------------------
14. TYPE OF REPORTING PERSON*
      IA, CO
- --------------------------------------------------------------------------------
                        *SEE INSTRUCTIONS BEFORE FILLING OUT!
<PAGE>
 
                                  SCHEDULE 13D

- -----------------------------                          -------------------------
CUSIP No.  87156 R 109                                 Page   5   of   7   Pages
- -----------------------------                          -------------------------


   This Amendment No. 2 (this "Amendment") relates to the Statement on Schedule
 13D dated March 19, 1997, as amended by Amendment No. 1 dated July 9, 1997 (as
 so amended, the "Statement"), filed with the Securities and Exchange Commission
 on behalf of BVF Partners L.P., a Delaware limited partnership ("Partners"),
 Biotechnology Value Fund, L.P., a Delaware limited partnership ("BVF") and BVF
 Inc., a Delaware corporation ("BVF Inc." and, together with BVF and Partners,
 the "Reporting Persons") with respect to the common stock, par value $0.01 per
 share (the "Stock"), of Synaptic Pharmaceutical Corporation, a Delaware
 corporation ("Synaptic").

     Item 3 is hereby amended to read in its entirety as follows:

ITEM 3.   SOURCE AND AMOUNT OF FUNDS OR OTHER CONSIDERATION.

     Since January 20, 1998, Partners, in its capacity as general partner of
BVF, has acquired on behalf of such limited partnership an aggregate number of
55,000 shares of the Stock for an aggregate consideration of $680,625, 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 managed accounts, has
acquired on behalf of such managed accounts an aggregate number of 109,900
shares of the Stock for an aggregate consideration of $1,297,347, utilizing
funds under management by Partners pursuant to investment manager agreements
between Partners and such managed accounts.

     Item 4 is hereby amended to read in its entirety as follows:

ITEM 4.   PURPOSE OF TRANSACTIONS.

     The sole purpose of the acquisitions and dispositions of the Stock reported
herein is and was for investment.  The Reporting Persons did not, at the time of
such acquisitions or dispositions of the Stock, and do not presently, have any
plan to acquire control of Synaptic or to entirely dispose of the Stock.  The
Reporting Persons may acquire or dispose of additional shares of the Stock from
time to time.

     Item 5 is hereby amended to read in its entirety as follows:

ITEM 5.   INTEREST IN SECURITIES OF THE ISSUER.

     (a) BVF beneficially owns 515,592 shares of the Stock, Partners
beneficially owns 1,022,192 shares of the Stock and BVF Inc. beneficially owns
1,022,192 shares of the Stock, approximately 4.9%, 9.7% and 9.7%, respectively,
of the aggregate number of shares outstanding as of November 5, 1997 (as
reported in Synaptic's most recent quarterly statement on Form 10-Q).
<PAGE>
 
                                  SCHEDULE 13D

- -----------------------------                          -------------------------
CUSIP No.  87156 R 109                                 Page   6   of   7   Pages
- -----------------------------                          -------------------------

     (b) BVF shares voting and dispositive power over the 515,592 shares of the
Stock it beneficially owns with Partners.  Partners and BVF Inc. share voting
and dispositive power over the 1,022,192 shares of the Stock they beneficially
own with, in addition to BVF, the managed accounts on whose behalf Partners, as
investment manager, purchased such shares. The managed accounts on whose behalf
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.").   ILL10, Palamundo, ZPG
and BVF Ltd. 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 c/o BVF Partners L.P., 333 West Wacker Drive,
Suite 1600, Chicago, Illinois 60606.

     (c) Exhibit B attached hereto contains information as to all transactions
in the Stock by the Reporting Persons during the past 60 days.  All such
transactions were made for cash in open market, over-the-counter transactions.
No other transactions in the Stock have been effected by the Reporting Persons
during the past 60 days.

     (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.   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>
 
                                  SCHEDULE 13D

- -----------------------------                          -------------------------
CUSIP No.  87156 R 109                                 Page   7   of   7   Pages
- -----------------------------                          -------------------------

     After reasonable inquiry and to the best of my knowledge and belief, I
certify that the information set forth in this Amendment is true, complete and
correct.

Dated:  February 27, 1998

     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, 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:  February 27, 1998

     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 LAST 60 DAYS
                            -----------------------


<TABLE>
<CAPTION>
Settlement       By          For the     Quantity     Price     Type of Trade   Broker
  Date       -----------   Account of    --------      per      -------------   ------
- ----------                 -----------                Share
                                                    ---------
======================================================================================
<C>          <S>           <C>           <C>        <C>         <C>             <C>
  01/20/98   BVF Ltd.      Partners        60,000    $11.3750   Purchase        MLCO
- --------------------------------------------------------------------------------------
  01/20/98   BVF Ltd.      Partners         3,900    $11.7500   Purchase        INET
- --------------------------------------------------------------------------------------
  01/23/98   BVF Ltd.      Partners         1,000    $12.0000   Purchase        INET
- --------------------------------------------------------------------------------------
  01/26/98   BVF           Partners        55,000    $12.3750   Purchase        BEST
- --------------------------------------------------------------------------------------
  01/26/98   PAL           Partners         5,000    $12.3750   Purchase        BEST
- --------------------------------------------------------------------------------------
  01/26/98   BVF Ltd.      Partners        40,000    $12.3750   Purchase        BEST
- --------------------------------------------------------------------------------------
</TABLE>

   INET  =   Instinet
   MLCO  =   Merrill Lynch & Co.
   BEST  =   Bear Stearns


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