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.

“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”.

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.

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#2009-1007.3 Third Amendment to Master Services Agreement

AAIPharma / Sunesis

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

#2009-1007.3 Third Amendment to Master Services Agreement

AAIPharma / Sunesis