NEUROGEN CORP
SC 13D/A, 1997-12-24
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. 3)/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)

                               December 17, 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         SCHEDULE 13D               PAGE 2 OF 7 PAGES
- -----------------------                                  ---------------------
 
- ------------------------------------------------------------------------------
      NAME OF REPORTING PERSON
 1    S.S. OR I.R.S. IDENTIFICATION NO. OF ABOVE PERSON
      
      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 PROCEEDINGS IS REQUIRED PURSUANT TO
 5    ITEMS 2(d) or 2(e)                                                   [_]
 

- ------------------------------------------------------------------------------
      CITIZENSHIP OR PLACE OF ORGANIZATION
 6    
      DELAWARE

- ------------------------------------------------------------------------------
                          SOLE VOTING POWER
                     7   
     NUMBER OF                 -0-   
 
      SHARES       -----------------------------------------------------------
                          SHARED VOTING POWER
   BENEFICIALLY      8
                          
     OWNED BY                  755,620
                   -----------------------------------------------------------
       EACH               SOLE DISPOSITIVE POWER
                     9    
    REPORTING                   -0-
 
      PERSON       -----------------------------------------------------------
                          SHARED DISPOSITIVE POWER
       WITH         10
                                755,620
- ------------------------------------------------------------------------------
      AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
11  
      755,620

- ------------------------------------------------------------------------------
      CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES CERTAIN SHARES*
12                  
                                                                           [_] 
 
- ------------------------------------------------------------------------------
      PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11)
13    
      5.3% 

- ------------------------------------------------------------------------------
      TYPE OF REPORTING PERSON*
14
      PN

- ------------------------------------------------------------------------------
                     *SEE INSTRUCTIONS BEFORE FILLING OUT!
<PAGE>
 
- -----------------------                                  ---------------------
  CUSIP NO. 64124 E 106         SCHEDULE 13D               PAGE 3 OF 7 PAGES
- -----------------------                                  ---------------------
 
- ------------------------------------------------------------------------------
      NAME OF REPORTING PERSON
 1    S.S. OR I.R.S. IDENTIFICATION NO. OF ABOVE PERSON
      
      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 PROCEEDINGS IS REQUIRED PURSUANT TO
 5    ITEMS 2(d) or 2(e)                                                   [_]
 
      
- ------------------------------------------------------------------------------
      CITIZENSHIP OR PLACE OF ORGANIZATION
 6    
      DELAWARE

- ------------------------------------------------------------------------------
                          SOLE VOTING POWER
                     7   
     NUMBER OF                 -0-   
 
      SHARES       -----------------------------------------------------------
                          SHARED VOTING POWER
   BENEFICIALLY      8
                          
     OWNED BY                  1,437,306
                   -----------------------------------------------------------
       EACH               SOLE DISPOSITIVE POWER
                     9    
    REPORTING                   -0-
 
      PERSON       -----------------------------------------------------------
                          SHARED DISPOSITIVE POWER
       WITH         10
                                1,437,306
- ------------------------------------------------------------------------------
      AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
11  
      1,437,306

- ------------------------------------------------------------------------------
      CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES CERTAIN SHARES*
12                  
                                                                           [_] 
                                                                            
- ------------------------------------------------------------------------------
      PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11)
13    
      10.0%

- ------------------------------------------------------------------------------
      TYPE OF REPORTING PERSON*
14
      PN

- ------------------------------------------------------------------------------
                     *SEE INSTRUCTIONS BEFORE FILLING OUT!
<PAGE>
 
- -----------------------                                  ---------------------
  CUSIP NO. 64124 E 106         SCHEDULE 13D               PAGE 4 OF 7 PAGES
- -----------------------                                  ---------------------
 
- ------------------------------------------------------------------------------
      NAME OF REPORTING PERSON
 1    S.S. OR I.R.S. IDENTIFICATION NO. OF ABOVE PERSON
      
      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 PROCEEDINGS IS REQUIRED PURSUANT TO
 5    ITEMS 2(d) or 2(e)                                                   [_]
 

- ------------------------------------------------------------------------------
      CITIZENSHIP OR PLACE OF ORGANIZATION
 6    
      DELAWARE

- ------------------------------------------------------------------------------
                          SOLE VOTING POWER
                     7   
     NUMBER OF                 -0-   
 
      SHARES       -----------------------------------------------------------
                          SHARED VOTING POWER
   BENEFICIALLY      8
                          
     OWNED BY                  1,437,306
                   -----------------------------------------------------------
       EACH               SOLE DISPOSITIVE POWER
                     9    
    REPORTING                   -0-
 
      PERSON       -----------------------------------------------------------
                          SHARED DISPOSITIVE POWER
       WITH         10
                                1,437,306
- ------------------------------------------------------------------------------
      AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
11  
      1,437,306

- ------------------------------------------------------------------------------
      CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES CERTAIN SHARES*
12                  
                                                                           [_] 
 
- ------------------------------------------------------------------------------
      PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11)
13    
      10.0%

- ------------------------------------------------------------------------------
      TYPE OF REPORTING PERSON*
14
      IA,CO

- ------------------------------------------------------------------------------
                     *SEE INSTRUCTIONS BEFORE FILLING OUT!
<PAGE>
 
- -----------------------                                  ---------------------
  CUSIP NO. 64124 E 106         SCHEDULE 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"). The principal executive office of Neurogen is located at 35
Northeast Industrial Road, Branford, CT 06405.

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

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

     Since December 8, 1997, Partners, in its capacity as general partner of
BVF, has purchased on behalf of such limited partnership an aggregate number of
111,900 shares of the Stock for an aggregate consideration of $1,583,647,
utilizing funds provided by BVF from its working capital pursuant to the terms
of its limited partnership agreement with Partners and sold 7,800 shares for an
aggregate consideraton of $158,841.  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 102,000 shares of the
Stock for an aggregate consideration of $1,414,775, utilizing funds under
management by Partners pursuant to an investment management agreement between
Partners and such managed accounts and sold 7,000 shares for an aggregate
consideration of $142,535.

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

ITEM 5.   INTEREST IN SECURITIES OF THE ISSUER.

     (a) BVF beneficially owns 755,620 shares of the Stock, Partners
beneficially owns 1,437,306 shares of the Stock, and BVF Inc. beneficially owns
1,437,306 shares of the Stock, approximately 5.3%, 9.99% and 9.99%,
respectively, of the 14,390,786 shares outstanding as of November 13, 1997 (as
reported in Neurogen's most recent quarterly statement on Form 10-Q).

     (b) BVF shares voting and dispositive power over the 755,620 shares of the
Stock it beneficially owns with Partners.  Partners and BVF Inc. share voting
and dispositive power over the 1,437,306 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 
<PAGE>
 
- -----------------------                                  ---------------------
  CUSIP NO. 64124 E 106         SCHEDULE 13D               PAGE 6 OF 7 PAGES
- -----------------------                                  ---------------------

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 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         SCHEDULE 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:  December 24, 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:  December 24, 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>

- --------------------------------------------------------------------------------------- 
                                                       Price
                                                       ----   
Settlement                   For the                    per
- ----------                   -------                    ---                           
  Date           By        Account of    Quantity      Share   Type of Trade    Broker  
- ----------   -----------   -----------   ---------    --------  -------------   ------ 
- --------------------------------------------------------------------------------------- 
<S>          <C>           <C>           <C>          <C>       <C>             <C> 
  12/08/97   Partners      BVF              2,900     $19.9591   Purchase        INET
- --------------------------------------------------------------------------------------- 
  12/12/97   Partners      BVF             (7,800)    $20.3750   Sale            INET
- ---------------------------------------------------------------------------------------
  12/12/97   Partners      ZPG             (7,000)    $20.3750   Sale            INET
- ---------------------------------------------------------------------------------------
  12/12/97   Partners      BVF             15,000     $13.5000   Purchase        SBSH
- ---------------------------------------------------------------------------------------
  12/12/97   Partners      BVF, Ltd.       35,000     $13.5000   Purchase        SBSH
- ---------------------------------------------------------------------------------------
  12/17/97   Partners      BVF             75,000     $14.1250   Purchase        GROW
- ---------------------------------------------------------------------------------------
  12/17/97   Partners      BVF, Ltd.       50,000     $14.1250   Purchase        GROW
- ---------------------------------------------------------------------------------------
  12/18/97   Partners      BVF             16,000     $13.8750   Purchase        SBSH
- ---------------------------------------------------------------------------------------
  12/18/97   Partners      ILL10            2,000     $13.8750   Purchase        SBSH
- ---------------------------------------------------------------------------------------
  12/18/97   Partners      PAL              1,000     $13.8750   Purchase        SBSH
- ---------------------------------------------------------------------------------------
  12/18/97   Partners      ZPG              1,000     $13.8750   Purchase        SBSH
- ---------------------------------------------------------------------------------------
  12/18/97   Partners      BVF, Ltd.       10,000     $13.8750   Purchase        SBSH
- ---------------------------------------------------------------------------------------
  12/18/97   Partners      BVF              3,000     $13.8854   Purchase        INET
- ---------------------------------------------------------------------------------------
  12/18/97   Partners      BVF, Ltd.        3,000     $13.8854   Purchase        INET
- ---------------------------------------------------------------------------------------
</TABLE>


     INET      =    Instinet
     SBSH      =    Smith Barney
     GROW      =    Pacific Growth Inc.


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