NEUROGEN CORP
SC 13D/A, 1997-08-29
PHARMACEUTICAL PREPARATIONS
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<PAGE>
 
                      SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, DC  20549

                             ---------------------

                                 SCHEDULE 13D
                                (RULE 13D-101)

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


                             NEUROGEN CORPORATION
                             --------------------
                               (Name of Issuer)

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

                                  64124 E 106
                                  -----------
                                (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)

                                August 25, 1997
                                ---------------
            (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>
 
- -----------------------                                  ---------------------
 CUSIP NO. 64124 E 106                  13D                PAGE 2 OF 7 PAGES
- -----------------------                                  ---------------------
 
- ------------------------------------------------------------------------------
      NAME OF REPORTING PERSONS
 1    S.S. OR I.R.S. IDENTIFICATION NOS. OF ABOVE PERSONS
      BIOTECHNOLOGY VALUE FUND, L.P.

- ------------------------------------------------------------------------------
      CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*
 2                                                        (a) [X]    (b) [_]
                                                 
- ------------------------------------------------------------------------------
      SEC USE ONLY
 3
 
- ------------------------------------------------------------------------------
      SOURCE OF FUNDS*
 4    WC

- ------------------------------------------------------------------------------
      CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDING IS
 5    REQUIRED PURSUANT TO ITEMS 2(d) OR 2(e)                            [_]

- ------------------------------------------------------------------------------
      CITIZENSHIP OR PLACE OF ORGANIZATION
 6    DELAWARE
      
- ------------------------------------------------------------------------------
                          SOLE VOTING POWER
      NUMBER         7    -0-
      
        OF         -----------------------------------------------------------
                          SHARED VOTING POWER
      SHARES         8    639,920
                          
   BENEFICIALLY    -----------------------------------------------------------
                          SOLE DISPOSITIVE POWER
     OWNED BY        9    -0-     
                     
    REPORTING      -----------------------------------------------------------
                          SHARED DISPOSITIVE POWER
      PERSON        10    639,920
                          
       WITH         
- ------------------------------------------------------------------------------
      AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH 
11    REPORTING PERSON
      639,920

- ------------------------------------------------------------------------------
      CHECK BOX IF THE AGGREGATE AMOUNT IN ROW 11 EXCLUDES 
12    CERTAIN SHARES*                                                    [_]
 
- ------------------------------------------------------------------------------
      PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 11
13    4.5%
      
- ------------------------------------------------------------------------------
      TYPE OF REPORTING PERSON*
14    PN

- ------------------------------------------------------------------------------

                     *SEE INSTRUCTIONS BEFORE FILLING OUT!
<PAGE>
 
- -----------------------                                  ---------------------
 CUSIP NO. 64124 E 106                  13D                PAGE 3 OF 7 PAGES
- -----------------------                                  ---------------------
 
- ------------------------------------------------------------------------------
      NAME OF REPORTING PERSONS
 1    S.S. OR I.R.S. IDENTIFICATION NOS. OF ABOVE PERSONS
      BVF PARTNERS L.P.

- ------------------------------------------------------------------------------
      CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*
 2                                                        (a) [X]    (b) [_]
                                                 
- ------------------------------------------------------------------------------
      SEC USE ONLY
 3
 
- ------------------------------------------------------------------------------
      SOURCE OF FUNDS*
 4    OO

- ------------------------------------------------------------------------------
      CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDING IS
 5    REQUIRED PURSUANT TO ITEMS 2(d) OR 2(e)                            [_]

- ------------------------------------------------------------------------------
      CITIZENSHIP OR PLACE OF ORGANIZATION
 6    DELAWARE
      
- ------------------------------------------------------------------------------
                          SOLE VOTING POWER
      NUMBER         7    -0-
      
        OF         -----------------------------------------------------------
                          SHARED VOTING POWER
      SHARES         8    1,221,106
                          
   BENEFICIALLY    -----------------------------------------------------------
                          SOLE DISPOSITIVE POWER
     OWNED BY        9    -0-     
                     
    REPORTING      -----------------------------------------------------------
                          SHARED DISPOSITIVE POWER
      PERSON        10    1,221,106      
                          
       WITH         
- ------------------------------------------------------------------------------
      AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH 
11    REPORTING PERSON
      1,221,106

- ------------------------------------------------------------------------------
      CHECK BOX IF THE AGGREGATE AMOUNT IN ROW 11 EXCLUDES 
12    CERTAIN SHARES*                                                    [_]
 
- ------------------------------------------------------------------------------
      PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 11
13    8.5%
      
- ------------------------------------------------------------------------------
      TYPE OF REPORTING PERSON*
14    PN

- ------------------------------------------------------------------------------

                     *SEE INSTRUCTIONS BEFORE FILLING OUT!
<PAGE>
 
- -----------------------                                  ---------------------
 CUSIP NO. 64124 E 106                  13D                PAGE 4 OF 7 PAGES
- -----------------------                                  ---------------------
 
- ------------------------------------------------------------------------------
      NAME OF REPORTING PERSONS
 1    S.S. OR I.R.S. IDENTIFICATION NOS. OF ABOVE PERSONS
      BVF INC.

- ------------------------------------------------------------------------------
      CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*
 2                                                        (a) [X]    (b) [_]
                                                 
- ------------------------------------------------------------------------------
      SEC USE ONLY
 3
 
- ------------------------------------------------------------------------------
      SOURCE OF FUNDS*
 4    WC, OO

- ------------------------------------------------------------------------------
      CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDING IS
 5    REQUIRED PURSUANT TO ITEMS 2(d) OR 2(e)                            [_]

- ------------------------------------------------------------------------------
      CITIZENSHIP OR PLACE OF ORGANIZATION
 6    DELAWARE
      
- ------------------------------------------------------------------------------
                          SOLE VOTING POWER
      NUMBER         7    -0-
      
        OF         -----------------------------------------------------------
                          SHARED VOTING POWER
      SHARES         8    1,221,106
                          
   BENEFICIALLY    -----------------------------------------------------------
                          SOLE DISPOSITIVE POWER
     OWNED BY        9    -0-     
                     
    REPORTING      -----------------------------------------------------------
                          SHARED DISPOSITIVE POWER
      PERSON        10    1,221,106      
                          
       WITH         
- ------------------------------------------------------------------------------
      AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH 
11    REPORTING PERSON
      1,221,106

- ------------------------------------------------------------------------------
      CHECK BOX IF THE AGGREGATE AMOUNT IN ROW 11 EXCLUDES 
12    CERTAIN SHARES*                                                    [_]
 
- ------------------------------------------------------------------------------
      PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 11
13    8.5%
      
- ------------------------------------------------------------------------------
      TYPE OF REPORTING PERSON*
14    IA,CO

- ------------------------------------------------------------------------------

                     *SEE INSTRUCTIONS BEFORE FILLING OUT!
<PAGE>
 
- -----------------------                                  ---------------------
 CUSIP NO. 64124 E 106                  13D                PAGE 5 OF 7 PAGES
- -----------------------                                  ---------------------


     This Amendment No. 2 (this "Amendment") relates to the Statement on
Schedule 13D, dated March 18, 1997, as amended by Amendment No. 1, dated April
16, 1997 (as so amended, the "Statement"), 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 $.025 per share (the "Stock"), of Neurogen Corporation
("Neurogen").

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

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

     Since June 25, 1997, Partners, in its capacity as general partner of BVF,
has purchased on behalf of such limited partnership an aggregate number of
68,000 shares of the Stock for an aggregate consideration of $1,364,040.00,
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
purchased on behalf of such managed accounts an aggregate number of 68,000
shares of the Stock for an aggregate consideration of $1,359,180.25, utilizing
funds under management by Partners pursuant to an investment management
agreement between Partners and such managed accounts.

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

ITEM 5.   INTEREST IN SECURITIES OF THE ISSUER.

     (a) BVF beneficially owns 639,920 shares of the Stock, Partners
beneficially owns 1,221,106 shares of the Stock, and BVF Inc. beneficially owns
1,221,106 shares of the Stock, approximately 4.5%, 8.5% and 8.5%, respectively,
of the aggregate number of shares outstanding as of August 26, 1997.

     (b) BVF shares voting and dispositive power over the 639,920 shares of the
Stock it beneficially owns with Partners.  Partners and BVF Inc. share voting
and dispositive power over the 1,221,106 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 
<PAGE>
 
- -----------------------                                  ---------------------
 CUSIP NO. 64124 E 106                  13D                PAGE 6 OF 7 PAGES
- -----------------------                                  ---------------------


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 sixty 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 sixty 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 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 days.
<PAGE>
 
- -----------------------                                  ---------------------
 CUSIP NO. 64124 E 106                  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:  August 29, 1997

     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:  August 29, 1997

     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>
Settlement                  For the                 Price per                 
  Date           By        Account of    Quantity     Share     Type of Trade   Broker
- ----------   -----------   ----------    --------   ---------   -------------   ------   
<C>          <S>           <C>           <C>         <C>        <C>             <C>
  06/25/97   Partners      BVF              1,000    $17.5000   Purchase        NB
- --------------------------------------------------------------------------------------
  06/27/97   Partners      BVF              2,000    $21.1250   Purchase        INET
- --------------------------------------------------------------------------------------
  07/29/97   Partners      BVF             53,000    $20.1250   Purchase        GROW
- --------------------------------------------------------------------------------------
  07/29/97   Partners      ILL10            8,500    $20.1250   Purchase        GROW
- --------------------------------------------------------------------------------------
  07/29/97   Partners      PAL              4,700    $20.1250   Purchase        GROW
- --------------------------------------------------------------------------------------
  07/29/97   Partners      ZPG              4,000    $20.1250   Purchase        GROW
- --------------------------------------------------------------------------------------
  07/29/97   Partners      BVF, Ltd.       29,900    $20.1250   Purchase        GROW
- --------------------------------------------------------------------------------------
  08/25/97   Partners      BVF             10,000    $19.7500   Purchase        GROW
- --------------------------------------------------------------------------------------
  08/25/97   Partners      ILL10            3,000    $19.6250   Purchase        INET
- --------------------------------------------------------------------------------------
  08/25/97   Partners      PAL              3,000    $19.6250   Purchase        INET
- --------------------------------------------------------------------------------------
  08/25/97   Partners      ZPG              2,000    $19.6250   Purchase        INET
- --------------------------------------------------------------------------------------
  08/25/97   Partners      BVF, Ltd.       11,600    $19.6250   Purchase        INET
- --------------------------------------------------------------------------------------
  08/26/97   Partners      BVF              2,000    $19.7175   Purchase        PFTC
- --------------------------------------------------------------------------------------
  08/26/97   Partners      BVF, Ltd.        1,300    $19.7175   Purchase        PFTC
- --------------------------------------------------------------------------------------
</TABLE>

     INET    =   Instinet
     GROW    =   Pacific Growth Inc.
     NB      =   No Broker
     PFTC    =   Preferred Technologies


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