Exhibit 10.52

THIRD AMENDMENT

TO THE MASTER SERVICES AGREEMENT

THIS THIRD AMENDMENT (Third Amendment), effective as of November 3, 2009 (the Amendment Effective Date) is
to the existing Master Services Agreement between AAIPharma Services Corp. (assignee of AAIPharma Inc. and hereinafter referred to as AAIPharma) and Sunesis Pharmaceuticals, Inc. (hereinafter the Client) dated
November 3, 2003 (the Agreement), as amended September 11, 2006 and May 2, 2008 (respectively, the First Amendment and Second Amendment). All capitalized terms herein shall have the same meaning as
set forth in the Agreement.

WHEREAS, AAIPharma and Client desire to modify the existing Agreement to provide the terms and
conditions upon which Client may continue to engage AAIPharma, from time to time and agreed to by AAIPharma, to provide services for individual projects being conducted by Client.

NOW, THEREFORE, in consideration of the promises and mutual covenants contained in this Third Amendment, AAIPharma and Client hereby
agree to the terms and conditions set forth below.



| | 1. | Section 7.1 of the Agreement, as amended under the First Amendment, shall he deleted and replaced in its entirety with the following:
| | -- | -------------------------------------------------------------------------------------------------------------------------------------

Unless sooner terminated in a manner herein provided, this Agreement shall continue until December 31, 2012 (hereinafter the
Term). The Parties may extend or modify this Agreement by written mutual agreement at least sixty (60) days prior to the expiration of the Term.



| | 2. | AAIPharmas contact information in Section 8.1 of the Agreement shall be deleted and replaced in its entirety with the following:
| | -- | ---------------------------------------------------------------------------------------------------------------------------------



|      |  |                                 
|----- |  | --------------------------------
|AAI: |  | AAIPharma Services Corp.        
|      |  | 2320 Scientific Park Drive      
|      |  | Wilmington, North Carolina 28405
|      |  | Attention: Legal Department     
|      |  | Fax: 910-815-2340              

Except as
otherwise stated in this Third Amendment, all other terms and conditions of the Agreement and the Second Amendment shall remain in full force and effect.

[SIGNATURE PAGE FOLLOWS]



#2009-1007.3 Third Amendment
to Master Services Agreement

AAIPharma / Sunesis



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IN WITNESS WHEREOF, the Parties have caused this Third Amendment to be executed as of the
Amendment Effective Date set forth above.



|     |  |                                                                                                   |  |                                                                          |  |              |  |                        
|---- |  | ------------------------------------------------------------------------------------------------- |  | ------------------------------------------------------------------------ |  | ------------ |  | -----------------------
|     |  | Sunesis Pharmaceuticals, Inc. 395 Oyster Point Boulevard, Suite 400 South San Francisco, CA 94080 |  | AAIPharma Services Corp. 2320 Scientific Park Drive Wilmington, NC 28405
|     |  |                                                                                                   |  |                                                                         
|LOGO |  | By:                                                                                               |  | LOGO                                                                     |  | By:          |  | LOGO                   
|     |  | Print Name:                                                                                       |  | Eric Bjerkholt                                                           |  | Print Name:  |  | L. Lee Karras          
|     |  | Title:                                                                                            |  | Sr. VP & CFO                                                             |  | Title:       |  | Chief Executive Officer
|     |  | Date Signed:                                                                                      |  | 12-8-09                                                                  |  | Date Signed: |  | 12.3.09                

LOGO



#2009-1007.3 Third Amendment
to Master Services Agreement

AAIPharma / Sunesis