SYNAPTIC PHARMACEUTICAL CORP
SC 13D/A, 1999-03-31
COMMERCIAL PHYSICAL & BIOLOGICAL RESEARCH
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<PAGE>

                          SECURITIES AND EXCHANGE COMMISSION
                                WASHINGTON, DC  20549



                                     SCHEDULE 13D
                                    (RULE 13d-101)

           INFORMATION TO BE INCLUDED IN STATEMENTS FILED PURSUANT TO 13d-
                1(a) AND AMENDMENTS THERETO FILED PURSUANT TO 13d-2(a)

                                 (AMENDMENT NO. 2)(1)

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

                                     COMMON STOCK
                                     ------------
                            (Title of Class of Securities)

                                     87156R 10 9
                                     -----------
                                    (CUSIP Number)

                                   Marc Schneidman
                                  BVF Partners L.P.
                          227 West Monroe Street, Suite 4800
                               Chicago, Illinois  60606
                                    (312) 263-7777
                          ----------------------------------
                    (Name, Address and Telephone Number of Person
                  Authorized to Receive Notices and Communications)

                                    March 19, 1999
                                    --------------
               (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)


- ---------------
(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>

- -----------------------------                    -------------------------------
CUSIP NO. 87156R 10 9                 13D            Page 2 of 7 Pages
- -----------------------------                    -------------------------------

- --------------------------------------------------------------------------------
   1     NAME OF REPORTING PERSONS
         I.R.S. IDENTIFICATION NOS. OF ABOVE PERSONS (ENTITIES ONLY)
              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 PROCEEDINGS IS
         REQUIRED PURSUANT TO ITEMS 2(d) OR 2(e)     / /
- --------------------------------------------------------------------------------
   6     CITIZENSHIP OR PLACE OF ORGANIZATION
              DELAWARE
- --------------------------------------------------------------------------------
                     7    SOLE VOTING POWER
                               -0-
    NUMBER OF      -------------------------------------------------------------
      SHARES         8    SHARED VOTING POWER
   BENEFICIALLY                677,867
     OWNED BY      -------------------------------------------------------------
       EACH          9    SOLE DISPOSITIVE POWER
    REPORTING                  -0-
   PERSON WITH     -------------------------------------------------------------
                     10   SHARED DISPOSITIVE POWER
                               677,867
- --------------------------------------------------------------------------------
   11    AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
              677,867
- --------------------------------------------------------------------------------
   12    CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES
         CERTAIN SHARES*    / /
- --------------------------------------------------------------------------------
   13    PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11)
              6.3%
- --------------------------------------------------------------------------------
   14    TYPE OF REPORTING PERSON*
              PN
- --------------------------------------------------------------------------------


                        * SEE INSTRUCTIONS BEFORE FILLING OUT!
<PAGE>

- -----------------------------                    -------------------------------
CUSIP NO. 87156R 10 9                 13D            Page 3 of 7 Pages
- -----------------------------                    -------------------------------

- --------------------------------------------------------------------------------
    1    NAME OF REPORTING PERSONS
         I.R.S. IDENTIFICATION NOS. OF ABOVE PERSONS (ENTITIES ONLY)
              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 PROCEEDINGS IS
         REQUIRED PURSUANT TO ITEMS 2(d) OR 2(e)    / /
- --------------------------------------------------------------------------------
    6    CITIZENSHIP OR PLACE OF ORGANIZATION
              DELAWARE
- --------------------------------------------------------------------------------
                     7    SOLE VOTING POWER
                               -0-
    NUMBER OF      -------------------------------------------------------------
      SHARES         8    SHARED VOTING POWER
   BENEFICIALLY                1,317,317
     OWNED BY      -------------------------------------------------------------
       EACH          9    SOLE DISPOSITIVE POWER
    REPORTING                  -0-
   PERSON WITH     -------------------------------------------------------------
                     10   SHARED DISPOSITIVE POWER
                               1,317,317
- --------------------------------------------------------------------------------
   11    AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
              1,317,317
- --------------------------------------------------------------------------------
   12    CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES
         CERTAIN SHARES*     / /
- --------------------------------------------------------------------------------
   13    PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11)
              12.3%
- --------------------------------------------------------------------------------
   14    TYPE OF REPORTING PERSON*
              PN
- --------------------------------------------------------------------------------


                        * SEE INSTRUCTIONS BEFORE FILLING OUT!
<PAGE>

- -----------------------------                    -------------------------------
CUSIP NO. 87156R 10 9                 13D            Page 4 of 7 Pages
- -----------------------------                    -------------------------------

- --------------------------------------------------------------------------------
    1    NAME OF REPORTING PERSONS
         I.R.S. IDENTIFICATION NOS. OF ABOVE PERSONS (ENTITIES ONLY)
              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 PROCEEDINGS IS
         REQUIRED PURSUANT TO ITEMS 2(d) OR 2(e)     / /
- --------------------------------------------------------------------------------
    6    CITIZENSHIP OR PLACE OF ORGANIZATION
              DELAWARE
- --------------------------------------------------------------------------------
                     7    SOLE VOTING POWER
                               -0-
    NUMBER OF      -------------------------------------------------------------
      SHARES         8    SHARED VOTING POWER
   BENEFICIALLY                1,317,317
     OWNED BY      -------------------------------------------------------------
       EACH          9    SOLE DISPOSITIVE POWER
    REPORTING                  -0-
   PERSON WITH     -------------------------------------------------------------
                     10   SHARED DISPOSITIVE POWER
                               1,317,317
- --------------------------------------------------------------------------------
   11    AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
              1,317,317
- --------------------------------------------------------------------------------
   12    CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES
         CERTAIN SHARES*      / /
- --------------------------------------------------------------------------------
   13    PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11)
              12.3%
- --------------------------------------------------------------------------------
   14    TYPE OF REPORTING PERSON*
              IA, CO
- --------------------------------------------------------------------------------


                        * SEE INSTRUCTIONS BEFORE FILLING OUT!
<PAGE>

- -----------------------------                    -------------------------------
CUSIP NO. 87156R 10 9                 13D            Page 5 of 7 Pages
- -----------------------------                    -------------------------------

     This Amendment No. 2 (the "Amendment") to the Statement on Schedule 13D, 
dated September 8, 1998 and Amendment No. 1 thereto, dated December 17, 1998 
(as so amended, the "Statement"), is filed with the Securities and Exchange 
Commission on behalf of Biotechnology Value Fund, L.P., a Delaware limited 
partnership ("BVF"), BVF Partners L.P., a Delaware limited partnership 
("Partners"), 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 (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 22, 1999, Partners, in its capacity as general partner of 
BVF, has purchased on behalf of such limited partnership an aggregate number 
of 309,000 shares of the Stock for an aggregate consideration of 
$2,042,659.00, and has sold on behalf of such limited partnership an 
aggregate number of 36,100 shares of the Stock for an aggregate consideration 
of $546,407.00.  In addition, Partners, in its capacity as investment manager 
with respect to certain managed accounts, has purchased on behalf of such 
managed accounts an aggregate number of 295,200 shares of the Stock for an 
aggregate consideration of $1,950,608.17, and has sold on behalf of such 
managed accounts an aggregate number of 4,000 shares of the Stock for an 
aggregate consideration of $59,612.99.  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 BVF Partners L.P., 
227 West Monroe Street, Suite 4800, Chicago, Illinois 60606.

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

ITEM 5.   INTEREST IN SECURITIES OF THE ISSUER.

     (a)  BVF beneficially owns 677,867 shares of the Stock, Partners 
beneficially owns 1,317,317 shares of the Stock, and BVF Inc. beneficially 
owns 1,317,317 shares of the Stock, approximately 6.3%, 12.3% and 12.3%, 
respectively, of the aggregate number of shares outstanding as of February 
15, 1999 (as reported in Synaptic's most recent annual statement on Form 
10-K).

<PAGE>

- -----------------------------                    -------------------------------
CUSIP NO. 87156R 10 9                 13D            Page 6 of 7 Pages
- -----------------------------                    -------------------------------

     (b)   BVF shares voting and dispositive power over the 677,867 shares of 
the Stock it beneficially owns with Partners.  Partners and BVF Inc. share 
voting and dispositive power over the 1,317,317 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.

     (c)  Exhibit B attached hereto contains information as to all 
transactions in the Stock by the Reporting Persons in the last sixty (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 sixty 60 days.   On February 11, 1999, Partners transferred 11,000 
shares of Stock that it owned on behalf of ILL10 to BVF and transferred 
10,000 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 past sixty (60) days.

<PAGE>

- -----------------------------                    -------------------------------
CUSIP NO. 87156R 10 9                 13D            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 statement is true, complete 
and correct.


Dated:  March 30, 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 30, 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>
- ---------------------------------------------------------------------------------------------------------
                                    For the                      Price per     Type of
 Trade Date           By          Account of      Quantity         Share        Trade         Broker
 ----------           --          ----------      --------       ---------     -------        ------
- ---------------------------------------------------------------------------------------------------------
<S>                 <C>          <C>             <C>            <C>           <C>            <C>
 02/18/99            BVF          Partners          (3,000)       $16.9375      Sale           INET
- ---------------------------------------------------------------------------------------------------------
 02/24/99            BVF          Partners          (2,100)       $16.5625      Sale           INET
- ---------------------------------------------------------------------------------------------------------
 02/24/99            BVF          Partners         (20,000)       $16.6250      Sale           HMQT
- ---------------------------------------------------------------------------------------------------------
 02/24/99            BVF          Partners          (3,000)       $16.7500      Sale           INET
- ---------------------------------------------------------------------------------------------------------
 02/26/99            BVF          Partners          (3,000)       $16.0000      Sale           INET
- ---------------------------------------------------------------------------------------------------------
 02/26/99            BVF Ltd.     Partners          (2,000)       $16.0000      Sale           INET
- ---------------------------------------------------------------------------------------------------------
 03/04/99            ILL10        Partners          (1,000)       $13.8750      Sale           INET
- ---------------------------------------------------------------------------------------------------------
 03/04/99            ZPG          Partners          (1,000)       $13.8750      Sale           INET
- ---------------------------------------------------------------------------------------------------------
 03/04/99            BVF          Partners          13,000        $11.0000      Purchase       HMQT
- ---------------------------------------------------------------------------------------------------------
 03/04/99            BVF Ltd.     Partners          12,000        $11.0000      Purchase       HMQT
- ---------------------------------------------------------------------------------------------------------
 03/19/99            BVF          Partners           5,000         $6.5000      Purchase       HMQT
- ---------------------------------------------------------------------------------------------------------
 03/19/99            BVF Ltd.     Partners           5,000         $6.5000      Purchase       HMQT
- ---------------------------------------------------------------------------------------------------------
 03/19/99            BVF          Partners          50,000         $6.5781      Purchase       VECT
- ---------------------------------------------------------------------------------------------------------
 03/19/99            ILL10        Partners           5,000         $6.5781      Purchase       VECT
- ---------------------------------------------------------------------------------------------------------
 03/19/99            BVF Ltd.     Partners          45,000         $6.5781      Purchase       VECT
- ---------------------------------------------------------------------------------------------------------
 03/19/99            BVF          Partners          16,000         $6.8506      Purchase       INET
- ---------------------------------------------------------------------------------------------------------
 03/19/99            ILL10        Partners           3,300         $6.8506      Purchase       INET
- ---------------------------------------------------------------------------------------------------------
 03/19/99            BVF Ltd.     Partners          14,000         $6.8506      Purchase       INET
- ---------------------------------------------------------------------------------------------------------
 03/22/99            BVF          Partners          68,000         $6.6977      Purchase       INET
- ---------------------------------------------------------------------------------------------------------
 03/22/99            ILL10        Partners           4,000         $6.6977      Purchase       INET
- ---------------------------------------------------------------------------------------------------------
 03/22/99            BVF Ltd.     Partners          56,700         $6.6977      Purchase       INET
- ---------------------------------------------------------------------------------------------------------
 03/23/99            BVF          Partners          18,000         $6.5206      Purchase       INET
- ---------------------------------------------------------------------------------------------------------

<PAGE>

- ---------------------------------------------------------------------------------------------------------
 03/23/99            ILL10        Parnters           5,000         $6.5206      Purchase       INET
- ---------------------------------------------------------------------------------------------------------
 03/23/99            BVF Ltd.     Partners          14,000         $6.5206      Purchase       INET
- ---------------------------------------------------------------------------------------------------------
 03/24/99            BVF          Partners           9,000         $6.2500      Purchase       INET
- ---------------------------------------------------------------------------------------------------------
 03/24/99            ILL10        Partners           3,200         $6.2500      Purchase       INET
- ---------------------------------------------------------------------------------------------------------
 03/24/99            BVF Ltd.     Partners           8,000         $6.2500      Purchase       INET
- ---------------------------------------------------------------------------------------------------------
 03/25/99            BVF          Partners          (5,000)        $6.0625      Sale           HMQT
- ---------------------------------------------------------------------------------------------------------
 03/25/99            BVF          Partners         130,000         $6.1250      Purchase       JEFF
- ---------------------------------------------------------------------------------------------------------
 03/25/99            ILL10        Partners          10,000         $6.1250      Purchase       JEFF
- ---------------------------------------------------------------------------------------------------------
 03/25/99            BVF Ltd.     Partners         110,000         $6.1250      Purchase       JEFF
- ---------------------------------------------------------------------------------------------------------
</TABLE>

     HMQT      =    Hambrecht, Quist
     INET      =    Instinet
     JEFF      =    Jeffries & Co.
     VECT      =    Vector Securities




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