ARQULE INC
SC 13G/A, 1999-02-12
PHARMACEUTICAL PREPARATIONS
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                                  UNITED STATES
                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549

                                  SCHEDULE 13G

                    UNDER THE SECURITIES EXCHANGE ACT OF 1934

                               (AMENDMENT NO.     2      )*
                                              ----------

                                              
                                  ARQULE, INC.
- --------------------------------------------------------------------------------
                                (Name of Issuer)


                          COMMON STOCK, $.01 Par Value
- --------------------------------------------------------------------------------
                         (Title of Class of Securities)

                                   00004269E1
                      ------------------------------------
                                 (CUSIP Number)


- --------------------------------------------------------------------------------
             (Date of Event Which Requires Filing of this Statement)

Check the appropriate box to designate the rule pursuant to which this Schedule
is filed:

      [ ] Rule 13d-1(b)
      [ ] Rule 13d-1(c)
      [X] Rule 13d-1(d)

*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 the
disclosures provided in a prior cover page.

The information required in 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 ("Act") 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).


SEC 1745 (3-98)                Page 1 of 22 pages


<PAGE>   2



- --------------------------                            --------------------------
 CUSIP NO.  00004269E1                 13G             PAGE    2   OF   22
           -------------                                     -----    ------ 
- --------------------------                            --------------------------



- --------------------------------------------------------------------------------
1     NAMES OF REPORTING PERSONS
      I.R.S. IDENTIFICATION NOS. OF ABOVE PERSONS (ENTITIES ONLY)

      Atlas Venture Fund II, L.P.
- --------------------------------------------------------------------------------
2     CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP (SEE INSTRUCTIONS)
                                                                        (a) [ ]
                                                                        (b) [ ]
- --------------------------------------------------------------------------------
3     SEC USE ONLY

- --------------------------------------------------------------------------------
4     CITIZENSHIP OR PLACE OF ORGANIZATION

      Delaware Limited Partnership
- --------------------------------------------------------------------------------
                                5    SOLE VOTING POWER

          NUMBER OF                  0 shares
                              --------------------------------------------------
           SHARES               6    SHARED VOTING POWER
        BENEFICIALLY
          OWNED BY                   1,154,480 shares
                              --------------------------------------------------
            EACH                7    SOLE DISPOSITIVE POWER
         REPORTING
           PERSON                    0 shares
                              --------------------------------------------------
           WITH:                8    SHARED DISPOSITIVE POWER

                                     1,154,480 shares
- --------------------------------------------------------------------------------
9     AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

      1,154,480 shares
- --------------------------------------------------------------------------------
10    CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES 
      SEE INSTRUCTIONS)  [ ]

- --------------------------------------------------------------------------------
11    PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9

      9.5%
- --------------------------------------------------------------------------------
12    TYPE OF REPORTING PERSON (SEE INSTRUCTIONS)

      PN
- --------------------------------------------------------------------------------


                               Page 2 of 22 Pages


<PAGE>   3


- --------------------------                            --------------------------
 CUSIP NO.  00004269E1                 13G             PAGE    3   OF   22
           -------------                                     -----    ------ 
- --------------------------                            --------------------------


- --------------------------------------------------------------------------------
1     NAMES OF REPORTING PERSONS
      I.R.S. IDENTIFICATION NOS. OF ABOVE PERSONS (ENTITIES ONLY)

      Atlas Venture Associates II, L.P.
- --------------------------------------------------------------------------------
2     CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP (SEE INSTRUCTIONS)
                                                                        (a) [ ]
                                                                        (b) [ ]
- --------------------------------------------------------------------------------
3     SEC USE ONLY

- --------------------------------------------------------------------------------
4     CITIZENSHIP OR PLACE OF ORGANIZATION

      Delaware Limited Partnership
- --------------------------------------------------------------------------------
                                5    SOLE VOTING POWER

          NUMBER OF                  0 shares
                              --------------------------------------------------
           SHARES               6    SHARED VOTING POWER
        BENEFICIALLY
          OWNED BY                   1,154,480 shares
                              --------------------------------------------------
            EACH                7    SOLE DISPOSITIVE POWER
         REPORTING
           PERSON                    0 shares
                              --------------------------------------------------
           WITH:                8    SHARED DISPOSITIVE POWER

                                     1,154,480 shares
- --------------------------------------------------------------------------------
9     AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

      1,154,480 shares
- --------------------------------------------------------------------------------
10    CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES 
      SEE INSTRUCTIONS)  [ ]

- --------------------------------------------------------------------------------
11    PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9

      9.5%
- --------------------------------------------------------------------------------
12    TYPE OF REPORTING PERSON (SEE INSTRUCTIONS)

      PN
- --------------------------------------------------------------------------------


                               Page 3 of 22 Pages


<PAGE>   4


- --------------------------                            --------------------------
 CUSIP NO.  00004269E1                 13G             PAGE    4   OF   22
           -------------                                     -----    ------ 
- --------------------------                            --------------------------



- --------------------------------------------------------------------------------
1     NAMES OF REPORTING PERSONS
      I.R.S. IDENTIFICATION NOS. OF ABOVE PERSONS (ENTITIES ONLY)

      Christopher J. Spray
- --------------------------------------------------------------------------------
2     CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP (SEE INSTRUCTIONS)
                                                                        (a) [ ]
                                                                        (b) [ ]
- --------------------------------------------------------------------------------
3     SEC USE ONLY

- --------------------------------------------------------------------------------
4     CITIZENSHIP OR PLACE OF ORGANIZATION

      United Kingdom                   
- --------------------------------------------------------------------------------
                                5    SOLE VOTING POWER

          NUMBER OF                  0 shares
                              --------------------------------------------------
           SHARES               6    SHARED VOTING POWER
        BENEFICIALLY
          OWNED BY                   664,310 shares
                              --------------------------------------------------
            EACH                7    SOLE DISPOSITIVE POWER
         REPORTING
           PERSON                    0 shares
                              --------------------------------------------------
           WITH:                8    SHARED DISPOSITIVE POWER

                                     664,310 shares
- --------------------------------------------------------------------------------
9     AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

      664,310 shares
- --------------------------------------------------------------------------------
10    CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES 
      SEE INSTRUCTIONS)  [ ]

- --------------------------------------------------------------------------------
11    PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9

      5.5%
- --------------------------------------------------------------------------------
12    TYPE OF REPORTING PERSON (SEE INSTRUCTIONS)

      IN
- --------------------------------------------------------------------------------


                               Page 4 of 22 Pages


<PAGE>   5


- --------------------------                            --------------------------
 CUSIP NO.  00004269E1                 13G             PAGE    5   OF   22
           -------------                                     -----    ------ 
- --------------------------                            --------------------------



- --------------------------------------------------------------------------------
1     NAMES OF REPORTING PERSONS
      I.R.S. IDENTIFICATION NOS. OF ABOVE PERSONS (ENTITIES ONLY)

      Barry Fidelman
- --------------------------------------------------------------------------------
2     CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP (SEE INSTRUCTIONS)
                                                                        (a) [ ]
                                                                        (b) [ ]
- --------------------------------------------------------------------------------
3     SEC USE ONLY

- --------------------------------------------------------------------------------
4     CITIZENSHIP OR PLACE OF ORGANIZATION

      United States
- --------------------------------------------------------------------------------
                                5    SOLE VOTING POWER

          NUMBER OF                  0 shares
                              --------------------------------------------------
           SHARES               6    SHARED VOTING POWER
        BENEFICIALLY
          OWNED BY                   664,310 shares
                              --------------------------------------------------
            EACH                7    SOLE DISPOSITIVE POWER
         REPORTING
           PERSON                    0 shares
                              --------------------------------------------------
           WITH:                8    SHARED DISPOSITIVE POWER

                                     664,310 shares
- --------------------------------------------------------------------------------
9     AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

      664,310 shares
- --------------------------------------------------------------------------------
10    CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES 
      SEE INSTRUCTIONS)  [ ]

- --------------------------------------------------------------------------------
11    PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9

      5.5%
- --------------------------------------------------------------------------------
12    TYPE OF REPORTING PERSON (SEE INSTRUCTIONS)

      IN
- --------------------------------------------------------------------------------


                               Page 5 of 22 Pages

<PAGE>   6

- --------------------------                            --------------------------
 CUSIP NO.  00004269E1                 13G             PAGE    6   OF   22
           -------------                                     -----    ------ 
- --------------------------                            --------------------------



- --------------------------------------------------------------------------------
1     NAMES OF REPORTING PERSONS
      I.R.S. IDENTIFICATION NOS. OF ABOVE PERSONS (ENTITIES ONLY)

      Allan Ferguson
- --------------------------------------------------------------------------------
2     CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP (SEE INSTRUCTIONS)
                                                                        (a) [ ]
                                                                        (b) [ ]
- --------------------------------------------------------------------------------
3     SEC USE ONLY

- --------------------------------------------------------------------------------
4     CITIZENSHIP OR PLACE OF ORGANIZATION

      United States
- --------------------------------------------------------------------------------
                                5    SOLE VOTING POWER

          NUMBER OF                  12,0000 shares
                              --------------------------------------------------
           SHARES               6    SHARED VOTING POWER
        BENEFICIALLY
          OWNED BY                   676,310 shares
                              --------------------------------------------------
            EACH                7    SOLE DISPOSITIVE POWER
         REPORTING
           PERSON                    12,000 shares
                              --------------------------------------------------
           WITH:                8    SHARED DISPOSITIVE POWER

                                     676,310 shares
- --------------------------------------------------------------------------------
9     AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

      676,310 shares
- --------------------------------------------------------------------------------
10    CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES 
      SEE INSTRUCTIONS)  [ ]

- --------------------------------------------------------------------------------
11    PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9

      5.6%
- --------------------------------------------------------------------------------
12    TYPE OF REPORTING PERSON (SEE INSTRUCTIONS)

      IN
- --------------------------------------------------------------------------------


                               Page 6 of 22 Pages


<PAGE>   7


- --------------------------                            --------------------------
 CUSIP NO.  00004269E1                 13G             PAGE    7   OF   22
           -------------                                     -----    ------ 
- --------------------------                            --------------------------



- --------------------------------------------------------------------------------
1     NAMES OF REPORTING PERSONS
      I.R.S. IDENTIFICATION NOS. OF ABOVE PERSONS (ENTITIES ONLY)

      Jean-Francois Formela
- --------------------------------------------------------------------------------
2     CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP (SEE INSTRUCTIONS)
                                                                        (a) [ ]
                                                                        (b) [ ]
- --------------------------------------------------------------------------------
3     SEC USE ONLY

- --------------------------------------------------------------------------------
4     CITIZENSHIP OR PLACE OF ORGANIZATION

      France
- --------------------------------------------------------------------------------
                                5    SOLE VOTING POWER

          NUMBER OF                  0 shares
                              --------------------------------------------------
           SHARES               6    SHARED VOTING POWER
        BENEFICIALLY
          OWNED BY                   664,310 shares
                              --------------------------------------------------
            EACH                7    SOLE DISPOSITIVE POWER
         REPORTING
           PERSON                    0 shares
                              --------------------------------------------------
           WITH:                8    SHARED DISPOSITIVE POWER

                                     664,310 shares
- --------------------------------------------------------------------------------
9     AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

      664,310 shares
- --------------------------------------------------------------------------------
10    CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES 
      SEE INSTRUCTIONS)  [ ]

- --------------------------------------------------------------------------------
11    PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9

      5.5%
- --------------------------------------------------------------------------------
12    TYPE OF REPORTING PERSON (SEE INSTRUCTIONS)

      IN
- --------------------------------------------------------------------------------


                               Page 7 of 22 Pages


<PAGE>   8


- --------------------------                            --------------------------
 CUSIP NO.  00004269E1                 13G             PAGE    8   OF   22
           -------------                                     -----    ------ 
- --------------------------                            --------------------------



- --------------------------------------------------------------------------------
1     NAMES OF REPORTING PERSONS
      I.R.S. IDENTIFICATION NOS. OF ABOVE PERSONS (ENTITIES ONLY)

      Atlas Venture Europe Fund B. V.
- --------------------------------------------------------------------------------
2     CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP (SEE INSTRUCTIONS)
                                                                        (a) [ ]
                                                                        (b) [ ]
- --------------------------------------------------------------------------------
3     SEC USE ONLY

- --------------------------------------------------------------------------------
4     CITIZENSHIP OR PLACE OF ORGANIZATION

      The Netherlands 
- --------------------------------------------------------------------------------
                                5    SOLE VOTING POWER

          NUMBER OF                  0 shares
                              --------------------------------------------------
           SHARES               6    SHARED VOTING POWER
        BENEFICIALLY
          OWNED BY                   1,154,480 shares
                              --------------------------------------------------
            EACH                7    SOLE DISPOSITIVE POWER
         REPORTING
           PERSON                    0 shares
                              --------------------------------------------------
           WITH:                8    SHARED DISPOSITIVE POWER

                                     1,154,480 shares
- --------------------------------------------------------------------------------
9     AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

      1,154,480 shares
- --------------------------------------------------------------------------------
10    CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES 
      SEE INSTRUCTIONS)  [ ]

- --------------------------------------------------------------------------------
11    PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9

      9.5%
- --------------------------------------------------------------------------------
12    TYPE OF REPORTING PERSON (SEE INSTRUCTIONS)

      CO
- --------------------------------------------------------------------------------


                               Page 8 of 22 Pages


<PAGE>   9


- --------------------------                            --------------------------
 CUSIP NO.  00004269E1                 13G             PAGE    9   OF   22
           -------------                                     -----    ------ 
- --------------------------                            --------------------------



- --------------------------------------------------------------------------------
1     NAMES OF REPORTING PERSONS
      I.R.S. IDENTIFICATION NOS. OF ABOVE PERSONS (ENTITIES ONLY)

      Atlas InvesteringsGroep N.V.
- --------------------------------------------------------------------------------
2     CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP (SEE INSTRUCTIONS)
                                                                        (a) [ ]
                                                                        (b) [ ]
- --------------------------------------------------------------------------------
3     SEC USE ONLY

- --------------------------------------------------------------------------------
4     CITIZENSHIP OR PLACE OF ORGANIZATION

      The Neterlands
- --------------------------------------------------------------------------------
                                5    SOLE VOTING POWER

          NUMBER OF                  0 shares
                              --------------------------------------------------
           SHARES               6    SHARED VOTING POWER
        BENEFICIALLY
          OWNED BY                   1,154,480 shares
                              --------------------------------------------------
            EACH                7    SOLE DISPOSITIVE POWER
         REPORTING
           PERSON                    0 shares
                              --------------------------------------------------
           WITH:                8    SHARED DISPOSITIVE POWER

                                     1,154,480 shares
- --------------------------------------------------------------------------------
9     AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

      1,154,480 shares
- --------------------------------------------------------------------------------
10    CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES 
      SEE INSTRUCTIONS)  [ ]

- --------------------------------------------------------------------------------
11    PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9

      9.5%
- --------------------------------------------------------------------------------
12    TYPE OF REPORTING PERSON (SEE INSTRUCTIONS)

      CO
- --------------------------------------------------------------------------------


                               Page 9 of 22 Pages
<PAGE>   10


                                  SCHEDULE 13G

Item 1(a).  NAME OF ISSUER: ArQule, Inc.

Item 1(b).  ADDRESS OF ISSUER'S PRINCIPAL EXECUTIVE OFFICES:
            200 Boston Avenue, Medford, Massachusetts  02155.

Item 2(a).  NAMES OF PERSONS FILING: Atlas Venture Fund II, L.P., Atlas Venture
            Associates II, L.P., Christopher J. Spray, Barry Fidelman, Allan
            Ferguson, Jean-Francois Formela, Atlas Venture Europe Fund B.V. and
            Atlas InvesteringsGroep N.V.

            Atlas Venture Associates II, L.P. is the sole general partner of
            Atlas Venture Fund II, L.P. Messrs. Spray, Fidelman, Ferguson and
            Formela are the individual general partners of Atlas Venture
            Associates II, L.P. Atlas InvesteringsGroep N.V. is the sole
            shareholder of Atlas Venture Europe Fund B.V.

Item 2(b).  ADDRESS OF PRINCIPAL BUSINESS OFFICE OR, IF NONE, RESIDENCE: The
            address of the principal business office of Atlas Venture Fund II,
            L.P., Atlas Venture Associates II, L.P. and Messrs. Spray, Fidelman,
            Ferguson and Formela is Atlas Venture, 222 Berkeley Street, Boston,
            Massachusetts 02116. The address of the principal business office of
            Atlas Venture Europe Fund B.V. and Atlas InvesteringsGroep N.V. is
            Atlas InvesteringsGroep N.V., Naarderpoort 1, 1411 MA Naarden, The
            Netherlands.

Item 2(c).  CITIZENSHIP: Atlas Venture Fund II, L.P. and Atlas Venture
            Associates II, L.P. are each a limited partnership organized under
            the laws of the State of Delaware. Messrs. Fidelman and Ferguson are
            citizens of the United States. Mr. Spray is a citizen of the United
            Kingdom. Mr. Formela is a citizen of France. Atlas Venture Europe
            Fund B.V. and Atlas InvesteringsGroep N.V. are each a corporation
            organized under the laws of The Netherlands.

Item 2(d).  TITLE OF CLASS OF SECURITIES:  Common Stock, $.01 par value.
            
Item 2(e).  CUSIP NUMBER:  00004269E1

Item 3.     IF THIS STATEMENT IS FILED PURSUANT TO RULES 13D-1(b), OR 13d-2(b) 
            or (c), CHECK WHETHER THE PERSON FILING IS A:


            Not Applicable.

Item 4.     OWNERSHIP.

      (a)   Amount Beneficially Owned:

            Each of Atlas Venture Fund II, L.P., Atlas Venture Associates II,
            L.P., Atlas Venture Europe Fund B.V. and Atlas InvesteringsGroep
            N.V. (individually an "Entity" and collectively the "Entities") may
            be deemed to own beneficially 1,154,480 shares of Common Stock as of
            December 31, 1998. Each of Messrs. Spray, Fidelman and Formela may
            be deemed to own beneficially 664,310 


                              Page 10 of 22 Pages


<PAGE>   11


            shares of Common Stock as of December 31, 1998. Mr. Ferguson may be
            deemed to own beneficially 676,310 shares (including 12,000 options)
            of Common Stock as of December 31, 1998.

            As of December 31, 1998, Atlas Venture Fund II, L.P. is the record
            owner of 664,310 shares of Common Stock, Atlas InvesteringsGroep
            N.V. is the record owner of 114,859 shares of Common Stock and Atlas
            Venture Europe Fund B.V. is the record owner of 375,311 shares of
            Common Stock (referred to as the "Record Shares"). By virtue of the
            affiliate relationships among the Entities, each Entity may be
            deemed to own beneficially all of the Record Shares. Hence, each
            Entity may be deemed to own beneficially 1,154,480 shares of Common
            Stock. In their capacities as individual general partners of Atlas
            Venture Associates II, L.P., each of Messrs. Spray, Fidelman and
            Formela may be deemed to own beneficially 664,310 shares of Common
            Stock. Mr. Ferguson may be deemed to own beneficially 676,310 shares
            (including 12,000 options) of Common Stock.

      (b)   Percent of Class:

                  Atlas Venture Fund II, L.P.                           9.5%
                  Atlas Venture Associates II, L.P.                     9.5%
                  Christopher J. Spray                                  5.5%
                  Barry Fidelman                                        5.5%
                  Allan Ferguson                                        5.6%
                  Jean-Francois Formela                                 5.5%
                  Atlas Venture Europe Fund B.V.                        9.5%
                  Atlas InvesteringsGroep N.V.                          9.5%

      The foregoing percentages are calculated based on the 12,165,403 shares of
      Common Stock reported to be outstanding in a Quarterly Report on Form 10-Q
      for ArQule, Inc. for the Quarter Ended September 30, 1998, as adjusted 
      pursuant to Rule 13d-3(d)(1).

      (c)   Number of shares as to which such person has:

                  (i)   sole power to vote or to direct the vote:

                        Allan Ferguson                          12,000 shares

                        0 shares as to each other reporting person


                              Page 11 of 22 Pages


<PAGE>   12


                  (ii)  shared power to vote or to direct the vote:

                        Atlas Venture Fund II, L.P.          1,154,480 shares
                        Atlas Venture Associates II, L.P.    1,154,480 shares
                        Christopher J. Spray                   664,310 shares
                        Barry Fidelman                         664,310 shares
                        Allan Ferguson                         676,310 shares
                        Jean-Francois Formela                  664,310 shares
                        Atlas Venture Europe Fund B.V.       1,154,480 shares
                        Atlas InvesteringsGroep N.V.         1,154,480 shares

                  (iii) sole power to dispose or to direct the disposition of:

                        Allan Ferguson                     12,000 shares

                        0 shares as to each other reporting person

                  (iv)  shared power to dispose or to direct the disposition of:

                        Atlas Venture Fund II, L.P.          1,154,480 shares
                        Atlas Venture Associates II, L.P.    1,154,480 shares
                        Christopher J. Spray                   664,310 shares
                        Barry Fidelman                         664,310 shares
                        Allan Ferguson                         676,310 shares
                        Jean-Francois Formela                  664,310 shares
                        Atlas Venture Europe Fund B.V.       1,154,480 shares
                        Atlas InvesteringsGroep N.V.         1,154,480 shares

            Each of the reporting persons expressly disclaims beneficial
            ownership of any shares of Common Stock of ArQule, Inc., except in
            the case of (i) Atlas Venture Fund II, L.P. for the 664,310 shares
            which it holds of record, (ii) Allan Ferguson for the 12,000 shares
            which he holds of record, (iii) Atlas InvesteringsGroep N.V. for the
            114,859 shares which it holds of record, and (iv) Atlas Venture
            Europe Fund B.V. for the 375,311 shares which it holds of record.

Item  5. OWNERSHIP OF FIVE PERCENT OR LESS OF A CLASS.

         Not Applicable

Item  6. OWNERSHIP OF MORE THAN FIVE PERCENT ON BEHALF OF ANOTHER PERSON.

         Not Applicable.

Item  7. IDENTIFICATION AND CLASSIFICATION OF THE SUBSIDIARY WHICH ACQUIRED THE
         SECURITY BEING REPORTED ON BY THE PARENT HOLDING COMPANY.

         Not Applicable.



                              Page 12 of 22 Pages


<PAGE>   13


Item  8.  IDENTIFICATION AND CLASSIFICATION OF MEMBERS OF THE GROUP.

          Not Applicable.

          The reporting persons expressly disclaim membership in a "group" as
          defined in Rule 13d-1(b)(1)(ii)(J).

Item  9.  NOTICE OF DISSOLUTION OF GROUP.

          Not Applicable.

Item  10. CERTIFICATIONS.

          Not Applicable. This statement on Schedule 13G is not filed pursuant
          to Rule 13d-1(b) or Rule 13d-1(c).


                              Page 13 of 22 Pages


<PAGE>   14



                                   SIGNATURES

     After reasonable inquiry and to the best of our knowledge and belief, we
certify that the information set forth in this statement is true, complete and
correct. We also hereby agree to file this statement jointly pursuant to the
Agreement listed on EXHIBIT 1 hereto.

Dated:  February 10, 1999

ATLAS VENTURE FUND II, L.P.                  ATLAS INVESTERINGSGROEP N.V.


By: Atlas Venture Associates II, L.P.

                                             By:             *                 
                                                 ---------------------------
                                                 Michiel de Haan,
                                                 Managing Director

By:               *            
    ---------------------------
    Christopher J. Spray,
    General Partner                                          *                
                                                 ---------------------------
                                                 Christopher J. Spray

ATLAS VENTURE ASSOCIATES II, L.P.


                                                             *                 
                                                 ---------------------------
By:               *                              Barry Fidelman
    ---------------------------
    Christopher J. Spray,
    General Partner

                                                             *          
                                                 ---------------------------  
                                                 Allan Ferguson

ATLAS VENTURE EUROPE FUND B.V.


By: Atlas InvesteringsGroep N.V.                             *          
                                                 ---------------------------
                                                 Jean-Francois Formela

By:              *                            
   ---------------------------
   Michiel de Haan,
   Managing Director


*  The undersigned attorney-in-fact, by signing her name below, does hereby
   sign this statement on behalf of the above indicated filers pursuant to
   Powers of Attorney filed hereto as EXHIBIT 2.


   /s/ Jeanne Larkin Henry                                 
   ---------------------------
   Jeanne Larkin Henry
   Attorney-in-fact


                              Page 14 of 22 Pages



<PAGE>   1

                                                                     EXHIBIT 1

                                    AGREEMENT

     Pursuant to Rule 13d-1(k)(1) under the Securities Exchange Act of 1934, the
undersigned hereby agree that only one statement containing the information
required by Schedule 13G need be filed with respect to the ownership by each of
the undersigned of shares of Common Stock of ArQule, Inc.

     This agreement may be executed in any number of counterparts, each of which
shall be deemed an original.


     EXECUTED this 10th day of February, 1999.


ATLAS VENTURE FUND II, L.P.                     ATLAS INVESTERINGSGROEP N.V.


By: Atlas Venture Associates II, L.P.
                                                By:              *            
                                                    ----------------------------
                                                    Michiel de Haan,
                                                    Managing Director

By:               *            
   ---------------------------------
   Christopher J. Spray,
   General Partner                                               *              
                                                    ----------------------------
                                                    Christopher J. Spray


ATLAS VENTURE ASSOCIATES II, L.P.


                                                                 *              
                                                    ----------------------------
By:               *                                 Barry Fidelman
   ---------------------------------
   Christopher J. Spray,
   General Partner

                                                                 *              
                                                    ----------------------------
                                                    Allan Ferguson


ATLAS VENTURE EUROPE FUND B.V.


By: Atlas InvesteringsGroep N.V.                                 *              
                                                    ----------------------------
                                                    Jean-Francois Formela

By:               *                            
   ---------------------------------
   Michiel de Haan,
   Managing Director


*    The undersigned attorney-in-fact, by signing her name below, does hereby
     sign this statement on behalf of the above indicated filers pursuant to
     Powers of Attorney filed hereto as EXHIBIT 2.

     /s/ Jeanne Larkin Henry                                 
     -------------------------------
     Jeanne Larkin Henry
     Attorney-in-fact


                              Page 15 of 22 Pages



<PAGE>   1


                                                                     EXHIBIT 2

                                POWER OF ATTORNEY

     KNOW ALL MEN BY THESE PRESENTS, that each person whose signature appears
below hereby constitutes and appoints each and any of Christopher J. Spray and
Jeanne Larkin Henry his true and lawful attorney-in-fact and agent, with full
power of substitution and resubstitution, for him and in his name, place and
stead, in any and all capacities (until revoked in writing) to sign any and all
instruments, certificates and documents required to be executed on behalf of
himself individually or on behalf of each or any of Atlas Venture Fund, L.P.,
Atlas Venture Associates, L.P., Atlas Venture Partners III, B.V., Atlas Venture
Fund II, L.P., Atlas Venture Associates II, L.P., Atlas Venture Europe Fund
B.V., Atlas InvesteringsGroep N.V., and Atlas Venture Beheer II B.V. pursuant to
sections 13 and 16 of the Securities Exchange Act of 1934, as amended (the
"Exchange Act"), and any and all regulations promulgated thereunder, and to file
the same, with all exhibits thereto, and any other documents in connection
therewith, with the Securities and Exchange Commission, and with any other
entity when and if such is mandated by the Exchange Act or by the By-laws of the
National Association of Securities Dealers, granting unto said attorney-in-fact
and agent full power and authority to do and perform each and every act and
thing requisite and necessary fully to all intents and purposes as he might or
could do in person thereby ratifying and confirming all that said
attorney-in-fact and agent, or his substitute or substitutes, may lawfully do or
cause to be done by virtue hereof.



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                              Page 16 of 22 Pages


<PAGE>   2


     IN WITNESS WHEREOF, this Power of Attorney has been signed as of the 31st
day of January, 1997.

                            /s/ Christopher J. Spray 
                            ------------------------------------
                            Christopher J. Spray



Commonwealth of Massachusetts)
                             ) ss:
County of Suffolk            )

     On this 31st day of January, 1997, before me personally came Christopher J.
Spray, known to me to be the person described and who executed the foregoing
instrument that he acknowledged that he executed the same.


[Notary Seal]               /s/ Elizabeth  A. Leblanc 
                            ------------------------------------
                            Notary Public

                            My commission expires: July 3, 1998



                              Page 17 of 22 Pages


<PAGE>   3


     IN WITNESS WHEREOF, this Power of Attorney has been signed as of the 31st
day of January, 1997.


                                            /s/ Barry Fidelman           
                                            -----------------------------------
                                            Barry Fidelman


Commonwealth of Massachusetts)
                             ) ss:
County of Suffolk            )

     On this 31st day of January, 1997, before me personally came Barry
Fidelman, known to me to be the person described and who executed the foregoing
instrument that he acknowledged that he executed the same.


[Notary Seal]                               /s/ Elizabeth  A. Leblanc 
                                            ------------------------------------
                                            Notary Public


                                            My commission expires: July 3, 1998


                              Page 18 of 22 Pages


<PAGE>   4


     IN WITNESS WHEREOF, this Power of Attorney has been signed as of the 31st
day of January, 1997.


                                            /s/ Michiel de Haan
                                            ---------------------------------
                                            Michiel de Haan


Commonwealth of Massachusetts)
                             ) ss:
County of Suffolk            )


     On this 31st day of January, 1997, before me personally came Michiel de
Haan, known to me to be the person described and who executed the foregoing
instrument that he acknowledged that he executed the same.


[Notary Seal]                               /s/ Elizabeth  A. Leblanc 
                                            ---------------------------------
                                            Notary Public

                                            My commission expires: July 3, 1998



                              Page 19 of 22 Pages


<PAGE>   5


     IN WITNESS WHEREOF, this Power of Attorney has been signed as of the 31st
day of January, 1997.

                                            /s/ Allan R. Ferguson 
                                            ----------------------------------
                                            Allan R. Ferguson

Commonwealth of Massachusetts)
                             ) ss:
County of Suffolk            )

     On this 31st day of January, 1997, before me personally came Allan R.
Ferguson, known to me to be the person described and who executed the foregoing
instrument that he acknowledged that he executed the same.

[Notary Seal]                               /s/ Elizabeth  A. Leblanc 
                                            ----------------------------------
                                            Notary Public

                                            My commission expires: July 3, 1998


                              Page 21 of 22 Pages


<PAGE>   6



     IN WITNESS WHEREOF, this Power of Attorney has been signed as of the 31st
day of January, 1997.

                                            /s/ Jean-Francois Formela
                                            ----------------------------------
                                            Jean-Francois Formela

Commonwealth of Massachusetts)
                             ) ss:
County of Suffolk            )

     On this 31st day of January, 1997, before me personally came Jean-Francois
Formela, known to me to be the person described and who executed the foregoing
instrument that he acknowledged that he executed the same.

[Notary Seal]                               /s/ Elizabeth  A. Leblanc 
                                            ----------------------------------
                                            Notary Public

                                            My commission expires: July 3, 1998



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