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

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

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).

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

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

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

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

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

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

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

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

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

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

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

One Wall Street

Burlington, Massachusetts 01803

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

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.”

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

04269E107

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.

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).

See Cover Pages Items 5-9.

See Cover Pages Items 5-9.

See Cover Pages Items 5-9.

See Cover Pages Items 5-9.

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].

Not Applicable

Not Applicable.

See Exhibit 99.1

Not Applicable.

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.

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

Exhibit 99.1

Joint Filing Agreement

The undersigned hereby agree that the Statement on Schedule 13G dated February 14, 2020 with respect to the common stock, par value $0.01 per share, of ArQule, Inc., and any further amendments thereto executed by each and any of the undersigned shall be filed on behalf of each of the undersigned pursuant to and in accordance with the provisions of Rule 13d-1(k)(1) under the Securities Exchange Act of 1934, as amended.