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. 9)¹

ArQule, Inc.

(Name of Issuer)

Common Stock, par value $0.01 per share

(Title of Class of Securities)

04269E107

(CUSIP Number)

December 31, 2019

(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)

☐

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 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 (“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

NAME OF REPORTING PERSON

Biotechnology Value Fund, L.P.

CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP

(a) ☒

(b) ☐

SEC USE ONLY

CITIZENSHIP OR PLACE OF ORGANIZATION

Delaware

NUMBER OF

SOLE VOTING POWER

BENEFICIALLY

0 shares

OWNED BY

SHARED VOTING POWER

EACH

REPORTING

2,471,860 (1)

PERSON WITH

SOLE DISPOSITIVE POWER

0 shares

SHARED DISPOSITIVE POWER

2,471,860 (1)

AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

2,471,860 (1)

CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES

☐

PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9)

1.3% (1)

TYPE OF REPORTING PERSON

(1) Includes 966,000 shares of Common Stock currently issuable upon the exercise of certain warrants.

CUSIP No. 04269E107

NAME OF REPORTING PERSON

BVF I GP LLC

CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP

(a) ☒

(b) ☐

SEC USE ONLY

CITIZENSHIP OR PLACE OF ORGANIZATION

Delaware

NUMBER OF

SOLE VOTING POWER

BENEFICIALLY

0 shares

OWNED BY

SHARED VOTING POWER

EACH

REPORTING

2,471,860 (1)

PERSON WITH

SOLE DISPOSITIVE POWER

0 shares

SHARED DISPOSITIVE POWER

2,471,860 (1)

AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

2,471,860 (1)

CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES

☐

PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9)

1.3% (1)

TYPE OF REPORTING PERSON

(1) Includes 966,000 shares of Common Stock currently issuable upon the exercise of certain warrants.

CUSIP No. 04269E107

NAME OF REPORTING PERSON

Biotechnology Value Fund II, L.P.

CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP

(a) ☒

(b) ☐

SEC USE ONLY

CITIZENSHIP OR PLACE OF ORGANIZATION

Delaware

NUMBER OF

SOLE VOTING POWER

BENEFICIALLY

0 shares

OWNED BY

SHARED VOTING POWER

EACH

REPORTING

1,936,143 (1)

PERSON WITH

SOLE DISPOSITIVE POWER

0 shares

SHARED DISPOSITIVE POWER

1,936,143 (1)

AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

1,936,143 (1)

CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES

☐

PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9)

Less than 1% (1)

TYPE OF REPORTING PERSON

(1) Includes 763,500 shares of Common Stock currently issuable upon the exercise of certain warrants.

CUSIP No. 04269E107

NAME OF REPORTING PERSON

BVF II GP LLC

CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP

(a) ☒

(b) ☐

SEC USE ONLY

CITIZENSHIP OR PLACE OF ORGANIZATION

Delaware

NUMBER OF

SOLE VOTING POWER

BENEFICIALLY

0 shares

OWNED BY

SHARED VOTING POWER

EACH

REPORTING

1,936,143 (1)

PERSON WITH

SOLE DISPOSITIVE POWER

0 shares

SHARED DISPOSITIVE POWER

1,936,143 (1)

AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

1,936,143 (1)

CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES

☐

PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9)

Less than 1% (1)

TYPE OF REPORTING PERSON

(1) Includes 763,500 shares of Common Stock currently issuable upon the exercise of certain warrants.

CUSIP No. 04269E107

NAME OF REPORTING PERSON

Biotechnology Value Trading Fund OS LP

CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP

(a) ☒

(b) ☐

SEC USE ONLY

CITIZENSHIP OR PLACE OF ORGANIZATION

Cayman Islands

NUMBER OF

SOLE VOTING POWER

BENEFICIALLY

0 shares

OWNED BY

SHARED VOTING POWER

EACH

REPORTING

339,220 (1)

PERSON WITH

SOLE DISPOSITIVE POWER

0 shares

SHARED DISPOSITIVE POWER

339,220 (1)

AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

339,220 (1)

CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES

☐

PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9)

Less than 1% (1)

TYPE OF REPORTING PERSON

(1) Includes 133,300 shares of Common Stock currently issuable upon the exercise of certain warrants.

CUSIP No. 04269E107

NAME OF REPORTING PERSON

BVF Partners OS Ltd.

CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP

(a) ☒

(b) ☐

SEC USE ONLY

CITIZENSHIP OR PLACE OF ORGANIZATION

Cayman Islands

NUMBER OF

SOLE VOTING POWER

BENEFICIALLY

0 shares

OWNED BY

SHARED VOTING POWER

EACH

REPORTING

339,220 (1)

PERSON WITH

SOLE DISPOSITIVE POWER

0 shares

SHARED DISPOSITIVE POWER

339,220 (1)

AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

339,220 (1)

CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES

☐

PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9)

Less than 1% (1)

TYPE OF REPORTING PERSON

(1) Includes 133,300 shares of Common Stock currently issuable upon the exercise of certain warrants.

CUSIP No. 04269E107

NAME OF REPORTING PERSON

BVF GP HOLDINGS LLC

CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP

(a) ☒

(b) ☐

SEC USE ONLY

CITIZENSHIP OR PLACE OF ORGANIZATION

Delaware

NUMBER OF

SOLE VOTING POWER

BENEFICIALLY

0 shares

OWNED BY

SHARED VOTING POWER

EACH

REPORTING

4,408,003 (1)

PERSON WITH

SOLE DISPOSITIVE POWER

0 shares

SHARED DISPOSITIVE POWER

4,408,003 (1)

AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

4,408,003 (1)

CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES

☐

PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9)

3.6% (1)

TYPE OF REPORTING PERSON

(1) Includes 1,729,500 shares of Common Stock currently issuable upon the exercise of certain warrants.

CUSIP No. 04269E107

NAME OF REPORTING PERSON

BVF Partners L.P.

CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP

(a) ☒

(b) ☐

SEC USE ONLY

CITIZENSHIP OR PLACE OF ORGANIZATION

Delaware

NUMBER OF

SOLE VOTING POWER

BENEFICIALLY

0 shares

OWNED BY

SHARED VOTING POWER

EACH

REPORTING

4,902,383 (1)

PERSON WITH

SOLE DISPOSITIVE POWER

0 shares

SHARED DISPOSITIVE POWER

4,902,383 (1)

AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

4,902,383 (1)

CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES

☐

PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9)

4.0% (1)

TYPE OF REPORTING PERSON

PN, IA

(1) Includes 1,923,700 shares of Common Stock currently issuable upon the exercise of certain warrants.

CUSIP No. 04269E107

NAME OF REPORTING PERSON

BVF Inc.

CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP

(a) ☒

(b) ☐

SEC USE ONLY

CITIZENSHIP OR PLACE OF ORGANIZATION

Delaware

NUMBER OF

SOLE VOTING POWER

BENEFICIALLY

0 shares

OWNED BY

SHARED VOTING POWER

EACH

REPORTING

4,902,383 (1)

PERSON WITH

SOLE DISPOSITIVE POWER

0 shares

SHARED DISPOSITIVE POWER

4,902,383 (1)

AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

4,902,383 (1)

CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES

☐

PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9)

4.0% (1)

TYPE OF REPORTING PERSON

(1) Includes 1,923,700 shares of Common Stock currently issuable upon the exercise of certain warrants.

CUSIP No. 04269E107

NAME OF REPORTING PERSON

Mark N. Lampert

CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP

(a) ☒

(b) ☐

SEC USE ONLY

CITIZENSHIP OR PLACE OF ORGANIZATION

United States

NUMBER OF

SOLE VOTING POWER

BENEFICIALLY

0 shares

OWNED BY

SHARED VOTING POWER

EACH

REPORTING

4,902,383 (1)

PERSON WITH

SOLE DISPOSITIVE POWER

0 shares

SHARED DISPOSITIVE POWER

4,902,383 (1)

AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

4,902,383 (1)

CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES

☐

PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9)

4.0% (1)

TYPE OF REPORTING PERSON

(1) Includes 1,923,700 shares of Common Stock currently issuable upon the exercise of certain warrants.

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:

One Wall Street

Burlington, Massachusetts 01803

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”)

44 Montgomery St., 40th Floor

San Francisco, California 94104

Citizenship: Delaware

BVF I GP LLC (“BVF GP”)

44 Montgomery St., 40th Floor

San Francisco, California 94104

Citizenship: Delaware

Biotechnology Value Fund II, L.P. (“BVF2”)

44 Montgomery St., 40th Floor

San Francisco, California 94104

Citizenship: Delaware

BVF II GP LLC (“BVF2 GP”)

44 Montgomery St., 40th Floor

San Francisco, California 94104

Citizenship: Delaware

Biotechnology Value Trading Fund OS LP (“Trading Fund OS”)

PO Box 309 Ugland House

Grand Cayman, KY1-1104

Cayman Islands

Citizenship: Cayman Islands

BVF Partners OS Ltd. (“Partners OS”)

PO Box 309 Ugland House

Grand Cayman, KY1-1104

Cayman Islands

Citizenship: Cayman Islands

BVF GP Holdings LLC (“BVF GPH”)

44 Montgomery St., 40th Floor

San Francisco, California 94104

Citizenship: Delaware

BVF Partners L.P. (“Partners”)

44 Montgomery St., 40th Floor

San Francisco, California 94104

Citizenship: Delaware

CUSIP No. 04269E107

BVF Inc.

44 Montgomery St., 40th Floor

San Francisco, California 94104

Citizenship: Delaware

Mark N. Lampert (“Mr. Lampert”)

44 Montgomery St., 40th 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.”

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: ____

CUSIP No. 04269E107

Item 4.

Ownership

(a)

Amount beneficially owned:

As of the close of business on December 31, 2019, the Reporting Persons held 1,923,700 Warrants exercisable for an aggregate of 1,923,700 shares of Common Stock (the “Warrants”). The Warrants are subject to an exercise limitation, and may not be exercised if, after such exercise, the Reporting Persons would beneficially own in the aggregate, as determined in accordance with Section 13(d) of the Securities Exchange Act of 1934, more than 19.9% of the number of shares of Common Stock then issued and outstanding. Such Warrants have an initial exercise price of $1.75 per share, subject to adjustment pursuant to the terms of the Warrants, and expire on October 11, 2021. As of December 31, 2019, the Warrant exercise limitation described above does not limit the exercise of the Warrants by the Reporting Persons.

As of December 31, 2019 (i) BVF beneficially owned 2,471,860 shares of Common Stock, including 966,000 shares of Common Stock issuable upon the exercise of Warrants, (ii) BVF2 beneficially owned 1,936,143 shares of Common Stock, including 763,500 shares of Common Stock issuable upon the exercise of Warrants and (iii) Trading Fund OS beneficially owned 339,220 shares of Common Stock, including 133,300 shares of Common Stock issuable upon the exercise of Warrants.

BVF GP, as the general partner of BVF, may be deemed to beneficially own the 2,471,860 shares of Common Stock beneficially owned by BVF.

BVF2 GP, as the general partner of BVF2, may be deemed to beneficially own the 1,936,143 shares of Common Stock beneficially owned by BVF2.

Partners OS, as the general partner of Trading Fund OS, may be deemed to beneficially own the 339,220 shares of Common Stock beneficially owned by Trading Fund OS.

BVF GPH, as the sole member of each of BVF GP and BVF2 GP, may be deemed to beneficially own the 4,408,003 shares of Common Stock beneficially owned in the aggregate by BVF and BVF2.

Partners, as the investment manager of BVF, BVF2, and Trading Fund OS, and the sole member of Partners OS, may be deemed to beneficially own the 4,902,383 shares of Common Stock beneficially owned in the aggregate by BVF, BVF2, Trading Fund OS, and a certain Partners managed account (the “Partners Managed Account”), including 155,160 shares of Common Stock, which includes 60,900 shares of Common Stock issuable upon exercise of the Warrants, held in the Partners Managed Account.

BVF Inc., as the general partner of Partners, may be deemed to beneficially own the 4,902,383 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 4,902,383 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. BVF GP disclaims beneficial ownership of the shares of Common Stock beneficially owned by BVF. BVF2 GP disclaims beneficial ownership of the shares of Common Stock beneficially owned by BVF2. Partners OS disclaims beneficial ownership of the shares of Common Stock beneficially owned by Trading Fund OS. BVF GPH disclaims beneficial ownership of the shares of Common Stock beneficially owned by BVF and BVF2. Each of Partners, BVF Inc. and Mr. Lampert disclaims beneficial ownership of the shares of Common Stock beneficially owned by BVF, BVF2, Trading Fund OS, and the Partners Managed Account, 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.

CUSIP No. 04269E107

(b)

Percent of class:

The following percentages are based on a denominator which is the sum of: (i) 120,787,771 shares of Common Stock outstanding as of December 5, 2019, as set forth in the Issuer’s Agreement and Plan of Merger, dated December 6, 2019, included as Exhibit 2.1 to the Issuer’s Current Report on Form 8-K filed with the Securities and Exchange Commission on December 9, 2019, and (ii) certain or all of the 1,923,700 shares of Common Stock underlying Warrants, as applicable.

As of December 31, 2019 (i) BVF beneficially owned approximately 1.3% of the outstanding shares of Common Stock, (ii) BVF2 beneficially owned less than 1% of the outstanding shares of Common Stock, (iii) Trading Fund OS beneficially owned less than 1% of the outstanding shares of Common Stock, (iv) BVF GP may be deemed to beneficially own approximately 1.3% of the outstanding shares of Common Stock, (v) BVF2 GP may be deemed to beneficially own less than 1% of the outstanding shares of Common Stock, (vi) Partners OS may be deemed to beneficially own less than 1% of the outstanding shares of Common Stock, (vii) BVF GPH may be deemed to beneficially own approximately 3.6% of the outstanding shares of Common Stock and (viii) each of Partners, BVF Inc. and Mr. Lampert may be deemed to beneficially own approximately 4.0% of the outstanding shares of Common Stock (less than 1% of which is held in the Partners Managed Account).

(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.

Item 5.

Ownership of Five Percent or Less of a Class.

If this statement is being filed to report the fact that as of the date hereof the reporting person has ceased to be the beneficial owner of more than five percent of the class of securities, check the following [X].

CUSIP No. 04269E107

Item 6.

Ownership of More than Five Percent on Behalf of Another Person.

Not Applicable

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

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.

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: February 14, 2020

BIOTECHNOLOGY VALUE FUND, L.P.		BIOTECHNOLOGY VALUE TRADING FUND OS LP

By:	BVF I GP LLC., its general partner	By:	BVF Partners L.P., its investment manager
		By:	BVF Inc., its general partner
By:	/s/ Mark N. Lampert
	Mark N. Lampert	By:	/s/ Mark N. Lampert
	Chief Executive Officer		Mark Lampert
			President

BVF I GP LLC
		BVF GP HOLDINGS LLC
By:	/s/ Mark N. Lampert
	Mark N. Lampert	By:	/s/ Mark N. Lampert
	Chief Executive Officer		Mark Lampert
			Chief Executive Officer

BIOTECHNOLOGY VALUE FUND II, L.P.
		BVF PARTNERS L.P.
By:	BVF II GP LLC its general partner
		By:	BVF Inc., its general partner
By:	/s/ Mark N. Lampert
	Mark N. Lampert	By:	/s/ Mark N. Lampert
	Chief Executive Officer		Mark N. Lampert
			President

BVF II GP LLC
		BVF INC.
By:	/s/ Mark N. Lampert
	Mark N. Lampert	By:	/s/ Mark N. Lampert
	Chief Executive Officer		Mark Lampert
			President

BVF PARTNERS OS LTD.
		/s/ Mark N. Lampert
By:	BVF Partners L.P., its sole member	MARK N. LAMPERT
By:	BVF Inc., its general partner

By:	/s/ Mark N. Lampert
	Mark N. Lampert
	President

ARQULE INC SC 13G/A