NPS PHARMACEUTICALS INC
SC 13D/A, 1998-03-30
BIOLOGICAL PRODUCTS, (NO DIAGNOSTIC SUBSTANCES)
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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/



                           NPS PHARMACEUTICALS, INC.
                           -------------------------
                               (Name of Issuer)

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

                                  62936 P 103
                                  -----------
                                (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)

                                March 24, 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).

                                       1
<PAGE>
 
- -----------------------                                  ---------------------
  CUSIP NO. 62936 P 103              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 REQUIRED PURSUANT 
      TO ITEMS 2(d) OR 2(e) [_]
 5    
- ------------------------------------------------------------------------------
      CITIZENSHIP OR PLACE OF ORGANIZATION
 6    
      DELAWARE
- ------------------------------------------------------------------------------
                          SOLE VOTING POWER
                     7     
      NUMBER              -0-
                             
        OF         -----------------------------------------------------------
                          SHARED VOTING POWER
      SHARES         8    
                          675,900
   BENEFICIALLY                  
                   -----------------------------------------------------------
    OWNED BY              SOLE DISPOSITIVE POWER
                     9     
    REPORTING             -0-
                         
      PERSON       -----------------------------------------------------------
                          SHARED DISPOSITIVE POWER
       WITH          10   
                                 675,900
- ------------------------------------------------------------------------------
      AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
11    
      
      675,900
- ------------------------------------------------------------------------------
      CHECK BOX IF THE AGGREGATE AMOUNT IN ROW 11 EXCLUDES CERTAIN SHARES*
12                  
      [_]
- ------------------------------------------------------------------------------
      PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 11
13    
                  5.6%
- ------------------------------------------------------------------------------
      TYPE OF REPORTING PERSON*
14
      PN
- ------------------------------------------------------------------------------
                     *SEE INSTRUCTIONS BEFORE FILLING OUT!

                                       2
<PAGE>
 
- -----------------------                                  ---------------------
  CUSIP NO. 62936 P 103              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 REQUIRED PURSUANT 
      TO ITEMS 2(d) OR 2(e) [_]
 5    
- ------------------------------------------------------------------------------
      CITIZENSHIP OR PLACE OF ORGANIZATION
 6    
       DELAWARE
- ------------------------------------------------------------------------------
                          SOLE VOTING POWER
                     7     
      NUMBER              
                             -0-
        OF         -----------------------------------------------------------
                          SHARED VOTING POWER
      SHARES         8    
                          1,361,800
   BENEFICIALLY                  
                   -----------------------------------------------------------
     OWNED BY             SOLE DISPOSITIVE POWER
                     9     
    REPORTING             
                           -0-
      PERSON       -----------------------------------------------------------
                          SHARED DISPOSITIVE POWER
       WITH          10   
                                 1,361,800
- ------------------------------------------------------------------------------
      AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
11    
      1,361,800
      
- ------------------------------------------------------------------------------
      CHECK BOX IF THE AGGREGATE AMOUNT IN ROW 11 EXCLUDES CERTAIN SHARES*
12                  
      [_]
- ------------------------------------------------------------------------------
      PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 11
13    
                  11.3%
- ------------------------------------------------------------------------------
      TYPE OF REPORTING PERSON*
14
      PN
- ------------------------------------------------------------------------------
                     *SEE INSTRUCTIONS BEFORE FILLING OUT!

                                       3
<PAGE>
 
- -----------------------                                  ---------------------
  CUSIP NO. 62936 P 103              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 REQUIRED PURSUANT 
      TO ITEMS 2(d) OR 2(e) [_]
 5    
- ------------------------------------------------------------------------------
      CITIZENSHIP OR PLACE OF ORGANIZATION
 6    
       DELAWARE
- ------------------------------------------------------------------------------
                          SOLE VOTING POWER
                     7     
      NUMBER               
                             -0-
        OF         -----------------------------------------------------------
                          SHARED VOTING POWER
      SHARES         8    
                          1,361,800
   BENEFICIALLY                  
                   -----------------------------------------------------------
     OWNED BY             SOLE DISPOSITIVE POWER
                     9     
    REPORTING             -0-
                         
      PERSON       -----------------------------------------------------------
                          SHARED DISPOSITIVE POWER
       WITH          10   
                                 1,361,800
- ------------------------------------------------------------------------------
      AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
11    
      1,361,800
      
- ------------------------------------------------------------------------------
      CHECK BOX IF THE AGGREGATE AMOUNT IN ROW 11 EXCLUDES CERTAIN SHARES*
12                  
      [_]
- ------------------------------------------------------------------------------
      PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 11
13    
                  11.3%
- ------------------------------------------------------------------------------
      TYPE OF REPORTING PERSON*
14
      IA, CO
- ------------------------------------------------------------------------------
                     *SEE INSTRUCTIONS BEFORE FILLING OUT!

                                       4
<PAGE>
 
- -----------------------                                  ---------------------
  CUSIP NO. 62936 P 103              13D                   PAGE 5 OF 7 PAGES
- -----------------------                                  ---------------------


     This Amendment No. 3 (this "Amendment") relates to the Statement on
Schedule 13D, dated April 25, 1997, as amended by Amendment No. 1, dated
December 1, 1997 and Amendment No. 2, dated January 30, 1998 (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 $0.001 per
share (the "Stock"), of NPS Pharmaceuticals, Inc., a Delaware corporation
("NPS"). The principal executive office of NPS is located at 420 Chipeta Way,
Suite 240, Salt Lake City, UT 84108-1256.


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

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

     Since the last Statement, Partners, in its capacity as general partner of
BVF, has purchased on behalf of such limited partnership an aggregate number of
106,000 shares of the Stock for an aggregate consideration of $794,703.20,
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 114,000
shares of the Stock for an aggregate consideration of $854,710.80 utilizing
funds under management by Partners pursuant to investment management agreements
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 675,900 shares of the Stock, Partners
beneficially owns 1,361,800 shares of the Stock, and BVF Inc. beneficially owns
1,361,800 shares of the Stock, approximately 5.6%, 11.3% and 11.3%,
respectively, of the aggregate number of shares outstanding as of September 30,
1997 (as reported in NPS's most recent quarterly statement on Form 10-Q).

     (b)  BVF shares voting and dispositive power over the 675,900 shares of the
Stock it beneficially owns with Partners.  Partners and BVF Inc. share voting
and dispositive power over the 1,361,800 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 

                                       5
<PAGE>
 
- -----------------------                                  ---------------------
  CUSIP NO. 62936 P 103              13D                   PAGE 6 OF 7 PAGES
- -----------------------                                  ---------------------


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., 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 since the last Statement.  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
since the last Statement.

     (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 since the
last Statement.

                                       6
<PAGE>
 
- -----------------------                                  ---------------------
  CUSIP NO. 62936 P 103              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 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, 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 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
              --------------------------------------------------
                           SINCE THE LAST STATEMENT
                           ------------------------

<TABLE>
<CAPTION>
- -------------------------------------------------------------------------------------------------
Settlement                 For the                    Price per 
- ----------                 -------                    ---------
 Date              By     Account of   Quantity        Share         Type of Trade       Broker 
 ----              --     ----------   --------        -----         -------------       ------
=================================================================================================
<S>           <C>         <C>          <C>            <C>            <C>                 <C>
03/24/98        Partners   BVF          106,000       $7.4972        Purchase             VECT 
- ------------------------------------------------------------------------------------------------- 
03/24/98        Partners   PAL            9,000       $7.4972        Purchase             VECT 
- ------------------------------------------------------------------------------------------------- 
03/24/98        Partners   ZPG            5,000       $7.4972        Purchase             VECT 
- ------------------------------------------------------------------------------------------------- 
03/24/98        Partners   BVF Ltd.     100,000       $7.4972        Purchase             VECT  
- ------------------------------------------------------------------------------------------------- 
</TABLE> 

     VECT               =         Vector Securities           


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