Exhibit 10.1

Execution Version

SUNESIS PHARMACEUTICALS, INC.

CONTROLLED EQUITY OFFERINGSM

AMENDMENT NO. 2 TO

SALES AGREEMENT

March 12, 2015

Cantor Fitzgerald & Co.

499 Park Avenue

New York, NY 10022

Ladies and Gentlemen:

Reference is made to the Sales Agreement, dated August 11, 2011 as amended on
April 10, 2013, including the Schedules thereto (the “Sales Agreement”), between
Cantor Fitzgerald & Co. (“CF&Co”) and Sunesis Pharmaceuticals, Inc., a Delaware
corporation (the “Company”), pursuant to which the Company agreed to sell
through CF&Co, as sales agent, shares of common stock, par value $0.0001 per
share, of the Company. All capitalized terms used in this Amendment No. 2 to
Sales Agreement between CF&Co and the Company (this “Amendment”) and not
otherwise defined herein shall have the respective meanings assigned to such
terms in the Sales Agreement. CF&Co and the Company agree as follows:

A. Amendments to Sales Agreement. The Sales Agreement is amended as follows:

1. The first sentence of Section 1 of the Sales Agreement is hereby deleted and
replaced with the following:

“The Company agrees that, from time to time after March 12, 2015 and during the
term of this Agreement, on the terms and subject to the conditions set forth
herein, it may issue and sell through CF&Co, acting as agent and/or principal,
shares (the “Placement Shares”) of common stock of the Company, par value
$0.0001 per share (the “Common Stock”), having an aggregate offering price of up
to $30,000,000 and such amount of Placement Shares shall be available for offer
and sale in addition to any offers and sales of Placement Shares registered
under the Prospectus Supplement filed by the Company on August 11, 2011, the
Prospectus Supplement filed by the Company on April 10, 2013, and the Prospectus
Supplement declared effective on April 30, 2013 pursuant to this Agreement,
subject to any limitations set forth in Section 6(e) hereof (“Maximum Amount”).”

2. The first sentence of the second paragraph of Section 1 of the Sales
Agreement is amended by deleting the parenthetical “(No. 333-166366)” and
replacing it with “(File No. 333-195779).”

3. (i) Section 11(d) of the Sales Agreement is hereby deleted in its entirety
and Section 11(e) is relabeled as Section 11(d); (ii) Newly labeled
Section 11(d) of the Sales Agreement is hereby deleted and replaced in its
entirety with the following: “This

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Agreement shall remain in full force and effect unless terminated pursuant to
Sections 8(k),11(a), (b), or (c) above or otherwise by mutual agreement of the
parties”; (iii) Section 11(f) of the Sales Agreement is relabeled as
Section 11(e); and (iv) Section 11(g) of the Sales Agreement is relabeled as
Section 11(f).

4. Schedule 1 is amended by adding the words “and March 12, 2015” after “April
10, 2013.”

5. Schedule 2 is amended by adding under Cantor Fitzgerald & Co. after “Josh
Feldman (jfeldman@cantor.com)”:

“Sameer Vasudev (svasudev@cantor.com)

With copies to:

CFControlledEquityOffering@cantor.com”

6. The first sentence of the Form of Representation Date Certificate attached as
Exhibit 7(m) is amended to add “and March 12, 2015” after “April 10, 2013.”

B. Prospectus Supplement. The Company shall file a Rule 424(b) Prospectus
Supplement reflecting this Amendment within 2 business days of the date hereof.

C. No Other Amendments. Except as set forth in Part A above, all the terms and
provisions of the Sales Agreement shall continue in full force and effect.

D. Counterparts. This Amendment may be executed in two or more counterparts,
each of which shall be deemed an original, but all of which together shall
constitute one and the same instrument. Delivery of an executed Amendment by one
party to the other may be made by facsimile or email transmission.

E. Governing Law. This Amendment shall be governed by, and construed in
accordance with, the internal laws of the State of New York without regard to
the principles of conflicts of laws.

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2

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If the foregoing correctly sets forth the understanding between us, please so
indicate in the space provided below for that purpose.

 

Very truly yours, SUNESIS PHARMACEUTICALS, INC. By:  

/s/ Eric H. Bjerkholt

Name: Eric H. Bjerkholt Title: Executive Vice President, Corporate Development
and Finance, and Chief Financial Officer ACCEPTED as of the date first above
written: CANTOR FITZGERALD & CO. By:

/s/ Jeffrey Lumby

Name: Jeffrey Lumby Title: Senior Managing Director

 

SIGNATURE PAGE

SUNESIS PHARMACEUTICALS, INC. – AMENDMENT NO. 2 TO SALES AGREEMENT