Exhibit 10.1

THIRD AMENDMENT TO EXCLUSIVE CHANNEL PARTNER AGREEMENT

This THIRD AMENDMENT TO THE EXCLUSIVE CHANNEL PARTNER AGREEMENT (the “Third
Amendment”) is effective as of June 29, 2016 (the “Third Amendment Effective
Date”) by and between INTREXON CORPORATION, a Virginia corporation with offices
at 20374 Seneca Meadows Parkway, Germantown, MD 20876 (“Intrexon”) and ZIOPHARM
ONCOLOGY, INC., a Delaware corporation having its principal place of business at
1180 Avenue of the Americas, 19th Floor, New York, NY 10036 (“ZIOPHARM”).
Intrexon and ZIOPHARM may be referred to herein individually as a “Party” and
collectively as the “Parties.”

RECITALS

A. WHEREAS Intrexon and ZIOPHARM are parties to that certain Exclusive Channel
Partner Agreement, effective January 6, 2011 (the “Agreement”), pursuant to
which Intrexon appointed ZIOPHARM as its exclusive channel collaborator for
developing and commercializing certain products for the treatment or prophylaxis
of cancer in humans;

B. WHEREAS Intrexon and ZIOPHARM have previously amended the Agreement by mutual
written agreements executed by the Parties on September 13, 2011 (the “First
Amendment”) and on March 27, 2015 (the “Second Amendment”), and the Parties now
desire to further amend the Agreement; and

C. WHEREAS, the Parties now mutually desire to further amend the Agreement;

D. NOW, THEREFORE, the Parties agree to amend the terms of the Agreement (as
previously amended) as provided below, effective as of the Third Amendment
Effective Date.

 

1. GENERALLY

1.1 Capitalized terms present within this Third Amendment that are not proper
names or titles, that are nor conventionally capitalized, or that are not
otherwise defined within this Third Amendment shall have the meaning set forth
in the Agreement (as previously amended).

1.2 The Parties, in conjunction with and contemporaneously with this Third
Amendment, have entered into Preferred Stock Purchase Agreement of even date
herewith (the “Preferred Stock Agreement”).

 

2. AMENDMENT TO THE AGREEMENT

2.1 Profit Sharing on ZIOPHARM Sales. All references to “fifty percent (50%)” in
Section 5.2(a) of the Agreement are hereby amended to now read “twenty percent
(20%)”. For clarity, neither Section 5.2(b) of the Agreement nor Section 4.1 of
the Second Amendment is amended under this Third Amendment.

 

3. CLARIFICATION OF THE SECOND AMENDMENT

3.1 Equity Purchase Commitment. It is hereby clarified and agreed that
Section 6.1 of the Second Amendment (and the revised equity purchase obligation
of Intrexon effected thereby) shall survive termination and/or expiration of the
Merck Agreement and/or the Second Amendment.

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4. COMPENSATION

4.1 Payments from ZIOPHARM. In partial consideration for the amendments agreed
to herein by Intrexon, ZIOPHARM shall issue to Intrexon certain shares of
ZIOPHARM preferred stock in accordance with the terms and conditions of the
Preferred Stock Agreement. Provided that all closing conditions for delivery of
stock under the Preferred Stock Agreement that are within the reasonable control
of Intrexon have been satisfied or waived, the issuance of all shares under the
Preferred Stock Agreement in satisfaction of this Section 4.1 is a condition
subsequent to the effectiveness of this Third Amendment.

 

5. MISCELLANEOUS

5.1 Full Force and Effect. This Third Amendment amends the terms of the
Agreement (as previously amended by the First Amendment and Second Amendment)
and is deemed incorporated into the Agreement. The provisions of the Agreement
as amended remain in full force and effect.

5.2 Entire Agreement. The Agreement, together with the Preferred Stock
Agreement, the First Amendment, the Second Amendment, and this Third Amendment,
constitute the entire agreement, both written and oral, between the Parties with
respect to the subject matter hereof, and any and all prior agreements with
respect to the subject matter hereof, either written or oral, expressed or
implied, are superseded hereby, merged and canceled, and are null and void and
of no effect.

5.3 Counterparts. This Third Amendment may be executed in one or more
counterparts, each of which will be an original and all of which together will
constitute one instrument.

 

2

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IN WITNESS WHEREOF, Intrexon and ZIOPHARM have executed this Third Amendment by
their respective duly authorized representatives as of the Third Amendment
Effective Date.

 

INTREXON CORPORATION       ZIOPHARM ONCOLOGY, INC. By:  

/s/ Randal J. Kirk

      By:  

/s/ Laurence J. N. Cooper, M.D., Ph.D.

Name: Randal J. Kirk       Name: Laurence J. N. Cooper, M.D., Ph.D. Title: Chief
Executive Officer       Title: Chief Executive Officer

Signature Page to Third Amendment to Exclusive Channel Partner Agreement