sc13ga207422arq_05262015.htm
UNITED STATES
SECURITIES AND EXCHANGE COMMISSION
Washington, D.C. 20549

SCHEDULE 13G
(Rule 13d-102)

INFORMATION TO BE INCLUDED IN STATEMENTS FILED PURSUANT
TO RULES 13d-1(b), (c), AND (d) AND AMENDMENTS THERETO FILED
PURSUANT TO RULE 13d-2(b)
 
(Amendment No. 2)1
 

ArQule, Inc.
 (Name of Issuer)
 
Common Stock, par value $0.01 per share
 (Title of Class of Securities)
 
04269E107
 (CUSIP Number)
 
May 26, 2015
 (Date of Event Which Requires Filing of this Statement)
 
 

Check the appropriate box to designate the rule pursuant to which this Schedule is filed:
 
   o  Rule 13d-1(b)
 
   x  Rule 13d-1(c)
 
   o  Rule 13d-1(d)
 
 

_______________
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 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).
 
 
 
 
CUSIP NO. 04269E107
 
 
1
NAME OF REPORTING PERSON
 
Biotechnology Value Fund, L.P.
2
CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP
  (a) x
  (b) o
3
SEC USE ONLY
 
4
CITIZENSHIP OR PLACE OF ORGANIZATION
 
Delaware
NUMBER OF SHARES BENEFICIALLY OWNED BY EACH REPORTING PERSON WITH
5
SOLE VOTING POWER
 
0 shares
6
SHARED VOTING POWER
 
 2,931,016
7
SOLE DISPOSITIVE POWER
 
0 shares
8
SHARED DISPOSITIVE POWER
 
 2,931,016
9
AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
 
 2,931,016
10
CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES
 
¨
11
PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9)
 
4.7%
12
TYPE OF REPORTING PERSON
 
PN

 
2
 
CUSIP NO. 04269E107
 
1
NAME OF REPORTING PERSON
 
Biotechnology Value Fund II, L.P.
2
CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP
  (a) x
  (b) o
3
SEC USE ONLY
 
4
CITIZENSHIP OR PLACE OF ORGANIZATION
 
Delaware
NUMBER OF SHARES BENEFICIALLY OWNED BY EACH REPORTING PERSON WITH
5
SOLE VOTING POWER
 
0 shares
6
SHARED VOTING POWER
 
1,779,082
7
SOLE DISPOSITIVE POWER
 
0 shares
8
SHARED DISPOSITIVE POWER
 
1,779,082
9
AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
 
1,779,082
10
CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES
 
¨
11
PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9)
 
2.8%
12
TYPE OF REPORTING PERSON
 
PN

 
3
 
CUSIP NO. 04269E107
 
1
NAME OF REPORTING PERSON
 
BVF Investments, L.L.C.
2
CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP
  (a) x
  (b) o
3
SEC USE ONLY
 
4
CITIZENSHIP OR PLACE OF ORGANIZATION
 
Delaware
NUMBER OF SHARES BENEFICIALLY OWNED BY EACH REPORTING PERSON WITH
5
SOLE VOTING POWER
 
0 shares
6
SHARED VOTING POWER
 
0 shares
7
SOLE DISPOSITIVE POWER
 
0 shares
8
SHARED DISPOSITIVE POWER
 
0 shares
9
AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
 
0
10
CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES
 
¨
11
PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9)
 
0%
12
TYPE OF REPORTING PERSON
 
OO

 
4
 
CUSIP NO. 04269E107
 
1
NAME OF REPORTING PERSON
 
Investment 10, L.L.C.
2
CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP
  (a) x
  (b) o
3
SEC USE ONLY
 
4
CITIZENSHIP OR PLACE OF ORGANIZATION
 
Illinois
NUMBER OF SHARES BENEFICIALLY OWNED BY EACH REPORTING PERSON WITH
5
SOLE VOTING POWER
 
0 shares
6
SHARED VOTING POWER
 
681,799
7
SOLE DISPOSITIVE POWER
 
0 shares
8
SHARED DISPOSITIVE POWER
 
681,799
9
AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
 
681,799
10
CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES
 
¨
11
PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9)
 
1.1%
12
TYPE OF REPORTING PERSON
 
OO

 
5
 
CUSIP NO. 04269E107
 
1
NAME OF REPORTING PERSON
 
MSI BVF SPV, LLC
2
CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP
  (a) x
  (b) o
3
SEC USE ONLY
 
4
CITIZENSHIP OR PLACE OF ORGANIZATION
 
Delaware
NUMBER OF SHARES BENEFICIALLY OWNED BY EACH REPORTING PERSON WITH
5
SOLE VOTING POWER
 
0 shares
6
SHARED VOTING POWER
 
964,221
7
SOLE DISPOSITIVE POWER
 
0 shares
8
SHARED DISPOSITIVE POWER
 
964,221
9
AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
 
964,221
10
CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES
 
¨
11
PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9)
 
1.5%
12
TYPE OF REPORTING PERSON
 
OO

 
6
 
CUSIP NO. 04269E107
 
1
NAME OF REPORTING PERSON
 
BVF Partners L.P.
2
CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP
  (a) x
  (b) o
3
SEC USE ONLY
 
4
CITIZENSHIP OR PLACE OF ORGANIZATION
 
Delaware
NUMBER OF SHARES BENEFICIALLY OWNED BY EACH REPORTING PERSON WITH
5
SOLE VOTING POWER
 
0 shares
6
SHARED VOTING POWER
 
6,356,118
7
SOLE DISPOSITIVE POWER
 
0 shares
8
SHARED DISPOSITIVE POWER
 
6,356,118
9
AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
 
6,356,118
10
CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES
 
¨
11
PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9)
 
10.1%
12
TYPE OF REPORTING PERSON
 
PN, IA

 
7
 
CUSIP NO. 04269E107
 
1
NAME OF REPORTING PERSON
 
BVF Inc.
2
CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP
  (a) x
  (b) o
3
SEC USE ONLY
 
4
CITIZENSHIP OR PLACE OF ORGANIZATION
 
Delaware
NUMBER OF SHARES BENEFICIALLY OWNED BY EACH REPORTING PERSON WITH
5
SOLE VOTING POWER
 
0 shares
6
SHARED VOTING POWER
 
6,356,118
7
SOLE DISPOSITIVE POWER
 
0 shares
8
SHARED DISPOSITIVE POWER
 
6,356,118
9
AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
 
6,356,118
10
CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES
 
¨
11
PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9)
 
10.1%
12
TYPE OF REPORTING PERSON
 
CO

 
8
 
CUSIP NO. 04269E107
 
1
NAME OF REPORTING PERSON
 
Mark N. Lampert
2
CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP
  (a) x
  (b) o
3
SEC USE ONLY
 
4
CITIZENSHIP OR PLACE OF ORGANIZATION
 
United States
NUMBER OF SHARES BENEFICIALLY OWNED BY EACH REPORTING PERSON WITH
5
SOLE VOTING POWER
 
0 shares
6
SHARED VOTING POWER
 
6,356,118
7
SOLE DISPOSITIVE POWER
 
0 shares
8
SHARED DISPOSITIVE POWER
 
6,356,118
9
AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
 
6,356,118
10
CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES
 
¨
11
PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9)
 
10.1%
12
TYPE OF REPORTING PERSON
 
IN

 
9
 
CUSIP NO. 04269E107
 
Item 1(a).
Name of Issuer:

ArQule, Inc., a Delaware corporation (the “Issuer”).

Item 1(b).
Address of Issuer's Principal Executive Offices:

19 Presidential Way
Woburn, Massachusetts 01801

Item 2(a).
Name of Person Filing
Item 2(b).
Address of Principal Business Office or, if None, Residence
Item 2(c).
Citizenship

Biotechnology Value Fund, L.P. (“BVF”)
1 Sansome Street, 30th Floor
San Francisco, California 94104
Citizenship: Delaware

Biotechnology Value Fund II, L.P. (“BVF2”)
1 Sansome Street, 30th Floor
San Francisco, California 94104
Citizenship: Delaware

BVF Investments, L.L.C. (“BVLLC”)
1 Sansome Street, 30th Floor
San Francisco, California 94104
Citizenship: Delaware

Investment 10, L.L.C. (“ILL10”)
900 North Michigan Avenue, Suite 1100
Chicago, Illinois 60611
Citizenship: Illinois

MSI BVF SPV, LLC (“MSI”)
c/o Magnitude Capital, LLC
601 Lexington Avenue, 59th Floor
New York, NY 10022
Citizenship: Delaware

BVF Partners L.P. (“Partners”)
1 Sansome Street, 30th Floor
San Francisco, California 94104
Citizenship: Delaware

BVF Inc.
1 Sansome Street, 30th Floor
San Francisco, California 94104
Citizenship: Delaware

Mark N. Lampert (“Mr. Lampert”)
1 Sansome Street, 30th Floor
San Francisco, California 94104
Citizenship: United States

Each of the foregoing is referred to as a “Reporting Person” and collectively as the “Reporting Persons.”
 
 
10
 
CUSIP NO. 04269E107
 
Item 2(d).
Title of Class of Securities:

Common Stock, par value $0.01 per share (the “Common Stock”)

Item 2(e).
CUSIP Number:

04269E107

Item 3.
If This Statement is Filed Pursuant to Rule 13d-1(b), or 13d-2(b) or (c), Check Whether the Person Filing is a:

 
 
/x/
Not applicable.

 
(a)
/ /
Broker or dealer registered under Section 15 of the Exchange Act.

 
(b)
/ /
Bank as defined in Section 3(a)(6) of the Exchange Act.

 
(c)
/ /
Insurance company as defined in Section 3(a)(19) of the Exchange Act.

 
(d)
/ /
Investment company registered under Section 8 of the Investment Company Act.

 
(e)
/ /
An investment adviser in accordance with Rule 13d-1(b)(1)(ii)(E).

 
(f)
/ /
An employee benefit plan or endowment fund in accordance with Rule 13d-1(b)(1)(ii)(F).

 
(g)
/ /
A parent holding company or control person in accordance with Rule 13d-1(b)(1)(ii)(G).

 
(h)
/ /
A savings association as defined in Section 3(b) of the Federal Deposit Insurance Act.

 
(i)
/ /
A church plan that is excluded from the definition of an investment company under Section 3(c)(14) of the Investment Company Act.

 
(j)
/ /
Group, in accordance with Rule 13d-1(b)(1)(ii)(J).

 
(k)
/ /
Group, in accordance with Rule 240.13d-1(b)(1)(ii)(K). If filing as a non-U.S. institution in accordance with Rule 240.13d-1(b)(1)(ii)(J), please specify the type of institution: ____

Item 4.
Ownership

 
(a)
Amount beneficially owned:
 
 
As of the close of business on May 28, 2015 (i) BVF beneficially owned  2,931,016  shares of Common Stock, (ii) BVF2 beneficially owned 1,779,082  shares of Common Stock, (iii) BVLLC did not own any shares of Common Stock, (iv) ILL10 beneficially owned 681,799 shares of Common Stock, and (v) MSI beneficially owned 964,221 shares of Common Stock.
 
 
11
 
CUSIP NO. 04269E107
 
 
Partners, as the general partner of BVF and BVF2, and the investment adviser of each of ILL10 and MSI, may be deemed to beneficially own the 6,356,118 shares of Common Stock beneficially owned in the aggregate by BVF, BVF2, ILL10 and MSI. Partners is the manager of BVLLC.
 
 
BVF Inc., as the general partner of Partners, may be deemed to beneficially own the 6,356,118 shares of Common Stock beneficially owned by Partners.
 
 
Mr. Lampert, as a director and officer of BVF Inc., may be deemed to beneficially own the 6,356,118 shares of Common Stock beneficially owned by BVF Inc.
 
 
The foregoing should not be construed in and of itself as an admission by any Reporting Person as to beneficial ownership of any shares of Common Stock owned by another Reporting Person.  Each of Partners, BVF Inc. and Mr. Lampert disclaims beneficial ownership of the shares of Common Stock beneficially owned by BVF, BVF2, ILL10 and MSI, and the filing of this statement shall not be construed as an admission that any such person or entity is the beneficial owner of any such securities.
 
 
(b)
Percent of class:
 
 
The following percentages are based on 62,819,191 shares of Common Stock outstanding as of April 22, 2015, as disclosed in the Issuer’s Quarterly Report on Form 10-Q filed with the Securities and Exchange Commission on May 6, 2015.
 
 
As of the close of business on May 28, 2015, (i) BVF beneficially owned approximately 4.7% of the outstanding shares of Common Stock, (ii) BVF2 beneficially owned approximately 2.8% of the outstanding shares of Common Stock, (iii) BVLLC did not own any percentage of the outstanding shares of Common Stock, (iv) ILL10 beneficially owned approximately 1.1% of the outstanding shares of Common Stock, (v) MSI beneficially owned approximately 1.5% of the outstanding shares of Common Stock, and (vi) each of Partners, BVF Inc. and Mr. Lampert may be deemed to beneficially own approximately 10.1% of the outstanding shares of Common Stock.
 
 
(c)
Number of shares as to which such person has:
 
 
(i)
Sole power to vote or to direct the vote
 
 
See Cover Pages Items 5-9.
 
 
(ii)
Shared power to vote or to direct the vote
 
 
See Cover Pages Items 5-9.
 
 
(iii)
Sole power to dispose or to direct the disposition of
 
 
See Cover Pages Items 5-9.
 
 
(iv)
Shared power to dispose or to direct the disposition of
 
 
See Cover Pages Items 5-9.
 
 
12
 
CUSIP NO. 04269E107
 
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.

Pursuant to the operating agreement of BVLLC, Partners is authorized, among other things, to invest the contributed capital of Samana Capital, L.P., the majority member of BVLLC, in the shares of Common Stock and other securities of the Issuer and to vote, exercise or convert and dispose of each security, and is entitled to receive fees based on assets under management and, subject to certain exceptions, allocations based on realized and unrealized gains on such assets. As of May 28, 2015, BVLLC does not own any shares of Common Stock of the Issuer.

Partners, BVF Inc. and Mr. Lampert share voting and dispositive power over the shares of Common Stock beneficially owned by BVF, BVF2, ILL10 and MSI.

Item 7.
Identification and Classification of the Subsidiary That Acquired the Security Being Reported on by the Parent Holding Company or Control Person.

Not Applicable.

Item 8.
Identification and Classification of Members of the Group.

See Exhibit 99.1 to the Schedule 13G filed by the Reporting Persons with the Securities and Exchange Commission on August 15, 2014.

Item 9.
Notice of Dissolution of Group.

Not Applicable.

Item 10.
Certifications.

By signing below each of the undersigned certifies that, to the best of its knowledge and belief, the securities referred to above were not acquired and are not held for the purpose of or with the effect of changing or influencing the control of the issuer of the securities and were not acquired and are not held in connection with or as a participant in any transaction having that purpose or effect.
 
 
13
 
CUSIP NO. 04269E107
 
SIGNATURE

After reasonable inquiry and to the best of his knowledge and belief, each of the undersigned certifies that the information set forth in this statement is true, complete and correct.

Dated:  May 28, 2015

BIOTECHNOLOGY VALUE FUND, L.P.
  
INVESTMENT 10, L.L.C.
 
 
      
By:
BVF Partners L.P., its general partner
  
By:
BVF Partners L.P., its investment adviser
By:
BVF Inc., its general partner
  
By:
BVF Inc., its general partner
 
 
    
 
By:
/s/ Mark N. Lampert
  
By:
/s/ Mark N. Lampert
 
Mark N. Lampert
    
Mark N. Lampert
 
President
    
President
 
 
      
 
 
      
BIOTECHNOLOGY VALUE FUND II, L.P.
  
MSI BVF SPV, LLC
 
 
      
By:
BVF Partners L.P., its general partner
  
By:
BVF Partners L.P., its investment adviser
By:
BVF Inc., its general partner
  
By:
BVF Inc., its general partner
 
 
    
 
By:
/s/ Mark N. Lampert
  
By:
/s/ Mark N. Lampert
 
Mark N. Lampert
    
Mark N. Lampert
 
President
    
President
       
 
     
BVF INC.
       
 
BVF PARTNERS L.P.
  
By:
/s/ Mark N. Lampert
       
Mark N. Lampert
By:
BVF Inc., its general partner
    
President
 
 
      
By:
/s/ Mark N. Lampert
    
 
 
Mark N. Lampert
    
/s/ Mark N. Lampert
 
President
    
MARK N. LAMPERT

BVF INVESTMENTS, L.L.C.
 
By:
BVF Partners L.P., its manager
By:
BVF Inc., its general partner
   
By:
/s/ Mark N. Lampert
 
Mark N. Lampert
 
President
 
 
14