UNITED STATES SECURITIES AND EXCHANGE
COMMISSION

Washington, D.C. 20549



Form 10-Q



|(Mark One) |  |                                                                                         
|---------- |  | ----------------------------------------------------------------------------------------
|þ          |  | QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 
|           |  | For the quarterly period ended June 30, 2012                                            
|OR        
| ̈          |  | TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934



Commission File Number 001-33038



ZIOPHARM Oncology, Inc.

(Exact name of registrant as specified
in its charter)



|Delaware                        |  | 84-1475642         
|------------------------------- |  | -------------------
|(State or other jurisdiction of |  | (I.R.S. Employer   
|incorporation or organization)  |  | Identification No.)



1180 Avenue of the Americas, 20th
Floor, New York, NY 10036

(646) 214-0700

(Address, including zip code, and telephone
number, including

area code, of registrant’s principal
executive offices)



Indicate by check mark whether the registrant (1) has filed
all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or
for such shorter period than the registrant was required to file such reports), and (2) has been subject to such filing requirements
for the past 90 days. Yes: þ    No:  ̈



Indicate by check mark whether the registrant has submitted
electronically and posted on its corporate Web site, if any, every Interactive Data File required to be submitted and posted pursuant
to Rule 405 of Regulation S-T during the preceding 12 months (or for such shorter period that the registrant was required to submit
and post such files). Yes: þ    No:  ̈



Indicate by check mark whether the registrant is a large accelerated
filer, an accelerated filer, a non-accelerated filer or smaller reporting company. See the definitions of “large accelerated
filer,” “accelerated filer,” and “smaller reporting company” in Rule 12b-2 of the Exchange Act.
(Check one):



|Large accelerated filer  ̈ | Accelerated filer þ                           | Non-accelerated filer ̈ | Smaller reporting company  ̈
|------------------------- | --------------------------------------------- | ---------------------- | ---------------------------
|                          | (Do not check if a smaller reporting company)



Indicate by check mark whether the registrant is a shell company
(as defined in Rule 12b-2 of the Exchange Act). Yes:  ̈    No: þ



The number of shares of the registrant’s common stock,
$.001 par value, outstanding as of  July 29, 2012, was 79,567,946 shares.











ZIOPHARM Oncology,
Inc. (a development stage company)



NOTE REGARDING FORWARD-LOOKING STATEMENTS



This report contains forward-looking statements that are based
on our current beliefs and expectations. These forward-looking statements may be accompanied by such words as “anticipate,”
“believe,” “estimate,” “expect,” “forecast,” “intend,” “may,”
“plan,” “project,” “target,” “will” and other words and terms of similar meaning.
Reference is made in particular to forward-looking statements regarding:



| | • | the anticipated amount, timing and accounting of deferred revenues, milestone and other payments
under licensing, collaboration or acquisition agreements, tax positions and contingencies, research and development costs and other
expenses, and amortization of intangible assets;
| | - | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------



| | • | our expectations regarding the application of certain accounting pronouncements
and their effect on our disclosures;
| | - | --------------------------------------------------------------------------------------------------------------------



| | • | the protection afforded by our patent rights;
| | - | ---------------------------------------------



| | • | our assessment of the potential impact on our future revenues of healthcare
reform legislation in the United States;
| | - | --------------------------------------------------------------------------------------------------------------------



| | • | the timing and impact of measures worldwide designed to reduce healthcare costs;
| | - | --------------------------------------------------------------------------------



| | • | the impact of the deterioration of the credit and economic conditions in certain countries in Europe;
| | - | -----------------------------------------------------------------------------------------------------



| | • | our ability to finance our operations and business initiatives and obtain funding for such activities;
| | - | ------------------------------------------------------------------------------------------------------



| | • | the sufficiency of our cash, investments and cash flows from operations
and our expected uses of cash;
| | - | ------------------------------------------------------------------------------------------------------



| | • | the costs and timing of the development and commercialization of our pipeline products and services;
| | - | ----------------------------------------------------------------------------------------------------



| | • | additional planned regulatory filings for and commercialization of Palifosfamide;
| | - | ---------------------------------------------------------------------------------



| | • | contract manufacturing activity;
| | - | --------------------------------



These forward-looking statements involve risks and uncertainties,
including those that are described in the “Risk Factors” section of this report and elsewhere within this report
that could cause actual results to differ materially from those reflected in such statements. You should not place undue reliance
on these statements. Forward-looking statements speak only as of the date of this report. We do not undertake any obligation to
publicly update any forward-looking statements.



NOTE REGARDING COMPANY REFERENCES



Throughout this report, “ZIOPHARM,” the “Company,”
“we,” “us” and “our” refer to ZIOPHARM Oncology, Inc .



NOTE REGARDING TRADEMARKS



Our registered trademarks include Zymafos and Zinapar. Our trademarks
include Zybulin. All other trademarks, trade names and service marks appearing in this Quarterly Report on Form 10-Q are the property
of their respective owners.



2







ZIOPHARM Oncology,
Inc. (a development stage company)



Table of Contents



|                               |  |                                                                                                                                                                                    |  | Page
|------------------------------ |  | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |  | ----
|Part I - Financial Information |  |                                                                                                                                                                                   
|                               |  |                                                                                                                                                                                    |  |     
|Item 1.                        |  | Financial Statements                                                                                                                                                               |  |     
|                               |  |                                                                                                                                                                                    |  |     
|                               |  | Balance Sheets as of June 30, 2012 and December 31, 2011 (unaudited)                                                                                                               |  | 4   
|                               |  |                                                                                                                                                                                   
|                               |  | Statements of Operations for the three and six months ended June 30, 2012 and 2011 and the period
    from September 9, 2003 (date of inception) through June 30, 2012 (unaudited) |  | 5   
|                               |  |                                                                                                                                                                                   
|                               |  | Statement of Stockholders’ Equity for the six months ended June 30, 2012 (unaudited)                                                                                               |  | 6   
|                               |  |                                                                                                                                                                                    |  |     
|                               |  | Statements of Cash Flows for the six months ended June 30, 2012 and 2011 and the period from September
    9, 2003 (date of inception) through June 30, 2012 (unaudited)           |  | 7   
|                               |  |                                                                                                                                                                                    |  |     
|                               |  | Notes to Financial Statements (unaudited)                                                                                                                                          |  | 8   
|                               |  |                                                                                                                                                                                    |  |     
|Item 2.                        |  | Management’s Discussion and Analysis of Financial Condition and Results of Operations                                                                                              |  | 21  
|                               |  |                                                                                                                                                                                    |  |     
|Item 3.                        |  | Quantitative and Qualitative Disclosures about Market Risk                                                                                                                         |  | 34  
|                               |  |                                                                                                                                                                                    |  |     
|Item 4.                        |  | Controls and Procedures                                                                                                                                                            |  | 34  
|                               |  |                                                                                                                                                                                   
|Part II - Other Information    |  |                                                                                                                                                                                   
|                               |  |                                                                                                                                                                                    |  |     
|Item 1.                        |  | Legal Proceedings                                                                                                                                                                  |  | 35  
|                               |  |                                                                                                                                                                                    |  |     
|Item 1A.                       |  | Risk Factors                                                                                                                                                                       |  | 35  
|                               |  |                                                                                                                                                                                    |  |     
|Item 2.                        |  | Unregistered Sale of Equity Securities and Use of Proceeds                                                                                                                         |  | 49  
|                               |  |                                                                                                                                                                                    |  |     
|Item 3.                        |  | Defaults upon Senior Securities                                                                                                                                                    |  | 49  
|                               |  |                                                                                                                                                                                    |  |     
|Item 4.                        |  | Mine Safety Disclosures                                                                                                                                                            |  | 49  
|                               |  |                                                                                                                                                                                    |  |     
|Item 5.                        |  | Other Information                                                                                                                                                                  |  | 49  
|                               |  |                                                                                                                                                                                    |  |     
|Item 6.                        |  | Exhibits                                                                                                                                                                           |  | 49  
|                               |  |                                                                                                                                                                                   
|SIGNATURES                     |  | 50                                                                                                                                                                                



3







Part I - Financial Information



Item 1. Consolidated Financial Statements



ZIOPHARM Oncology,
Inc. (a development stage company)



BALANCE SHEETS

(unaudited)



(in thousands, except share and per share
data)



|                                                                                                                                                                            |  | June 30, |          |   | December 31, |  
|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |  | -------- | -------- | - | ------------ | -
|                                                                                                                                                                            |  | 2012     |          |   | 2011         |  
|                                                                                                                                                                            |  |          |          |   |              |  
|ASSETS                                                                                                                                                                      |  |          |          |   |              |  
|Current assets:                                                                                                                                                             |  |          |          |   |              |  
|Cash and cash equivalents                                                                                                                                                   |  | $        | 110,391  |   |              | $
|Collaboration receivable                                                                                                                                                    |  |          | -        |   |              |  
|Prepaid expenses and other current assets                                                                                                                                   |  |          | 9,051    |   |              |  
|Total current assets                                                                                                                                                        |  |          | 119,442  |   |              |  
|                                                                                                                                                                            |  |          |          |   |              |  
|Property and equipment, net                                                                                                                                                 |  |          | 1,982    |   |              |  
|                                                                                                                                                                            |  |          |          |   |              |  
|Deposits                                                                                                                                                                    |  |          | 132      |   |              |  
|Other non-current assets                                                                                                                                                    |  |          | 824      |   |              |  
|Total assets                                                                                                                                                                |  | $        | 122,380  |   |              | $
|                                                                                                                                                                            |  |          |          |   |              |  
|LIABILITIES AND STOCKHOLDERS' EQUITY                                                                                                                                        |  |          |          |   |              |  
|Current liabilities:                                                                                                                                                        |  |          |          |   |              |  
|Accounts payable                                                                                                                                                            |  | $        | 1,470    |   |              | $
|Accrued expenses                                                                                                                                                            |  |          | 15,502   |   |              |  
|Deferred revenue - current portion                                                                                                                                          |  |          | 800      |   |              |  
|Deferred rent - current portion                                                                                                                                             |  |          | 4        |   |              |  
|Total current liabilities                                                                                                                                                   |  |          | 17,776   |   |              |  
|                                                                                                                                                                            |  |          |          |   |              |  
|Deferred revenue                                                                                                                                                            |  |          | 3,133    |   |              |  
|Deferred rent                                                                                                                                                               |  |          | 363      |   |              |  
|Warrant liabilities                                                                                                                                                         |  |          | 25,472   |   |              |  
|Total liabilities                                                                                                                                                           |  |          | 46,744   |   |              |  
|                                                                                                                                                                            |  |          |          |   |              |  
|Commitments and contingencies (note 7)                                                                                                                                      |  |          |          |   |              |  
|                                                                                                                                                                            |  |          |          |   |              |  
|Stockholders' equity:                                                                                                                                                       |  |          |          |   |              |  
|Preferred stock, $0.001 par value; 30,000,000 shares authorized and no shares issued and outstanding                                                                        |  |          | -        |   |              |  
|Common stock, $0.001 par value; 250,000,000 shares authorized; 79,625,290 and 69,206,044 shares issued and outstanding at June 30, 2012 and December 31, 2011, respectively |  |          | 80       |   |              |  
|Additional paid-in capital - common stock                                                                                                                                   |  |          | 304,219  |   |              |  
|Additional paid-in capital - warrants issued                                                                                                                                |  |          | 7,012    |   |              |  
|Deficit accumulated during the development stage                                                                                                                            |  |          | (235,675 | ) |              |  
|Total stockholders' equity                                                                                                                                                  |  |          | 75,636   |   |              |  
|Total liabilities and stockholders' equity                                                                                                                                  |  | $        | 122,380  |   |              | $



The accompanying notes are an integral part
of the unaudited interim financial statements.



4







ZIOPHARM Oncology,
Inc. (a development stage company)



STATEMENTS OF OPERATIONS

(unaudited)



(in thousands, except share and per share
data)



|                                                                                            |  |                                     |            |   |                                   |   |            |         |  |   |            |   |  | Period from         |           
|------------------------------------------------------------------------------------------- |  | ----------------------------------- | ---------- | - | --------------------------------- | - | ---------- | ------- |  | - | ---------- | - |  | ------------------- | ----------
|                                                                                            |  |                                     |            |   |                                   |   |            |         |  |   |            |   |  | September 9, 2003   |           
|                                                                                            |  |                                     |            |   |                                   |   |            |         |  |   |            |   |  | (date of inception) |           
|                                                                                            |  | For the Three Months Ended June 30, |            |   | For the Six Months Ended June 30, |   |            | through | 
|                                                                                            |  | 2012                                |            |   | 2011                              |   |            | 2012    |  |   | 2011       |   |  | June 30, 2012       |           
|                                                                                            |  |                                     |            |   |                                   |   |            |         |  |   |            |   |  |                     |           
|Research contract revenue                                                                   |  | $                                   | 200        |   |                                   | $ | 200        |         |  | $ | 400        |   |  | $                   | 267       
|                                                                                            |  |                                     |            |   |                                   |   |            |         |  |   |            |   |  |                     |           
|Operating expenses:                                                                         |  |                                     |            |   |                                   |   |            |         |  |   |            |   |  |                     |           
|Research and development, including costs of research contracts                             |  |                                     | 18,264     |   |                                   |   | 9,125      |         |  |   | 32,249     |   |  |                     | 33,766    
|General and administrative                                                                  |  |                                     | 4,902      |   |                                   |   | 3,923      |         |  |   | 9,750      |   |  |                     | 7,275     
|Total operating expenses                                                                    |  |                                     | 23,166     |   |                                   |   | 13,048     |         |  |   | 41,999     |   |  |                     | 41,041    
|                                                                                            |  |                                     |            |   |                                   |   |            |         |  |   |            |   |  |                     |           
|Loss from operations                                                                        |  |                                     | (22,966    | ) |                                   |   | (12,848    | )       |  |   | (41,599    | ) |  |                     | (40,774   
|                                                                                            |  |                                     |            |   |                                   |   |            |         |  |   |            |   |  |                     |           
|Other income, net                                                                           |  |                                     | 3          |   |                                   |   | 9          |         |  |   | (23        | ) |  |                     | 7         
|Change in fair value of warrants                                                            |  |                                     | (650       | ) |                                   |   | 2,115      |         |  |   | (6,461     | ) |  |                     | (8,965    
|Net income (loss)                                                                           |  | $                                   | (23,613    | ) |                                   | $ | (10,724    | )       |  | $ | (48,083    | ) |  | $                   | (49,732   
|                                                                                            |  |                                     |            |   |                                   |   |            |         |  |   |            |   |  |                     |           
|Net income (loss) per share - basic                                                         |  | $                                   | (0.30      | ) |                                   | $ | (0.16      | )       |  | $ | (0.62      | ) |  | $                   | (0.78     
|Net income (loss) per share - diluted                                                       |  | $                                   | (0.30      | ) |                                   | $ | (0.16      | )       |  | $ | (0.62      | ) |  | $                   | (0.78     
|                                                                                            |  |                                     |            |   |                                   |   |            |         |  |   |            |   |  |                     |           
|Weighted average common shares outstanding to compute net income (loss) per share - basic   |  |                                     | 78,514,718 |   |                                   |   | 67,229,098 |         |  |   | 77,067,424 |   |  |                     | 63,839,723
|                                                                                            |  |                                     |            |   |                                   |   |            |         |  |   |            |   |  |                     |           
|Weighted average common shares outstanding to compute net income (loss) per share - diluted |  |                                     | 78,514,718 |   |                                   |   | 67,229,098 |         |  |   | 77,067,424 |   |  |                     | 63,839,723



The accompanying notes are an integral part
of the unaudited interim financial statements.



5







ZIOPHARM Oncology, Inc. (a development
stage company)



STATEMENT OF STOCKHOLDERS’ EQUITY

For the Six Months Ended June 30, 2012

(unaudited)



(in thousands, except share and per share
data)



|                                                                                            |  | Stockholders' Equity |  
|------------------------------------------------------------------------------------------- |  | -------------------- | -
|                                                                                            |  |                      |  
|                                                                                            |  |                      |  
|                                                                                            |  | Preferred Stock      |  
|                                                                                            |  |                      |  
|                                                                                            |  | Shares               |  
|Balance at December 31, 2011                                                                |  |                      | -
|                                                                                            |  |                      |  
|Stock-based compensation                                                                    |  |                      | -
|Exercise of employee stock options                                                          |  |                      | -
|Exercise of warrants to purchase common stock                                               |  |                      | -
|Issuance of restricted common stock                                                         |  |                      | -
|Forfeiture of unvested restricted common stock                                              |  |                      | -
|Expired warrants                                                                            |  |                      | -
|Issuance of common stock in a securities offering, net of commission and expenses of $3,426 |  |                      | -
|Net loss                                                                                    |  |                      | -
|Balance at June 30, 2012                                                                    |  |                      | -



The accompanying notes are an integral part
of the unaudited interim financial statements.



6







ZIOPHARM Oncology,
Inc. (a development stage company)



STATEMENTS OF CASH FLOWS

(unaudited)



(in thousands)



|                                                                            |  | For the Six Months |         |   | (date of inception) |  
|--------------------------------------------------------------------------- |  | ------------------ | ------- | - | ------------------- | -
|                                                                            |  | Ended June 30,     |         |   | through             |  
|                                                                            |  | 2012               |         |   | 2011                |  
|Cash flows from operating activities:                                       |  |                    |         |   |                     |  
|Net loss                                                                    |  | $                  | (48,083 | ) |                     | $
|Adjustments to reconcile net loss to net cash used in operating activities: |  |                    |         |   |                     |  
|Depreciation and amortization                                               |  |                    | 265     |   |                     |  
|Stock-based compensation                                                    |  |                    | 2,290   |   |                     |  
|Change in fair value of warrants                                            |  |                    | 6,461   |   |                     |  
|Loss on disposal of fixed assets                                            |  |                    | -       |   |                     |  
|Common stock issued in exchange for in-process research and development     |  |                    | -       |   |                     |  
|Change in operating assets and liabilities:                                 |  |                    |         |   |                     |  
|(Increase) decrease in:                                                     |  |                    |         |   |                     |  
|Collaboration receivable                                                    |  |                    | 79      |   |                     |  
|Prepaid expenses and other current assets                                   |  |                    | (7,738  | ) |                     |  
|Other noncurrent assets                                                     |  |                    | (53     | ) |                     |  
|Deposits                                                                    |  |                    | (41     | ) |                     |  
|Increase (decrease) in:                                                     |  |                    |         |   |                     |  
|Accounts payable                                                            |  |                    | (258    | ) |                     |  
|Accrued expenses                                                            |  |                    | 4,681   |   |                     |  
|Deferred revenue                                                            |  |                    | (400    | ) |                     |  
|Deferred rent                                                               |  |                    | 172     |   |                     |  
|Net cash used in operating activities                                       |  |                    | (42,625 | ) |                     |  
|Cash flows from investing activities:                                       |  |                    |         |   |                     |  
|Purchases of property and equipment                                         |  |                    | (1,107  | ) |                     |  
|Proceeds from sale of property and equipment                                |  |                    | -       |   |                     |  
|Net cash used in investing activities                                       |  |                    | (1,107  | ) |                     |  
|Cash flows from financing activities:                                       |  |                    |         |   |                     |  
|Stockholders' capital contribution                                          |  |                    | -       |   |                     |  
|Proceeds from exercise of stock options                                     |  |                    | 30      |   |                     |  
|Payments to employees for repurchase of common stock                        |  |                    | -       |   |                     |  
|Proceeds from exercise of warrants                                          |  |                    | 210     |   |                     |  
|Proceeds from issuance of common stock and warrants, net                    |  |                    | 49,170  |   |                     |  
|Proceeds from issuance of preferred stock, net                              |  |                    | -       |   |                     |  
|Net cash provided by financing activities                                   |  |                    | 49,410  |   |                     |  
|Net increase (decrease) in cash and cash equivalents                        |  |                    | 5,678   |   |                     |  
|Cash and cash equivalents, beginning of period                              |  |                    | 104,713 |   |                     |  
|Cash and cash equivalents, end of period                                    |  | $                  | 110,391 |   |                     | $
|                                                                            |  |                    |         |   |                     |  
|Supplementary disclosure of cash flow information:                          |  |                    |         |   |                     |  
|Cash paid for interest                                                      |  | $                  | -       |   |                     | $
|Cash paid for income taxes                                                  |  | $                  | -       |   |                     | $
|                                                                            |  |                    |         |   |                     |  
|Supplementary disclosure of noncash investing and financing activities:     |  |                    |         |   |                     |  
|Warrants issued to placement agents and investors                           |  | $                  | -       |   |                     | $
|Preferred stock conversion to common stock                                  |  | $                  | -       |   |                     | $
|Exercise of equity-classified warrants to common shares                     |  | $                  | 166     |   |                     | $
|Exercise of liability-classified warrants to common shares                  |  | $                  | 412     |   |                     | $



The accompanying notes are an integral part
of the unaudited interim financial statements.



7







ZIOPHARM Oncology,
Inc. (a development stage company)



NOTES TO FINANCIAL STATEMENTS

(unaudited)



1. Business



Overview



ZIOPHARM Oncology, Inc. (“ZIOPHARM” or the “Company”)
is a biopharmaceutical company that seeks to acquire, develop and commercialize, on its own or with other commercial partners,
products for the treatment of important unmet medical needs in cancer.



The Company’s operations to date have consisted primarily
of raising capital and conducting research and development.  Accordingly, the Company is considered to be in the development
stage at June 30, 2012. The Company's fiscal year ends on December 31.



The Company has operated at a loss since its inception in 2003
and has minimal revenues. The Company anticipates that losses will continue for the foreseeable future. At June 30, 2012,
the Company’s accumulated deficit was approximately $235.7 million. The Company currently believes that it has sufficient
capital to fund development and commercialization activities into the second half of 2013. The Company’s ability to
continue operations after its current cash resources are exhausted depends on its ability to obtain additional financing or to
achieve profitable operations, as to which no assurances can be given. Cash requirements may vary materially from those now planned
because of changes in the Company’s focus and direction of its research and development programs, competitive and technical
advances, patent developments, regulatory changes or other developments. Additional financing will be required to continue operations
after the Company exhausts its current cash resources and to continue its long-term plans for clinical trials and new product development.
There can be no assurance that any such financing can be realized by the Company, or if realized, what the terms thereof may be,
or that any amount that the Company is able to raise will be adequate to support the Company’s working capital requirements
until it achieves profitable operations.



Basis of Presentation



The accompanying unaudited interim financial statements have
been prepared in accordance with the instructions to Form 10-Q pursuant to the rules and regulations of the Securities and Exchange
Commission. Certain information and note disclosures required by generally accepted accounting principles in the United States
have been condensed or omitted pursuant to such rules and regulations.



It is management’s opinion that the accompanying unaudited
interim financial statements reflect all adjustments (which are normal and recurring) that are necessary for a fair statement of
the results for the interim periods. The unaudited interim financial statements should be read in conjunction with the audited
financial statements and the notes thereto for the year ended December 31, 2011 included in the Company’s Form 10-K for such
fiscal year.



The year-end balance sheet data was derived from the audited
financial statements but does not include all disclosures required by generally accepted accounting principles in the United States.



The results disclosed in the Statements of Operations for the
three and six months ended June 30, 2012 are not necessarily indicative of the results to be expected for the full fiscal year.



Use of Estimates



The preparation of financial statements in conformity with accounting
principles generally accepted in the United States requires management to make estimates and assumptions that affect the reported
amounts of assets and liabilities and the disclosure of contingent assets and liabilities at the date of the financial statements
and the reported amounts of revenues and expenses during the reporting period. Although
the Company regularly assesses these estimates, actual results could differ from those estimates. Changes in estimates are recorded
in the period in which they become known.



8







ZIOPHARM Oncology, Inc. (a development
stage company)



NOTES TO FINANCIAL STATEMENTS (unaudited)



1. Business - (continued)



The Company’s most significant estimates and judgments
used in the preparation of its financial statements are:



| | · | Clinical trial expenses;
| | - | ------------------------



| | · | Fair value measurements for stock based compensation and warrants; and
| | - | ----------------------------------------------------------------------



| | · | Income taxes.
| | - | -------------



Subsequent Events



The Company evaluated all events and transactions that occurred
after the balance sheet date through the date of this filing.  Except as disclosed below, the Company did not have any
other material subsequent events that impacted its financial statements or disclosures.



On July 16, 2012, the Company announced that it has restructured
its management team and will also be closing its Germantown, MD office. As a result of this action, the Company expects to record
a restructuring charge, consisting primarily of severance and health benefit continuation costs, of approximately $1.1 million
in the third quarter of 2012.



2.Summary of Significant
Accounting Policies



The Company’s significant accounting policies were identified
in the Company’s Form 10-K for the fiscal year ended December 31, 2011.



3. Collaborations and Alliances



On March 7, 2011, the Company entered into a License and Collaboration
Agreement with Solasia Pharma K.K. (“Solasia”).



Pursuant to the License and Collaboration Agreement (the
“Agreement”), the Company granted Solasia an exclusive license to develop and commercialize darinaparsin in both intravenous
and oral forms and related organic arsenic molecules, in all indications for human use in a pan-Asian/Pacific territory comprised
of Japan, China, Hong Kong, Macau, Republic of Korea, Taiwan, Singapore, Australia, New Zealand, Malaysia, Indonesia, Philippines
and Thailand.



As consideration for the license, the Company received an upfront
payment of $5.0 million to be used exclusively for further clinical development of darinaparsin outside of the pan-Asian/Pacific
territory, and will be entitled to receive additional payments of up to $32.5 million in development-based milestones and up to
$53.5 million in sales-based milestones. The Company will also be entitled to receive double digit royalty payments from Solasia
based upon net sales of licensed products in the applicable territories, once commercialized, and a percentage of sublicense revenues
generated by Solasia.



The upfront payment for research and development funding is
earned over the period of effort. The Company currently estimates this period to be 75 months, which could be adjusted in the future.



Under the Agreement, the Company provides Solasia with drug
product to conduct clinical trials. These transfers are accounted for as a reduction of research and development costs and an increase
in collaboration receivables.



The Agreement provides that Solasia will be responsible for
the development and commercialization of darinaparsin in the pan-Asian/Pacific territory.



9







ZIOPHARM Oncology, Inc. (a development
stage company)



NOTES TO FINANCIAL STATEMENTS (unaudited)



4. Fair Value Measurements



The Company accounts for fair value measurements of its financial
assets and liabilities and non-financial assets and non-financial liabilities, except those that are recognized or disclosed in
the financial statements at fair value on a recurring basis. The accounting standard defines fair value, establishes a framework
for measuring fair value under generally accepted accounting principles and enhances disclosures about fair value measurements. Fair
value is defined as the exchange price that would be received for an asset or paid to transfer a liability (an exit price) in the
principal or most advantageous market for the asset or liability in an orderly transaction between market participants on the measurement
date. Valuation techniques used to measure fair value must maximize the use of observable inputs and minimize the use of unobservable
inputs.  The standard describes a fair value hierarchy based on three levels of inputs, of which the first two are considered
observable and the last unobservable, that may be used to measure fair value which are the following:



| | · | Level 1 - Quoted prices in active markets for identical assets or liabilities.
| | - | ------------------------------------------------------------------------------



| | · | Level 2 - Inputs other than Level 1 that are observable, either directly or indirectly, such
as quoted prices for similar assets or liabilities; quoted prices in markets that are not active; or other inputs that are observable
or can be corroborated by observable market data for substantially the full term of the assets or liabilities.
| | - | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------



| | · | Level 3 - Unobservable inputs that are supported by little or no market activity and that are
significant to the fair value of the assets or liabilities.
| | - | ---------------------------------------------------------------------------------------------------------------------------------------------------------



Assets and liabilities measured at fair value on a recurring
basis as of June 30, 2012 and December 31, 2011 are as follows:



|($ in thousands)  |  |                             |         |  | Fair Value Measurements at Reporting Date Using                            |  
|----------------- |  | --------------------------- | ------- |  | -------------------------------------------------------------------------- | -
|Description       |  | Balance as of June 30, 2012 |         |  | Quoted Prices in Active Markets for Identical Assets/Liabilities (Level 1) |  
|                  |  |                             |         |  |                                                                            |  
|Cash equivalents  |  | $                           | 109,455 |  |                                                                            | $
|                  |  |                             |         |  |                                                                            |  
|Warrant liability |  | $                           | 25,472  |  |                                                                            | $



10







ZIOPHARM Oncology, Inc. (a development
stage company)



NOTES TO FINANCIAL STATEMENTS (unaudited)



4. Fair Value Measurements – (continued)



|($ in thousands)  |  |                                 |         |  | Fair Value Measurements at Reporting Date Using                            |  
|----------------- |  | ------------------------------- | ------- |  | -------------------------------------------------------------------------- | -
|Description       |  | Balance as of December 31, 2011 |         |  | Quoted Prices in Active Markets for
Identical Assets/Liabilities (Level 1) |  
|                  |  |                                 |         |  |                                                                            |  
|Cash equivalents  |  | $                               | 103,736 |  |                                                                            | $
|                  |  |                                 |         |  |                                                                            |  
|Warrant liability |  | $                               | 19,425  |  |                                                                            | $



The cash equivalents represent deposits in a short term U.S.
treasury money market mutual fund quoted in an active market and classified as a Level I asset. The Company’s Level II financial
liabilities consist of long-term investor and placement agent warrants issued in connection with its December 2009 public offering.
The warrants were valued using Binomial/Monte Carlo valuation models. See Note 8 for additional disclosures on the valuation methodology
and significant assumptions.



5. Net Loss per Share



Basic net loss per share is computed by dividing net loss by
the weighted average number of shares of common stock outstanding for the period. The Company's potential dilutive shares, which
include outstanding common stock options, unvested restricted stock and warrants, have not been included in the computation of
diluted net loss per share for any of the periods presented as the result would be antidilutive. Such potential shares of common
stock at June 30, 2012 and 2011 consist of the following:



|                                 |  | For the Six Months |           
|-------------------------------- |  | ------------------ | ----------
|                                 |  | Ended June 30,     |           
|                                 |  | 2012               |           
|Stock options                    |  |                    | 5,397,154 
|Unvested restricted common stock |  |                    | 1,029,848 
|Warrants                         |  |                    | 11,268,678
|                                 |  |                    | 17,695,680



6. Related Party Transactions



On January 6, 2011, the Company entered into an Exclusive Channel
Partner Agreement (the “Channel Agreement”) with Intrexon Corporation (see Note 7 for additional disclosure relating
to the Channel Agreement). During the six months ended June 30, 2012, the Company paid Intrexon approximately $10.7 million, of
which $2.5 million was for services already incurred and the remaining $8.2 million expected to be incurred within a year. This
amount has been included as part of prepaid expenses and other current assets on the accompanying balance sheet as of June 30,
2012. The Company does not owe any amounts to Intrexon that have not already been accrued for as of June 30, 2012.



On January 25, 2012, Intrexon purchased 1,923,075 shares of
common stock in the Company’s public offering (see Note 9).



11







ZIOPHARM Oncology,
Inc. (a development stage company)



NOTES TO FINANCIAL STATEMENTS (unaudited)



7. Commitments and Contingencies



Patent and Technology License Agreement—The University
of Texas M. D. Anderson Cancer Center and the Texas A&M University System.



On August 24, 2004, the Company entered into a patent and technology
license agreement with The Board of Regents of the University of Texas System, acting on behalf of The University of Texas M. D.
Anderson Cancer Center and the Texas A&M University System (collectively, the “Licensors”). Under this agreement,
the Company was granted an exclusive, worldwide license to rights (including rights to U.S. and foreign patent and patent applications
and related improvements and know-how) for the manufacture and commercialization of two classes of organic arsenicals (water- and
lipid-based) for human and animal use. The class of water-based organic arsenicals includes darinaparsin.



As partial consideration for the license rights obtained, the
Company made an upfront payment in 2004 of $125 thousand and granted the Licensors 250,487 shares of the Company’s common
stock. In addition, the Company issued options to purchase an additional 50,222 shares outside the 2003 Stock Option Plan for $0.002
per share following the successful completion of certain clinical milestones, which vested with respect to 12,555 shares upon the
filing of an Investigation New Drug application (“IND”) for darinaparsin in 2005 and vested with respect to another
25,111 shares upon the completion of dosing of the last patient for both Phase 1 clinical trials in 2007. The Company recorded
$120 thousand of stock based compensation expense related to the vesting in 2007. The remaining 12,556 shares will vest upon enrollment
of the first patient in a multi-center pivotal clinical trial i.e. a human clinical trial intended to provide the substantial evidence
of efficacy necessary to support the filing of an approvable New Drug Application (“NDA”). In addition, the Licensors
are entitled to receive certain milestone payments, including $100 thousand that was paid in 2005 upon the commencement of Phase
1 clinical trial and $250 thousand that was paid in 2006 upon the dosing of the first patient in the Company-sponsored Phase 2
clinical trial for darinaparsin. The Company may be required to make additional payments upon achievement of certain other milestones
in varying amounts which on a cumulative basis could total up to an additional $4.5 million. In addition, the Licensors are entitled
to receive single-digit percentage royalty payments on sales from a licensed product and will also be entitled to receive a portion
of any fees that the Company may receive from a possible sublicense under certain circumstances. In addition, the Company also
paid the Licensors $100 thousand in 2006 and 2007 to conduct scientific research with the Company obtaining exclusive right to
all resulting intellectual property rights. The sponsored research agreements governing this research and any related extensions
expired in February 2008 with no payments being made subsequent to that date.



The license agreement also contains other provisions customary
and common in similar agreements within the industry, such as the right to sublicense the Company rights under the agreement. However,
if the Company sublicenses its rights prior to the commencement of a pivotal study, i.e. a human clinical trial intended to provide
the substantial evidence of efficacy necessary to support the filing of an approvable NDA, the Licensors will be entitled to receive
a share of the payments received by the Company in exchange for the sublicense (subject to certain exceptions). The term of the
license agreement extends until the expiration of all claims under patents and patent applications associated with the licensed
technology, subject to earlier termination in the event of defaults by the Company or the Licensors under the license agreement,
or if the Company becomes bankrupt or insolvent. No milestones under the license agreement were reached or expensed during the
years ended December 31, 2009, 2010, 2011 or for the six months ended June 30, 2012.



12







ZIOPHARM Oncology, Inc. (a development
stage company)



NOTES TO FINANCIAL STATEMENTS (unaudited)



7. Commitments and Contingencies – (continued)



License Agreement with DEKK-Tec, Inc.



On October 15, 2004, the Company entered into a license agreement
with DEKK-Tec, Inc., pursuant to which it was granted an exclusive, worldwide license for palifosfamide. As part of the signing
of license agreement with DEKK-Tec, the Company expensed an upfront $50 thousand payment to DEKK-Tec in 2004.



In consideration for the license rights, DEKK-Tec is entitled
to receive payments upon achieving certain milestones in varying amounts, which on a cumulative basis may total $4.0 million. Of
the aggregate milestone payments, most will be creditable against future royalty payments as referenced below. The Company expensed
a $100 thousand milestone payment upon achieving Phase 2 milestones during the year ended December 31, 2006. Additionally, in 2004
the Company issued DEKK-Tec an option to purchase 27,616 shares of the Company’s common stock for $0.02 per share. Upon the
execution of the license agreement, 6,904 shares vested and were subsequently exercised in 2005 and the remaining options will
vest upon certain milestone events, culminating with final FDA approval of the first NDA submitted by the Company (or by its sublicensee)
for palifosfamide. DEKK-Tec is entitled to receive single-digit percentage royalty payments on the sales of palifosfamide should
it be approved for commercial sale. On March 16, 2010, the Company expensed a $100 thousand milestone payment upon receiving a
United States Patent for palifosfamide. In December 2010, the Company expensed a $300 thousand milestone payment and vested 6,904
stock options upon achieving Phase 3 milestones. These options were subsequently exercised in 2011. The Company’s obligation
to pay royalties will terminate on a country-by-country basis upon the expiration of all valid claims of patents in such country
covering licensed product, subject to earlier termination in the event of defaults by the parties under the license agreement.
No milestones under the license agreement were reached or expensed during the years ended December 31, 2009, 2011 or for the six
months ended June 30, 2012.



Option Agreement with Southern Research Institute (“SRI”)



On December 22, 2004, the Company entered into an Option Agreement
with SRI (the “Option Agreement”), pursuant to which the Company was granted an exclusive option to obtain an exclusive
license to SRI’s interest in certain intellectual property, including exclusive rights related to certain isophosphoramide
mustard analogs.



Also on December 22, 2004, the Company entered into a Research
Agreement with SRI pursuant to which the Company agreed to spend a sum not to exceed $200 thousand between the execution of the
agreement and December 21, 2006, including a $25 thousand payment that was made simultaneously with the execution of the agreement,
to fund research and development work by SRI in the field of isophosphoramide mustard analogs. The Option Agreement was exercised
on February 13, 2007. Under the license agreement entered into upon exercise of the option, the Company is required to remit minimum
annual royalty payments of $25 thousand until the first commercial sale of a licensed product. These payments were made for the
years ended December 31, 2008, 2009, 2010 and 2011. The Company may be required to make payments upon achievement of certain milestones
in varying amounts which on a cumulative basis could total up to $775,000. In addition, SRI will be entitled to receive single
digit percentage royalty payments on the sales of a licensed product in any country until all licensed patents rights in that country
which are utilized in the product have expired. No milestones under the license agreement were reached or expensed during the years
ended December 31, 2009, 2010, 2011 or for the six months ended June 30, 2012.



13







ZIOPHARM Oncology, Inc. (a development
stage company)



NOTES TO FINANCIAL STATEMENTS (unaudited)



7. Commitments and Contingencies – (continued)



License Agreement with Baxter Healthcare Corporation



On November 3, 2006, the Company entered into a definitive Asset
Purchase Agreement for indibulin and a License Agreement to proprietary nanosuspension technology with affiliates of Baxter Healthcare
S.A. The purchase included the entire indibulin intellectual property portfolio as well as existing drug substance and capsule
inventories. The terms of the Asset Purchase Agreement included an upfront cash payment of approximately $1.1 million and an additional
$100 thousand payment for existing inventory, both of which were expensed in 2006. In addition to the upfront costs, the Asset
Purchase Agreement includes additional diligence and milestone payments that could amount to approximately $8 million in the aggregate
and royalties on net sales of products covered by a valid claim of a patent for the life of the patent on a country-by-country
basis. The Company expensed a $625 thousand milestone payment upon the successful U.S. IND application for indibulin in 2007. The
License Agreement requires payment of a $15 thousand annual patent and license prosecution/maintenance fee through the expiration
of the last of the licensed patents, which is expected to expire in 2025, and single-digit royalties on net sales of licensed products
covered by a valid claim of a patent for the life of the patent on a country-by-country basis. The term of the license agreement
extends until the expiration of the last to expire of the patents covering the licensed products, subject to earlier termination
in the event of defaults by the parties under the license agreement.



In October 2009, the Baxter License Agreement was amended to
allow the Company to manufacturer indibulin. No milestones under the license agreement were reached or expensed during the years
ended December 31, 2009, 2010, 2011 or for the six months ended June 30, 2012.



Exclusive Channel Partner Agreement with Intrexon Corporation



On January 6, 2011, we entered into the Channel Agreement, with
Intrexon that governs a “channel partnering” arrangement in which we use Intrexon’s technology directed towards
in vivo expression of effectors in connection with the development of ZIN-CTI-001 and ZIN-ATI-001 and generally to research,
develop and commercialize products, in each case in which DNA is administered to humans for expression of anti-cancer effectors
for the purpose of treatment or prophylaxis of cancer, which we collectively refer to as the Cancer Program. The Channel Agreement
establishes committees comprised of representatives of us and Intrexon that govern activities related to the Cancer Program in
the areas of project establishment, chemistry, manufacturing and controls, clinical and regulatory matters, commercialization efforts
and intellectual property.



The Channel Agreement grants us a worldwide license to use patents
and other intellectual property of Intrexon in connection with the research, development, use, importing, manufacture, sale, and
offer for sale of products involving DNA administered to humans for expression of anti-cancer effectors for the purpose of treatment
or prophylaxis of cancer (collectively the “ZIOPHARM Products”). Such license is exclusive with respect to any clinical
development, selling, offering for sale or other commercialization of ZIOPHARM Products, and otherwise is non-exclusive. Subject
to limited exceptions, we may not sublicense the rights described without Intrexon’s written consent.



Under the Channel Agreement, and subject to certain exceptions,
we are responsible for, among other things, the performance of the Cancer Program, including development, commercialization and
certain aspects of manufacturing of ZIOPHARM Products. Intrexon is responsible for the costs of establishing manufacturing capabilities
and facilities for the bulk manufacture of products developed under the Cancer Program, certain other aspects of manufacturing
and costs of discovery-stage research with respect to platform improvements and costs of filing, prosecution and maintenance of
Intrexon’s patents.



Subject to certain expense allocations and other offsets provided
in the Channel Agreement, we will pay Intrexon on a quarterly basis 50% of net profits derived in that quarter from the sale of
ZIOPHARM Products, calculated on a ZIOPHARM Product-by- ZIOPHARM Product basis. We have likewise agreed to pay Intrexon on a quarterly
basis 50% of revenue obtained in that quarter from a sublicensor in the event of a sublicensing arrangement. In addition, in partial
consideration for each party’s execution and delivery of the Channel Agreement, we entered into a Stock Purchase Agreement
with Intrexon.



14







ZIOPHARM Oncology, Inc. (a development
stage company)



NOTES TO FINANCIAL STATEMENTS (unaudited)



7. Commitments and Contingencies – (continued)



During the first 24 months of the agreement, either we or Intrexon
may terminate the Channel Agreement in the event of a material breach by the other and Intrexon may terminate the Channel Agreement
under certain circumstances if we assign our rights under the Channel Agreement without Intrexon’s consent. Following the
first 24 months of the agreement, Intrexon may also terminate the Channel Agreement if we fail to use diligent efforts to develop
and commercialize ZIOPHARM Products or if we elect not to pursue the development of a Cancer Program identified by Intrexon that
is a “Superior Therapy” as defined in the Channel Agreement. Also following the first 24 months of the agreement, we
may voluntarily terminate the Channel Agreement upon 90 days written notice to Intrexon.



Upon termination of the Channel Agreement, we may continue to
develop and commercialize any ZIOPHARM Product that, at the time of termination:



| | · | is being commercialized by us;
| | - | ------------------------------

| | · | has received regulatory approval;
| | - | ---------------------------------

| | · | is a subject of an application for regulatory approval that is pending before the applicable regulatory authority;
or
| | - | ---------------------------------------------------------------------------------------------------------------------

| | · | is the subject of at least an ongoing Phase 2 clinical trial (in the case of a termination by Intrexon due to an uncured breach
or a voluntary termination by us), or an ongoing Phase 1 clinical trial in the field (in the case of a termination by us due to
an uncured breach or a termination by Intrexon following an unconsented assignment by us or our election not to pursue development
of a Superior Therapy).
| | - | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------



Our obligation to pay 50% of net profits or revenue described
above with respect to these “retained” products will survive termination of the Channel Agreement.



Collaboration Agreement with Harmon Hill, LLC



On April 8, 2008, the Company signed a collaboration agreement
for Harmon Hill, LLC (“Harmon Hill”) to provide consulting and other services for the development and commercialization
of oncology therapeutics by ZIOPHARM. Under the agreement the Company has agreed to pay Harmon Hill $20 thousand per month for
the consulting services and has further agreed to pay Harmon Hill (a) $500 thousand upon the first patient dosing of the Specified
Drug in a pivotal trial, which trial uses a dosing regime introduced by Harmon Hill; and (b) provided that the Specified Drug receives
regulatory approval from the FDA, the European Medicines Agency or another regulatory agency for the marketing of the Specified
Drug, a 1% royalty of the Company’s net sales will be awarded to Harmon Hill. If the Specified Drug is sublicensed to a third
party, the agreement entitles Harmon Hill to 1% award of royalties or other payments received from a sublicense. The agreement
expired on May 8, 2012 and is currently being renegotiated through November 8, 2012. The Company expensed $240 thousand during
each of the years ended December 31, 2009, 2010 and 2011 and $120 thousand for the six months ended June 30, 2012 for consulting
services per the aforementioned agreement. No milestones under the license agreement were reached or expensed during the years
ended December 31, 2009, 2010, 2011 or for the six months ended June 30, 2012.



Collaboration Agreement with Solasia Pharma K.K.



On March 7, 2011, we entered into a License and Collaboration
Agreement with Solasia Pharma K.K., (“Solasia”).



Pursuant to the License and Collaboration Agreement, we granted
Solasia an exclusive license to develop and commercialize darinaparsin in both IV and oral forms and related organic arsenic molecules,
in all indications for human use in a pan- Asian/Pacific territory comprised of Japan, China, Hong Kong, Macau, Republic of Korea,
Taiwan, Singapore, Australia, New Zealand, Malaysia, Indonesia, Philippines and Thailand.



15







ZIOPHARM
Oncology, Inc. (a development stage company)



NOTES TO FINANCIAL STATEMENTS (unaudited)



7. Commitments and Contingencies – (continued)

As consideration for the license, we received an upfront payment
of $5.0 million to be used exclusively for further clinical development of darinaparsin outside of the pan-Asian/Pacific territory,
and will be entitled to receive additional payments of up to $32.5 million in development-based milestones and up to $53.5 million
in sales-based milestones. We will also be entitled to receive double-digit royalty payments from Solasia based upon net sales
of licensed products in the applicable territories, once commercialized, and a percentage of sublicense revenues generated by Solasia.



The upfront payment for research and development funding is
earned over the period of effort. We currently estimate this period to be 75 months, which could be adjusted in the future.



Under the License and Collaboration Agreement, we provide Solasia
with drug product to conduct clinical trials. These transfers are accounted for as a reduction of research and development costs
and an increase in collaboration receivables.



The agreement provides that Solasia will be responsible for
the development and commercialization of darinaparsin in the pan-Asian/Pacific territory.



CRO Services Agreement with PPD Development, L.P.



The Company and PPD Development, L.P. ("PPD") are
parties to a master clinical research organization services agreement dated January 29, 2010, a related work order dated June
25, 2010 and a related work order dated April 8, 2011 under which PPD provides clinical research organization ("CRO")
services in support of the Company's clinical trials. PPD is entitled to cumulative payments of up to $18.3 million
under these arrangements, which is payable by the Company in varying amounts upon PPD achieving specified milestones. During
the year ended December 31, 2010, the Company expensed $1.8 million upon contract execution and $1.1 million upon a clinical study
commencement of enrollment in North America. During the year ended December 31, 2011, additional milestones related to commencing
enrollment in Europe, Latin America and Asia, along with enrollment based milestones, were met and the Company recorded an aggregate
$4.0 million expense. During the six months ended June 30, 2012, two enrollment related milestones were met and the Company recorded
an expense of $2.6 million.



CRO Services Agreement with Pharmaceutical Research Associates,
Inc.



The Company and Pharmaceutical Research Associates, Inc. (“PRA”)
are parties to a master clinical research organization services agreement dated December 13, 2011 under which PRA provides CRO
services in support of the Company's clinical trials.  PRA is entitled to cumulative payments of up to $19.7 million
under these arrangements, which is payable by the Company in varying amounts upon PRA achieving specified milestones. During
the year ended December 31, 2011, the Company expensed $0.5 million upon execution of a letter of intent. During the six months
ended June 30, 2012, the Company expensed $0.4 million upon execution of extensions of the foregoing letter of intent, $0.7 million
upon work order execution and $1.0 million upon initial clinical study enrollment in the United States.



8. Warrants



The Company has issued both warrants that are accounted for
as liabilities and warrants that are accounted for as equity instruments. The number of warrants outstanding at June 30, 2012 and
December 31, 2011 were as follows:



|                              |  | June 30, |            |  | December 31, | 
|----------------------------- |  | -------- | ---------- |  | ------------ | 
|                              |  | 2012     |            |  | 2011         | 
|Liability-classified warrants |  |          | 8,050,709  |  |              | 
|Equity-classified warrants    |  |          | 3,217,969  |  |              | 
|                              |  |          |            |  |              | 
|Total warrants                |  |          | 11,268,678 |  |              | 



16







ZIOPHARM
Oncology, Inc. (a development stage company)



NOTES TO FINANCIAL STATEMENTS (unaudited)



8. Warrants – (continued)



Liability-Classified Warrants



In May 2005, the Company issued 419,786 warrants to placement
agents for services performed in connection with a 2005 private placement (the “2005 Warrants”) which were originally
valued at $1.6 million. Subject to certain exceptions, the 2005 Warrants provide for anti-dilution protection should common stock
or common stock equivalents be subsequently issued at a price less than the exercise price of the 2005 Warrants then in effect,
which was initially $4.75 per share. This provision was triggered when the Company sold stock in a 2006 private placement at $4.63
per share. Accordingly, the 2005 Warrants were re-priced at $4.69. The provision was triggered a second time upon completion of
a 2009 private placement in which the Company sold stock at $1.825 per share and issued common stock purchase warrants with an
exercise price of $2.04, and the 2005 Warrants were re-priced at $4.25. The provision was triggered again when the Company sold
stock in a December 2009 public offering at $3.10 per share and the 2005 Warrants were re-priced at $3.93. During the first six
months of 2012, 373,617 warrants were exercised and 579 expired on May 31, 2012.



Also, in connection with its December 2009 public securities
offering, the Company issued warrants to purchase an aggregate of 8,206,520 shares of common stock (including the investor warrants
and 464,520 warrants issued to the underwriters for the offering) (the “2009 Warrants”). The 2009 Warrants issued to
investors were exercisable immediately and the warrants issued to underwriters became exercisable six months after the date of
issuance. The 2009 Warrants have an exercise price of $4.02 per share and have a five-year term. The fair value of the 2009 Warrants
was estimated at $22.9 million using a Black-Scholes model with the following assumptions: expected volatility of 105%, risk free
interest rate of 2.14%, expected life of five years and no dividends.



The Company assessed whether the 2005 Warrants and the 2009
Warrants require accounting as derivatives.  The Company determined that these warrants were not indexed to the Company’s
own stock in accordance with accounting standards codification Topic 815, Derivatives and Hedging.  As such, the
Company has concluded these warrants did not meet the scope exception for determining whether the instruments require accounting
as derivatives and were classified as liabilities.



In December 2011, the Company changed from using a Black-Scholes
pricing model to estimate the value of the liability-classified warrants to a Binomial/Monte Carlo pricing model. The following
assumptions were used in the Binomial/Monte Carlo valuation model at June 30, 2012 and the Black-Scholes valuation model at June
30, 2011:



|                        |  | June 30, 2012 |      |   | June 30, 2011 | 
|----------------------- |  | ------------- | ---- | - | ------------- | 
|Risk-free interest rate |  |               | 0.37 | % |               | 
|Expected life in years  |  |               | 2.44 |   |               | 
|Expected volatility     |  |               | 70   | % |               | 
|Expected dividend yield |  |               | 0    |   |               | 
|Steps per year          |  |               | 12   |   |               | 



The change in the fair value of the warrant liability resulted
in losses of $0.6 million and $6.4 million for the three and six months ended June 30, 2012, respectively. The change in the fair
value of the warrant liability resulted in a gain of $2.1 million for the three months ended June 30, 2011 and a loss of $9.0 million
for the six months ended June 30, 2011. The change in the fair value of the warrant liability was charged to other income (expense)
in the Statements of Operations.



17







ZIOPHARM Oncology,
Inc. (a development stage company)



NOTES TO FINANCIAL STATEMENTS (unaudited)



8. Warrants – (continued)



During the first six months of 2012, warrant exercises were
as follows:



|                                  |  |          |         |  |           |  |         | Common |  |  | Liability |  |  |          |    
|--------------------------------- |  | -------- | ------- |  | --------- |  | ------- | ------ |  |  | --------- |  |  | -------- | ---
|                                  |  | Equity   |         |  | Liability |  |         | Stock  |  |  | Reclassed |  |  | Cash     |    
|(in thousands, except share data) |  | Warrants |         |  | Warrants  |  |         | Issued |  |  | to Equity |  |  | Received |    
|Cash exercises                    |  |          | 102,744 |  |           |  | -       |        |  |  | 102,744   |  |  | $        | -  
|Cashless exercises                |  |          | 12,329  |  |           |  | 373,617 |        |  |  | 89,859    |  |  |          | 412
|                                  |  |          | 115,073 |  |           |  | 373,617 |        |  |  | 192,603   |  |  | $        | 412



During the first six months of 2011, warrant exercises were
as follows:



|                                  |  |          |           |  |           |  |         | Common |  |  | Liability |  |  |          |    
|--------------------------------- |  | -------- | --------- |  | --------- |  | ------- | ------ |  |  | --------- |  |  | -------- | ---
|                                  |  | Equity   |           |  | Liability |  |         | Stock  |  |  | Reclassed |  |  | Cash     |    
|(in thousands, except share data) |  | Warrants |           |  | Warrants  |  |         | Issued |  |  | to Equity |  |  | Received |    
|Cash exercises                    |  |          | 2,259,770 |  |           |  | -       |        |  |  | 2,259,770 |  |  | $        | -  
|Cashless exercises                |  |          | 39,832    |  |           |  | 144,905 |        |  |  | 59,308    |  |  |          | 265
|                                  |  |          | 2,299,602 |  |           |  | 144,905 |        |  |  | 2,319,078 |  |  | $        | 265



During the six months ended June 30, 2012, 1,359,317 warrants
issued on February 23, 2007, exercisable at $5.75, expired unexercised on February 23, 2012 and 579 warrants issued on May 31,
2005, exercisable at $3.93, expired unexercised on May 31, 2012.



9. Common Stock



On January 20, 2012, the Company entered into an underwriting
agreement with J. P. Morgan Securities LLC, as representative of the several underwriters named therein, relating to the issuance
and sale of 9,650,000 shares of our common stock. The price to the public in the offering was $5.20 per share, and the underwriters
agreed to purchase the shares from the Company pursuant to the underwriting agreement at a purchase price of $4.888 per share.
Under the terms of the underwriting agreement, the Company also granted the underwriters an option, exercisable for 30 days, to
purchase up to an additional 1,447,500 shares of common stock at a purchase price of $4.888 per share.  The offering
was made pursuant to the Company’s effective registration statement on Form S-3 (Registration Statement No. 333-177793) previously
filed with the SEC, and a prospectus supplement thereunder.  The underwriters purchased the 9,650,000 shares on January 25,
2012 and purchased an additional 464,401 shares on January 31, 2012 pursuant to the partial exercise of their option to purchase
additional shares, resulting in our issuing a total of 10,114,401 shares. The net proceeds from the offering were approximately
$49.2 million after deducting underwriting discounts and offering expenses payable by the Company.



18







ZIOPHARM Oncology,
Inc. (a development stage company)



NOTES TO FINANCIAL STATEMENTS (unaudited)



10. Stock-Based Compensation



The Company recognized stock-based compensation expense on all
employee and non-employee awards as follows:



|                                          |  | For the three months |       |  | For the six months |  
|----------------------------------------- |  | -------------------- | ----- |  | ------------------ | -
|                                          |  | ended June 30,       |       |  | ended June 30,     |  
|                                          |  |                      |       |  |                    |  
|(in thousands)                            |  | 2012                 |       |  | 2011               |  
|Research and development                  |  | $                    | 426   |  |                    | $
|General and administrative                |  |                      | 652   |  |                    |  
|Stock-based employee compensation expense |  | $                    | 1,078 |  |                    | $



The Company granted 361,900 and 425,400
stock options during the three and six months ended June 30, 2012 that had a weighted-average grant date fair value of $3.51 and
$3.48 per share, respectively. The Company granted 516,000 and 1,063,900 stock options during the three and six months ended June
30, 2011 that had a weighted-average grant date fair value of $4.69 and$4.33 per share, respectively.



At June 30, 2012, total unrecognized
compensation costs related to unvested stock options outstanding amounted to $10.3million. The
cost is expected to be recognized over a weighted-average period of 1.59 years.



19







ZIOPHARM Oncology, Inc. (a development
stage company)



NOTES TO FINANCIAL STATEMENTS (unaudited)



10. Stock-Based Compensation – (continued)



For the three months ended
June 30, 2012 and 2011, the fair value of stock options was estimated on the date of grant using a Black-Scholes
option valuation model with the following assumptions:



|                        |  | For the three months ended June 30, |              
|----------------------- |  | ----------------------------------- | -------------
|                        |  | 2012                                |              
|Risk-free interest rate |  |                                     | 0.93 - 1.10  
|Expected life in years  |  |                                     | 6            
|Expected volatility     |  |                                     | 83.36 - 83.52
|Expected dividend yield |  |                                     | 0            



Stock option activity under the Company’s stock option
plan for the six months ended June 30, 2012 is as follows:



|(in thousands, except share and per share data)       |  | Number of Shares |           |   | Weighted- Average Exercise Price |   |      | Weighted- Average Contractual Term (Years) |  |  | Aggregate Intrinsic Value | 
|----------------------------------------------------- |  | ---------------- | --------- | - | -------------------------------- | - | ---- | ------------------------------------------ |  |  | ------------------------- | 
|                                                      |  |                  |           |   |                                  |   |      |                                            |  |  |                           | 
|Outstanding, December 31, 2011                        |  |                  | 5,138,486 |   |                                  | $ | 4.08 |                                            |  |  |                           | 
|                                                      |  |                  |           |   |                                  |   |      |                                            |  |  |                           | 
|Granted                                               |  |                  | 425,400   |   |                                  |   | 4.96 |                                            |  |  |                           | 
|Exercised                                             |  |                  | (8,300    | ) |                                  |   | 3.61 |                                            |  |  |                           | 
|Cancelled                                             |  |                  | (158,432  | ) |                                  |   | 5.90 |                                            |  |  |                           | 
|                                                      |  |                  |           |   |                                  |   |      |                                            |  |  |                           | 
|Outstanding, June 30, 2012                            |  |                  | 5,397,154 |   |                                  | $ | 4.10 |                                            |  |  | 7.19                      | 
|                                                      |  |                  |           |   |                                  |   |      |                                            |  |  |                           | 
|Vested and unvested expected to vest at June 30, 2012 |  |                  | 5,340,550 |   |                                  | $ | 4.10 |                                            |  |  | 7.19                      | 
|                                                      |  |                  |           |   |                                  |   |      |                                            |  |  |                           | 
|Options exercisable, June 30, 2012                    |  |                  | 3,124,387 |   |                                  | $ | 3.40 |                                            |  |  | 5.28                      | 
|                                                      |  |                  |           |   |                                  |   |      |                                            |  |  |                           | 
|Options exercisable, December 31, 2011                |  |                  | 2,911,186 |   |                                  | $ | 3.21 |                                            |  |  | 5.52                      | 
|                                                      |  |                  |           |   |                                  |   |      |                                            |  |  |                           | 
|Options available for future grant                    |  |                  | 3,678,000 |   |                                  |   |      |                                            |  |  |                           | 



A summary of the status of unvested restricted stock for the
six months ended June 30, 2012 is as follows:



|                              |  | Number of Shares |           |   | Weighted-Average Grant Date Fair Value |  
|----------------------------- |  | ---------------- | --------- | - | -------------------------------------- | -
|                              |  |                  |           |   |                                        |  
|Non-vested, December 31, 2011 |  |                  | 950,906   |   |                                        | $
|Granted                       |  |                  | 170,302   |   |                                        |  
|Vested                        |  |                  | (25,000   | ) |                                        |  
|Cancelled                     |  |                  | (66,360   | ) |                                        |  
|                              |  |                  |           |   |                                        |  
|Non-vested, June 30, 2012     |  |                  | 1,029,848 |   |                                        | $



At June 30, 2012, total unrecognized compensation costs related
to unvested restricted stock outstanding amounted to $6.4 million. The cost is expected to be recognized over a weighted-average
period of 1.76 years.



20







Item 2. Management’s Discussion and Analysis of
Financial Condition and Results of Operations



Forward Looking Statements



This quarterly report on Form 10-Q contains “forward-looking
statements” within the meaning of Section 27A of the Securities Act of 1933, as amended, and Section 21E of the Securities
Exchange Act of 1934, as amended. In particular, statements contained in this Form 10-Q, including but not limited to, statements
regarding our future results of operations and financial position, business strategy and plan prospects, projected revenue or costs
and objectives of management for future research, development or operations, are forward-looking statements. These statements relate
to our future plans, objectives, expectations and intentions and may be identified by words such as “may,” “will,”
“should,” “expects,” “plans,” “anticipates,” “intends,” “targets,”
“projects,” “contemplates,” “believes,” “seeks,” “goals,” “estimates,”
“predicts,” “potential” and “continue” or similar words. Readers are cautioned that these forward-looking
statements are only predictions and are subject to risks, uncertainties, and assumptions that are difficult to predict, including
those identified below, under Part II, Item 1A. “Risk Factors” and elsewhere herein. Therefore, actual results
may differ materially and adversely from those expressed in any forward-looking statements. We undertake no obligation to revise
or update any forward-looking statements for any reason.



Business Overview



ZIOPHARM Oncology, Inc. is a biopharmaceutical company that
seeks to develop and commercialize a diverse portfolio of cancer drugs that can address unmet medical needs through the licensing
and development of proprietary small molecule drug candidates and novel DNA-based biotherapeutics. Our small molecule drug candidates
are related to cancer therapeutics already on the market or in development and that can be administered by intravenous, or IV,
and/or oral dosing. Our small molecule clinical programs include palifosfamide (ZIO-201), indibulin (ZIO-301) and darinaparsin
(ZIO-101). We are also pursuing the development of novel DNA-based biotherapeutics in the field of cancer, using a synthetic biology
platform, pursuant to a partnering arrangement with Intrexon Corporation, or Intrexon. Under the arrangement, we obtained rights
to Intrexon’s effector platform for use in the field of oncology, which includes two existing clinical stage product candidates,
ZIN-CTI-001 (or DC-RTS-IL-12 + AL) and ZIN-ATI-001 (or Ad-RTS-IL-12 + AL). We plan to leverage Intrexon’s synthetic biology
platform to develop products to stimulate key pathways used by the body’s immune system to inhibit the growth and metastasis
of cancers, adding significantly to our small molecule drug development portfolio and utilizing our capabilities to translate science
to the patient setting. More detailed descriptions of palifosfamide, indibulin, darinaparsin, ZIN-CTI-001 and ZIN-ATI-001, and
our clinical development plans for each, are set forth below. More detailed descriptions of these product candidates and our clinical
development plans for each are also set forth in our Annual Report on Form 10-K for the fiscal year ended December 31, 2011 and
in other reports that we file from time to time with the Securities and Exchange Commission.



21







Product Candidates



Palifosfamide, ZIO-201



General. Palifosfamide is a novel bi-functional DNA alkylating
agent which is not metabolized by ALDH, nor a substrate for mutli-drug resistance pathways. Therefore, it is likely to have activity,
and be effective, in multiple drug tumors using typical resistance pathways. Also in preclinical cancer models, palifosfamide was
shown to be orally active and synergistic results have been obtained with palifosfamide in combination with doxorubicin, an agent
approved to treat sarcoma.



Further preclinical studies have shown that, in animal and laboratory
models, palifosfamide evidences activity against leukemia and solid tumors. These studies also indicate that palifosfamide may
have a better safety profile than other in-class agents, in part because it does not appear to produce certain toxic metabolites.
One such agent that is commonly used, ifosfamide, produces the toxic metabolites acrolein and chloroacetaldehyde. Acrolein, which
is toxic to the kidneys and bladder, can mandate the administration of a protective agent called mesna, which is inconvenient and
expensive. Chloroacetaldehyde is toxic to the central nervous system, causing “fuzzy brain” syndrome for which there
is currently no protective measure. Because of its distinct pharmaceutical composition, activity and tolerability profile, we believe
palifosfamide may be a new, more effective and well tolerated agent to treat cancer.



Lead Indications for palifosfamide: Soft Tissue Sarcoma.
Sarcomas are cancers of the bone, cartilage, fat, muscle, blood vessels, or other connective or supportive tissue. There are more
than 50 histological or tissue types of soft tissue sarcomas, or STS, but with considerable homogeneity when the disease is metastatic.
The prognosis for patients with soft tissue sarcoma depends on several factors, including the patient’s age, size of the
primary tumor, histological grade, and stage of the tumor. Factors associated with a poorer prognosis include being older than
60 years of age, having tumors larger than five centimeters, and having tumors of high-grade histology. While small, low-grade
tumors are usually curable by surgery alone, the higher-grade or larger sarcomas are associated with higher local treatment failure
rates and increased metastatic potential.



Intravenous palifosfamide may be a useful agent that, either
alone or in combination with other agents and doxorubicin, in particular, may deliver enhanced therapeutic activity with fewer
side effects of the type that have been associated with agents such as ifosfamide. In the United States, ifosfamide is often included
in combination regimens for the treatment of sarcomas, testicular cancers, head and neck cancer, certain types of non-Hodgkin’s
lymphomas, and other solid tumors including small-cell lung cancer, or SCLC, although ifosfamide is formally approved by FDA only
for the treatment of testicular cancer.  Doxorubicin, approved decades ago, is the only FDA-approved treatment for sarcoma.
We believe that palifosfamide in combination with doxorubicin may be more effective than doxorubicin alone or in combination with
minimal impact on the safety profile and better Quality of Life (QoL).



Small-Cell Lung Cancer.SCLC is almost exclusively associated
with smoking. Similar to sarcoma, standard of care for SCLC, which is etoposide and platinum therapy, has changed little in decades.
Published studies of ifosfamide in combination with standard of care have evidenced enhanced efficacy but also with enhanced side
effects, providing for an unfavorable benefit to risk association. We believe that combining palifosfamide with standard of care
could offer enhanced efficacy with an appropriate balance of benefit to toxicity.



Other Indications. Palifosfamide may be useful to treat
many other solid tumors, such as breast cancer, and for the treatment of pediatric cancer and hematological malignancies. With
an investigational new drug application, or IND, for the oral form of palifosfamide now approved by FDA and clinical study under
development, oral palifosfamide could also offer not only a significant advancement to current therapies but also greater patient
access and convenience.



22







Lead Indications for palifosfamide: STS and SCLC, Significant
Unmet Medical Need.Both first-line metastatic STS and SCLC represent significant unmet medical needs with standard of care
considerably dated. We believe approximately 100,000 patients worldwide are initially diagnosed with STS every year. For patients
diagnosed with STS, primary care is surgery, sometimes with radiation therapy. Many patients enter a period of remission that is
unpredictable and can even represent a “cure.” Metastatic STS arises when the disease is either first diagnosed in
the advanced setting or has and spread re-occurred and surgery is no longer an option. Chemotherapy is the standard of care for
first-line metastatic STS and doxorubicin is the only first-line therapy approved in the United States for its treatment. We believe
the annual projection in the United States for first-line metastatic STS treatment is approximately 9,000 patients. While data
sources for Europe are limited, we estimate, based on epidemiology, an annual projection in Europe for first-line metastatic STS
treatment of approximately 14,000 patients, for a combined U.S. and European estimate of 23,000 patients annually. Orphan Drug
Designation for palifosfamide has been obtained in both the United States and the European Union for the treatment of STS. For
SCLC, the estimated U.S. annual incidence is 30,000 – 35,000 patients and 200,000 patients worldwide. Approximately
80% - 90% of patients have extensive disease, the population for the planned pivotal trial. Platinum and etoposide are standard
of care in the first-line setting. A formal retrospective mortality study also suggests that the SCLC population in China is substantial
and projected from the study to be greater than 150,000 patients and growing.



Clinical Development Plan for Palifosfamide. Following
Phase 1 study with IV administration, we completed Phase 2 testing of palifosfamide as a single agent to treat advanced sarcoma.
In both Phase 1 and Phase 2 testing, palifosfamide has been administered without the “uroprotectant” mesna, as is required
with ifosfamide, and the toxicities associated with other ifosfamide metabolites, acrolein and chloroacetaldehyde, have not been
observed. We reported clinical activity of palifosfamide when used alone in the Phase 2 study addressing advanced sarcoma. Following
review of preclinical combination studies, we initiated a Phase 1 dose escalation study of palifosfamide in combination with doxorubicin,
primarily in patients with STS. We reported favorable results and safety profile from this study at the 2009 annual meeting of
the American Society of Clinical Oncology, or ASCO.



In light of reported favorable Phase 2 single agent clinical
activity data and with the combination being well tolerated in the Phase 1 trial, we initiated a Phase 2 randomized controlled
trial in the second half of 2008, which we refer to as PICASSO, to compare doxorubicin plus palifosfamide to doxorubicin alone
in patients with front- and second-line metastatic or unresectable STS. The study generated positive top-line interim data in 2009.
Upon successfully reaching a pre-specified efficacy milestone and following safety and efficacy data review by our Data Committee,
sarcoma experts, and our Medical Advisory Board, we elected to suspend enrollment in the trial in October 2009. We subsequently
presented further positive interim data from the trial at the 15th Annual Connective Tissue Oncology Society meeting held in November
2009 and again at the 2010 ASCO annual meeting in June 2010, where the presentation was selected for “Best of ASCO.”
As presented at ASCO in February 2012, the Phase 2 PICASSO trial randomized a total of 67 patients with 66 treated and 62 eligible
for evaluation. The study was designed to show a difference in progression free survival (“PFS”) between doxorubicin
in combination with palifosfamide versus doxorubicin alone. An analysis of the evaluable data reported a hazard ratio of 0.43 (p=0.019).
Safety data were similar between the two groups in the study. The most common grade 3-4 events were neutropenia and elevated creatinine,
both observed with similar frequency between treatment groups. Subsequently in February 2012, we announced the preliminary overall
survival data from the PICASSO trial; the hazard ratio for overall survival was 0.78 favoring the palifosfamide group (with a 2-year
survival rate of 40% compared to 30%).



In July 2010, we announced the initiation of a
worldwide registration trial on a protocol design developed through a FDA End-of-Phase 2 meeting and the Special Protocol
Assessment, or SPA, process. Although we did engage in the SPA process, we, with guidance from the FDA, elected to initiate
the trial without having obtained SPA agreement from the FDA. The Phase 3 trial is in first-line metastatic STS, entitled
PICASSO 3, and is an international, randomized, double-blinded, placebo-controlled trial with a targeted enrollment of 424
patients. The study completed enrollment in June 2012 and we now expect data from this trial to be reported in the fourth
quarter of 2012.



The study is designed to evaluate the safety and efficacy of
palifosfamide administered with doxorubicin compared with doxorubicin administered with placebo, with no cross-over between the
arms. Progression-free survival is the primary endpoint for accelerated approval, with overall survival as the primary endpoint
for full approval. PICASSO 3 has no interim efficacy analysis, while the trial is monitored by an Independent Data Monitoring Committee,
or IDMC, of outside, independent experts for safety and futility. The IDMC has met on four occasions to review all available study
data and in all instances has recommended trial continuation. Orphan Drug Designation for palifosfamide has been obtained in both
the United States and the European Union for the treatment of STS.



23







A Phase 1 trial has completed accrual with palifosfamide in
combination with etoposide and carboplatin and data to date have determined appropriate dosing for initiating a potentially pivotal,
adaptive Phase 3 trial in first-line, extensive SCLC. In June 2012, the Company initiated an international, multi-center, open-label,
adaptive, randomized study of palifosfamide in combination with carboplatin and etoposide (PaCE) chemotherapy versus carboplatin
and etoposide (CE) alone in chemotherapy naïve patients with extensive-stage small cell lung cancer (MATISSE). The MATISSE
study is designed to enroll up to 548 patients. The trial's primary endpoint is overall survival.  Secondary endpoints
include progression-free survival, objective response rate and quality of life. MATISSE will be conducted at centers in North
America, Europe, Australia and Asia.



The study’s adaptive design includes a prospectively planned
opportunity for modification of the study protocol by adjusting one or more specified components of the design in order to maintain
adequate power. Evaluation of the study’s powering will be conducted by an IDMC at a single, pre-planned interim analysis,
scheduled to occur following 125 events. At the interim analysis, the IDMC will review all efficacy and safety data and decide
whether to: 1) halt the study for efficacy or futility, 2) continue the study to its planned enrollment of 548 patients, 3) decrease
sample size, or 4) increase event size.



Additionally, an oral capsule form of palifosfamide has been
the subject of preclinical studies necessary for an Investigational New Drug, or IND, application to support commencing Phase 1
study, presently under development.



DNA-based biotherapeutics (synthetic biology) ZIN-CTI-001
(or DC-RTS-IL-12 + AL) and ZIN-ATI-001 (or Ad-RTS-IL-12 + AL)



General. On January 6, 2011, we entered into an Exclusive
Channel Partner Agreement with Intrexon pursuant to which we plan to supplement our small molecule drug development efforts by
pursuing the development and commercialization of novel DNA-based biotherapeutics in the field of cancer treatment using Intrexon’s
RheoSwitch® and UltraVector® synthetic biology technologies. The channel partnering arrangement contemplates
our using Intrexon’s technology directed towards in vivo expression of effectors in connection with the development
of ZIN-CTI-001 and ZIN-ATI-001 and generally to research, develop and commercialize products, in each case in which DNA is administered
to humans for expression of anti-cancer effectors for the purpose of treatment or prophylaxis of cancer. ZIN-CTI-001 (or DC-RTS-IL-12)
and ZIN-ATI-001 (or Ad-RTS-IL-12) are the two existing clinical-stage products currently in development under this channel partnering
arrangement. Under the arrangement, Intrexon assigned to us all regulatory filings and approvals relating to the two product candidates
and we assumed sponsorship of the ongoing clinical trials of ZIN-CTI-001.



Clinical Development Plan for DNA-based biotherapeutics.The Company completed enrollment in a Phase 1b dose escalation study of ZIN-CTI-001 in Q2 2012 in the United States. ZIN-CTI-001
employs intratumoral injection of modified dendritic cells from each patient and oral dosing of an activator ligand to turn on
in vivo expression of interleukin-12, or IL-12. ZIN-CTI-001, through the RheoSwitch Therapeutic System®,
or RTS®, controls the timing and level of transgene expression. The RTS® technology functions as
a “gene switch” for the regulated expression of human IL-12 in the patients’ dendritic cells which are transduced
with a replication deficient adenoviral vector carrying the IL-12 gene under the control of the RTS®, and in Phase
1 study, injected intratumorally for the treatment of patients with stage III or IV melanoma. The binding of the small molecule
activator to the fusion proteins of RTS® is intended to regulate the timing and level of IL-12 expression. In the
absence of the activator ligand, the level of IL-12 is below detectable levels.



The activator ligand has been the subject of a number of preclinical,
safety and pharmacology studies under FDA and International Conference on Harmonisation of Technical Requirements for Registration
of Pharmaceuticals for Human Use guidelines. Preclinical studies in the B16 mouse melanoma model consistently induced regression
of established melanoma lesions, both in those directly injected and those elsewhere in the animal. Preclinical studies have shown
DC-RTS-IL-12, in combination with an activator ligand, to have strong activity against a broad array of cancers, including brain,
colon, renal and pancreatic cancers and melanoma.



24







A Phase 1a clinical study of the activator ligand was conducted
in 65 healthy volunteers, with the two most common side-effects being dysgeusia (impairment of taste) and throat irritation. A
subsequent Phase 1b trial, which is ongoing in patients with advanced melanoma, has been amended to study efficacy and immunological
and biological effects in addition to safety with cohort-based dose escalation of the activator ligand during repeated treatment
cycles. Initial positive clinical results from the Phase 1b trial were presented at the June 2011 ASCO annual meeting. The trial
enrolled ten patients (median age 61) with unresectable stage III or IV melanoma. Among eight evaluable patients, partial or complete
regression of injected and some uninjected lesions was observed by computed axial tomography, or CT, scans in three patients, with
one patient having a RECIST PR of >11 months and three patients demonstrating stable disease by RECIST, for an overall disease
control rate of 50%. Treatment was generally well tolerated, adverse events were mild to moderate, with one to two patients each
experiencing nausea, vomiting, anorexia, arthralgia, fever or chills. One severe adverse event was reported 18 hours after treatment
onset with 60 mg AL + ZIN-CTI-001, and included diarrhea, followed by hypotension and reversible acute renal failure, which completely
resolved.



Clinical study of ZIN-ATI-001, essentially ZIN-CTI-001 without
dendritic cells, is in an ongoing Phase 1b study for metastatic melanoma. The Phase 1b study is evaluating safety in addition to
immunological and biological effects and efficacy of the therapeutic candidate in patients with melanoma. Enrollment in the Phase
1b study is ongoing and is expected to complete in 2012.



We expect to advance ZIN-ATI-001 into a Phase 2 study for melanoma
in 2012. The Company will also continue to focus on additional disease indications where there are significant unmet medical needs.



Furthermore, we are evaluating additional potential preclinical
candidates and continuing discovery efforts aimed at identifying other potential product candidates under our Channel Agreement
with Intrexon.



Indibulin, ZIO-301



General. Indibulin is a novel, orally available small
molecular-weight inhibitor of tubulin polymerization that we acquired from Baxter Healthcare in 2006, and is the subject of numerous
patents worldwide, including those in the United States, the European Union and Japan. The microtubule component, tubulin, is one
of the more well-established drug targets in cancer. Microtubule inhibitors interfere with the dynamics of tubulin polymerization,
resulting in inhibition of chromosome segregation during mitosis and consequently inhibition of cell division. A number of marketed
IV anti-cancer drugs target tubulin, such as the taxane family members, paclitaxel (Taxol®), docetaxel (Taxotere®),
the vinca alkaloid family members, vincristine and vinorelbine, and new classes of tubulin inhibitors including the epothilones.
This broad class of agents is typically the mainstay of therapy in a wide variety of indications. In spite of their effectiveness,
the use of these drugs is associated with significant toxicities, notably peripheral neurotoxicity.



Preclinical studies with indibulin demonstrate significant and
broad antitumor activity, including activity against taxane-refractory cell lines. The cytotoxic activity of indibulin was demonstrated
in several rodent and human tumor cell lines derived from prostate, brain, breast, pancreas, lung, ovary, and cervical tumor tissues
and in rodent tumor and human tumor xenograft models. In addition, indibulin was effective against multidrug resistant tumor cell
lines (breast, lung, and leukemia) bothin vitroand in vivo. Indibulin is potentially safer than other tubulin inhibitors
as no neurotoxicity has been observed at therapeutic doses in rodents and in the Phase 1 trials. Indibulin has also demonstrated
synergy with approved anti-cancer agents in preclinical studies. The availability of an oral formulation with the expected convenience
of once daily dosing we believe is a significant commercial opportunity.



Indibulin has a different pharmacological profile from other
tubulin inhibitors currently on the market as it binds to a unique site on tubulin and is active in multi-drug-resistant (MDR-1,
MRP-1) and taxane-resistant tumors. Indibulin binding causes destabilization of microtubules in vitro, an effect similar
to that of the vinca alkaloid family or colchicine, but opposite to that of paclitaxel and related drugs and different from the
epothilones.



Testing of indibulin for in vitro growth inhibitory activity
against a panel of human and rodent tumor-derived cell lines revealed that the drug candidate is active in a broad spectrum of
cell lines derived from different organs. In vivo, indibulin is active in a number of xenograft and rodent tumor models.
Its unique pharmacodynamic properties demonstrated in preclinical studies, as well as an excellent safety profile observed to date
in ongoing Phase 1 studies, warranted further evaluation in the clinic.



25







Clinical Development Plan for Indibulin.Phase 1 study
as a single agent in patients with a variety of advanced solid tumors has been completed. We have reported clinical activity at
well-tolerated doses using a continuous dosing scheme without the development of clinically relevant peripheral neuropathy. Following
encouraging preclinical results obtained with indibulin in combination with other chemotherapies, two Phase 1 combination studies
were initiated with TarcevaTM and XelodaTM, respectively. The favorable activity and safety profile of oral
indibulin with oral XelodaTM was reported at ASCO’s annual meeting in May 2009. In all studies, a maximum tolerated
dose, or MTD, has not been established.



Preclinical work established a dosing schedule to maximize activity
while managing toxicity and that regimen, five days on drug and nine days off, is now in Phase 1 study in late stage metastatic
breast cancer. In light of not establishing an MTD and the need to administer many capsules several times a day, we have recently
modified the dosage form to achieve once a day dosing which continues in the Phase 1 trial with the 5 and 9 schedule.



Darinaparsin, ZIO-101



General. Darinaparsin is an anti-mitochondrial (organic
arsenic) compound covered by issued patents and pending patent applications in the United States and in foreign countries. A form
of commercially available inorganic arsenic (arsenic trioxide [Trisenox®], or ATO) has been approved in the United
States, the European Union and Japan for the treatment of acute promyelocytic leukemia, a precancerous condition. In the United
States, ATO is on the compendia listing for the therapy of multiple myeloma, and has been studied for the treatment of various
other cancers. Nevertheless, ATO has been shown to be toxic to the heart, liver, and brain, which limits its use as an anti-cancer
agent. ATO carries a “black box” warning for electrocardiogram abnormalities since arsenic trioxide has been shown
to cause QT interval prolongation and complete atrioventricular block. QT prolongation can lead to a torsade de pointes-type
ventricular arrhythmia, which can be fatal. Inorganic arsenic has also been shown to cause cancer of the skin and lung in humans.
The toxicity of arsenic is generally correlated to its accumulation in organs and tissues. Our preclinical and clinical studies
to date have demonstrated that darinaparsin is considerably less toxic than ATO, particularly with regard to cardiac toxicity.



In vitro testing of darinaparsin using the National Cancer
Institute’s human cancer cell panel demonstrated activity against a series of tumor cell lines including lung, colon, brain,
melanoma, ovarian, and kidney cancer. Moderate activity was shown against breast and prostate cancer tumor cell lines. In addition
to solid tumors, in vitro testing in both the National Cancer Institute’s cancer cell panel and in vivo testing
in a leukemia animal model demonstrated substantial activity against hematological cancers (cancers of the blood and blood-forming
tissues) such as leukemia, lymphoma, myelodysplastic syndromes, and multiple myeloma. Results indicate significant activity against
the HuT 78 cutaneous T-cell lymphoma, the NK-G2MI natural killer-cell NHL, KARPAS-299 T-cell NHL, SU-DHL-8 B-cell NHL, SU-DHL-10
B-cell NHL and SU-DHL-16 B-cell NHL cell lines. Preclinical studies have also established anti-angiogenic properties of darinaparsin,
providing support for the development of an oral form of the drug, and established synergy of darinaparsin in combination with
other approved anti-cancer agents.



Potential Lead Indication: Lymphoma. Three Phase 2 IV
studies of darinaparsin evaluating hematological malignancies, myeloma and liver cancer, have been completed and data from these
trials has been reported, the most promising being in lymphomas and particularly in peripheral T-cell lymphoma.



Clinical Development Plan for darinaparsin: Phase 1 testing
of the IV form of darinaparsin in solid tumors and hematological cancers was completed and we reported clinical activity and a
safety profile from these studies as predicted by preclinical results. We subsequently completed Phase 2 studies in advanced myeloma,
primary liver cancer and in certain other hematological cancers. At the May 2009 annual meeting of ASCO, we reported favorable
results from the IV trial in lymphoma, particularly peripheral T-cell lymphoma, or PTCL. A Phase 1 trial in solid tumors with an
oral form of darinaparsin has completed enrollment. We have obtained Orphan Drug Designation for darinaparsin in the United States
and Europe for the treatment of PTCL and have entered into a licensing agreement with Solasia for the Asia/Pacific territory with
the present IV darinaparsin clinical priority a focus on advancing PTCL study in that region. Further clinical studies are currently
ongoing with Solasia.



26







Development Plans



We are currently pursuing several clinical programs for our
small molecule and DNA-based biotherapeutic candidates, which include:



| | • | palifosfamide (ZIO-201) — completing our Phase 3 pivotal trial in first-line metastatic STS, entitled PICASSO
3, and continuing enrollment in our Phase 3 trial in SCLC, entitled MATISSE.
| | - | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------



| | • | ZIN-CTI-001 — completing a Phase 1b trial in patients with metastatic melanoma.
| | - | -------------------------------------------------------------------------------



| | • | ZIN-ATI-001 — completing a Phase 1b trial in patients with late-stage melanoma and advancing into a Phase 2
trial.
| | - | ------------------------------------------------------------------------------------------------------------------



| | • | indibulin (ZIO-301) — completing a Phase 1 trial in patients with metastatic breast cancer.
| | - | -------------------------------------------------------------------------------------------



| | • | darinaparsin (ZIO-101) — completing an ongoing Phase 1 study and determining future study with the oral form
and working with Solasia with IV administration in PTCL in the licensed territory.
| | - | -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------



We are also evaluating additional potential preclinical candidates
and continuing discovery efforts aimed at identifying other potential product candidates under our channel partnership with Intrexon.



Our current plans involve using our principal internal financial
resources to develop palifosfamide and to extend the DNA-based biotherapeutic program, with the intention of ultimately partnering
or otherwise raising additional resources to support further development activities for all of our product candidates. Based
on these plans, we expect to incur the following expenses during the next twelve months: approximately $82.9 million on research
and development expenses and approximately $24.0 million on general corporate and administrative expenses. This forecast of expenses
is forward-looking information that involves risks and uncertainties, and the actual amount of our expenses over the next twelve
months could vary materially and adversely as a result of a number of factors, including the factors discussed in the ‘‘Risk
Factors’’ section of this report and the uncertainties applicable to ourforecast for the overall sufficiency
of our capital resources, which are discussed under “—Liquidity and Capital Resources” below. We have based our estimates on assumptions that may prove to be wrong, and our expenses could prove to be significantly higher
than we currently anticipate.



Furthermore, the successful development of our product candidates
is highly uncertain. Product development costs and timelines can vary significantly for each product candidate, are difficult to
accurately predict, and will require us to obtain additional funding, either alone or in connection with partnering arrangements.
Various statutes and regulations also govern or influence the manufacturing, safety, labeling, storage, record keeping and marketing
of each product. The lengthy process of seeking approval and the subsequent compliance with applicable statutes and regulations
require the expenditure of substantial resources. Any failure by us to obtain, or any delay in obtaining, regulatory approvals
could materially, adversely affect our business. To date, we have not received approval for the sale of any product candidates
in any market and, therefore, have not generated any revenues from our product candidates.



27







Financial Overview



Overview of Results of Operations



Three and six months ended June 30, 2012 compared to three
and six months ended June 30, 2011



Revenue. Revenue during the three and six months
ended June 30, 2012 and 2011 were as follows:



|                      |  | Three months ended June 30, |     |  |      |   |     |        |  |   | Six months ended June 30, |  |  |      |   |   |        |  
|--------------------- |  | --------------------------- | --- |  | ---- | - | --- | ------ |  | - | ------------------------- |  |  | ---- | - | - | ------ | -
|                      |  | 2012                        |     |  | 2011 |   |     | Change |  |   | 2012                      |  |  | 2011 |   |   | Change |  
|($ in thousands)      |  |                             |     |  |      |   |     |        |  |   |                           |  |  |      |   |   |        |  
|                      |  |                             |     |  |      |   |     |        |  |   |                           |  |  |      |   |   |        |  
|Collaboration revenue |  | $                           | 200 |  |      | $ | 200 |        |  | $ | -                         |  |  |      | 0 | % |        | $



Revenue for the three months ended June 30, 2012 was the same
as the three months ended June 30, 2011.



Revenue for the six months ended June 30, 2012 increased by
$133 thousand from the six months ended June 30, 2011. The increase is due to our entry into the collaboration agreement on March
7, 2011, resulting in a partial period under the agreement during the first six months of 2011. We are recognizing the research
and development funding revenue over the estimated period of performance (75 months).



Research and development expenses. Research and
development expenses during the three and six months ended June 30, 2012 and 2011 were as follows:



|                         |  | Three months ended June 30, |        |  |      |   |       |        |  |   | Six months ended June 30, |  |  |      |     |   |        |  
|------------------------ |  | --------------------------- | ------ |  | ---- | - | ----- | ------ |  | - | ------------------------- |  |  | ---- | --- | - | ------ | -
|                         |  | 2012                        |        |  | 2011 |   |       | Change |  |   | 2012                      |  |  | 2011 |     |   | Change |  
|($ in thousands)         |  |                             |        |  |      |   |       |        |  |   |                           |  |  |      |     |   |        |  
|                         |  |                             |        |  |      |   |       |        |  |   |                           |  |  |      |     |   |        |  
|Research and development |  | $                           | 18,264 |  |      | $ | 9,125 |        |  | $ | 9,139                     |  |  |      | 100 | % |        | $



Research and development expenses for
the three months ended June 30, 2012 increased by $9.1 million from the three months ended June 30, 2011. The increase was due
primarily to increased trial costs of $4.0 million related primarily to the Phase 3 palifosfamide study in STS and the Phase 3
palifosfamide study in SCLC, increased preclinical trials of $2.1 million, increased manufacturing activity of $1.2 million, increased
salary and employee-related costs of $1.1 million, and other costs of $0.7 million.



Research and development expenses for
the six months ended June 30, 2012 decreased by $1.5 million from the six months ended June 30, 2011. The decrease was primarily
due to the payment in the first six months of 2011 of a one-time $17.5 million non-cash expense related to our Channel Agreement,
including our associated license of Intrexon technology, partially offset by increases in trial costs of $7.0 million related primarily
to the Phase 3 palifosfamide study in STS and the Phase 3 palifosfamide study in SCLC, preclinical trial costs of $3.1 million,
salary and employee-related costs of $2.7 million, manufacturing activity costs of $1.5 million, other costs of $0.6 million, and
a one-time expense of $0.7 million relating to a new safety database.



We expect our research and development expenses to increase,
as compared to prior periods, as we continue our Phase 3 palifosfamide trials and other studies for palifosfamide, DNA therapeutics,
indibulin and darinaparsin.



28







Our research and development expense consists primarily of salaries
and related expenses for personnel, costs of contract manufacturing services, costs of facilities and equipment, fees paid to professional
service providers in conjunction with our clinical trials, fees paid to research organizations in conjunction with preclinical
animal studies, costs of materials used in research and development, consulting, license and milestone payments and sponsored research
fees paid to third parties.



We have not accumulated and tracked our internal historical
research and development costs or our personnel and personnel-related costs on a program-by-program basis. Our employee and infrastructure
resources are allocated across several projects, and many of our costs are directed to broadly applicable research endeavors. As
a result, we cannot state the costs incurred for each of our oncology programs on a program-by-program basis.



In 2012, our clinical projects have consisted primarily of two
Phase 3 projects for our lead product candidate palifosfamide. The expenses for our Phase 3 palifosfamide study in STS incurred
by us to third parties were $9.9 million for the six months ended June 30, 2012 and $30.2 million from the project inception in
July 2010 through June 30, 2012. The expenses for our Phase 3 palifosfamide study in SCLC incurred by us to third parties were
$3.9 million for the six months ended June 30, 2012 and $3.9 million from the project inception in December 2011 through June 30,
2012.



Our future research and development expenses in support of our
current and future programs will be subject to numerous uncertainties in timing and cost to completion. We test potential products
in numerous preclinical studies for safety, toxicology and efficacy. We may conduct multiple clinical trials for each product.
As we obtain results from trials, we may elect to discontinue or delay clinical trials for certain products in order to focus our
resources on more promising products or indications. Completion of clinical trials may take several years or more, and the length
of time generally varies substantially according to the type, complexity, novelty and intended use of a product. It is not unusual
for preclinical and clinical development of each of these types of products to require the expenditure of substantial resources.



We estimate that clinical trials of the type generally needed
to secure new drug approval are typically completed over the following timelines:



|Clinical Phase |  | Estimated Completion Period
|-------------- |  | ---------------------------
|               |  |                            
|Phase 1        |  | 1 - 2 years                
|Phase 2        |  | 2 - 3 years                
|Phase 3        |  | 2 - 4 years                



The duration and the cost of clinical trials may vary significantly
over the life of a project as a result of differences arising during clinical development, including, among others, the following:



| | · | the number of clinical sites included in the trials;
| | - | ----------------------------------------------------



| | · | the length of time required to enroll suitable patents;
| | - | -------------------------------------------------------



| | · | the number of patients that ultimately participate in the
trials;
| | - | -----------------------------------------------------------------



| | · | the duration of patient follow-up to ensure the absence
of long-term product-related adverse events; and
| | - | --------------------------------------------------------------------------------------------------------



| | · | the efficacy and safety profile of the product.
| | - | -----------------------------------------------



As a result of the uncertainties discussed above, we are unable
to determine the duration and completion costs of our programs or when and to what extent we will receive cash inflows from the
commercialization and sale of a product. Our inability to complete our programs in a timely manner or our failure to enter into
appropriate collaborative agreements could significantly increase our capital requirements and could adversely impact our liquidity.
These uncertainties could force us to seek additional, external sources of financing from time-to-time in order to continue with
our product development strategy. Our inability to raise additional capital, or to do so on terms reasonably acceptable to us,
would jeopardize the future success of our business.



29







General and administrative expenses. General and
administrative expenses during the three and six months ended June 30, 2012 and 2011 were as follows:



|                           |  | Three months ended June 30, |       |  |      |   |       |        |  |   | Six months ended June 30, |  |  |      |    |   |        |  
|-------------------------- |  | --------------------------- | ----- |  | ---- | - | ----- | ------ |  | - | ------------------------- |  |  | ---- | -- | - | ------ | -
|                           |  | 2012                        |       |  | 2011 |   |       | Change |  |   | 2012                      |  |  | 2011 |    |   | Change |  
|($ in thousands)           |  |                             |       |  |      |   |       |        |  |   |                           |  |  |      |    |   |        |  
|                           |  |                             |       |  |      |   |       |        |  |   |                           |  |  |      |    |   |        |  
|General and administrative |  | $                           | 4,902 |  |      | $ | 3,923 |        |  | $ | 979                       |  |  |      | 25 | % |        | $



General and administrative expenses for the three months ended
June 30, 2012 increased by $1.0 million from the three months ended June 30, 2011. The increase was primarily due to increases
in salary and employee-related costs of $0.6 million, non-employee contracted costs of $0.1 million and other costs of $0.3 million.



General and administrative expenses for the six months ended
June 30, 2012 increased by $2.5 million from the six months ended June 30, 2011. The increase was primarily due to increases in
salary and employee-related costs of $1.2 million, non-employee contracted costs of $0.9 million and other costs of $0.4 million.



We expect our general and administrative expenses to increase
moderately to support increased activity in clinical studies.



Other income (expense). Other income (expense)
for the three and six months ended June 30, 2012 and 2011 were as follows:



|                                 |  | Three months ended June 30, |      |   |      |   |       |        |  |   | Six months ended June 30, |   |  |      |      |   |        |  
|-------------------------------- |  | --------------------------- | ---- | - | ---- | - | ----- | ------ |  | - | ------------------------- | - |  | ---- | ---- | - | ------ | -
|                                 |  | 2012                        |      |   | 2011 |   |       | Change |  |   | 2012                      |   |  | 2011 |      |   | Change |  
|($ in thousands)                 |  |                             |      |   |      |   |       |        |  |   |                           |   |  |      |      |   |        |  
|                                 |  |                             |      |   |      |   |       |        |  |   |                           |   |  |      |      |   |        |  
|Other income, net                |  | $                           | 3    |   |      | $ | 9     |        |  | $ | (6                        | ) |  |      | -67  | % |        | $
|Change in fair value of warrants |  |                             | (650 | ) |      |   | 2,115 |        |  |   | (2,765                    | ) |  |      | -131 | % |        |  
|                                 |  |                             |      |   |      |   |       |        |  |   |                           |   |  |      |      |   |        |  
|Total                            |  | $                           | (647 | ) |      | $ | 2,124 |        |  | $ | (2,771                    | ) |  |      |      |   |        | $



The increase in total other income (expense) of $2.8 million
from the three months ended June 30, 2012 compared to the three months ended June 30, 2011 was due primarily to decreased non-cash
expense recorded from the change in the fair value of liability-classified warrants.



The decrease in total other income (expense) of $2.5 million
from the six months ended June 30, 2012 compared to the six months ended June 30, 2011 was due primarily to decreased non-cash
expense recorded from the change in the fair value of liability-classified warrants. Additional changes are attributable to increased
state tax payments.



30







Liquidity and Capital Resources



As of June 30, 2012, we had approximately $110.4 million in
cash and cash equivalents, compared to $104.7 million in cash and cash equivalents as of December 31, 2011. We anticipate that
our cash resources will be sufficient to fund our operations into the second half of 2013. However, changes may occur that would
consume our existing capital prior to that time, including the scope and progress of our research and development efforts and changes
in governmental regulation. Actual costs may ultimately vary from our current expectations, which could materially impact our use
of capital and our forecast of the period of time through which our financial resources will be adequate to support our operations.
We have estimated the sufficiency of our cash resources based in part on the trial design for our PICASSO 3 pivotal trial for first-line
metastatic STS and our adaptive Phase 3 trial for first-line SCLC for IV palifosfamide and our current timing expectations for
enrollment of the studies, which may change based on the progression of enrollment. We also assumed responsibility for the advancement
of two product candidates in the clinic under our exclusive channel partnership with Intrexon, and we expect that the costs associated
with these and additional product candidates will increase the level of our overall research and development expenses significantly
going forward.



Although
all human clinical trials are expensive and difficult to design and implement, we believe that due to complexity, costs
associated with clinical trials forDNA-based biotherapeuticproducts
are greater than the corresponding costs associated with clinical trials for small molecule candidates. In addition to increased
research and development costs, we have added, and will continue to add, headcount to support our exclusive channel partnership
endeavors, which will add to our general and administrative expenses going forward.



In addition to these factors, our actual cash requirements may
vary materially from our current expectations for a number of other factors that may include, but are not limited to, changes in
the focus and direction of our development programs, competitive and technical advances, costs associated with the development
of our product candidates, our ability to secure partnering arrangements, and costs of filing, prosecuting, defending and enforcing
our intellectual property rights. If we exhaust our capital reserves more quickly than anticipated, regardless of the reason, and
we are unable to obtain additional financing on terms acceptable to us or at all, we will be unable to proceed with development
of some or all of our product candidates on expected timelines and will be forced to prioritize among them.



31







We expect that we will need additional financing to support
our long-term plans for clinical trials and new product development. We expect to finance our cash needs through the sale of equity
securities, strategic collaborations and/or debt financings, or through other sources that may be dilutive to existing stockholders.
There can be no assurance that we will be able to obtain funding from any of these sources or, if obtained, what the terms of such
funding(s) may be, or that any amount that we are able to obtain will be adequate to support our working capital requirements until
we achieve profitable operations. We have no current committed sources of additional capital. Recently, capital markets have experienced
a period of instability that may severely hinder our ability to raise capital within the time periods needed or on terms we consider
acceptable, if at all. If we are unable to raise additional funds when needed, we may not be able to continue development and regulatory
approval of our products, or we could be required to delay, scale back or eliminate some or all our research and development programs.



The following table summarizes our net increase (decrease) in
cash and cash equivalents for the six months ended June 30, 2012 and 2011:



|                                          |  | Six months ended June 30, |        
|----------------------------------------- |  | ------------------------- | -------
|                                          |  | 2012                      |        
|($ in thousands)                          |  |                           |        
|Net cash provided by (used in):           |  |                           |        
|Operating activities                      |  | $                         | (42,625
|Investing activities                      |  |                           | (1,107 
|Financing activities                      |  |                           | 49,410 
|                                          |  |                           |        
|Net increase in cash and cash equivalents |  | $                         | 5,678  



Net cash used in operating activities was $42.6 million for
the six months ended June 30, 2012 compared to $14.0 million for the six months ended June 30, 2011. The $28.6 million increase
was due to an increase in prepaid expenses and other current assets attributable to a related party prepayment (see Note 6), as
well as an increase in the net loss from operations, caused by increased research and development activities, excluding non-cash
expenses of the change in fair value of warrants, stock-based compensation, and in process research and development.



Net cash used in investing activities was $1.1 million for the
six months ended June 30, 2012 compared to $0.4 million for the six months ended June 30, 2011. The increase was due to build out
of additional space in the Boston office including leasehold improvements and furniture and fixtures along with software additions.



Net cash provided by financing activities was $49.4 million
for the six months ended June 30, 2012 compared to $84.3 million for the six months ended June 30, 2011. The change is primarily
attributable to a $49.2 million financing that occurred during the first six months of 2012 versus a $71.2 million financing and
warrant exercises of $12.3 million that occurred during the first six months of 2011.



32







Operating capital and capital expenditure requirements



We anticipate that losses will continue for the foreseeable
future. At June 30, 2012, our accumulated deficit was approximately $235.7 million. Our actual cash requirements may vary materially
from those planned because of a number of factors including:



| | · | Changes in the focus, direction and pace of our development programs;
| | - | ---------------------------------------------------------------------



| | · | Competitive and technical advances;
| | - | -----------------------------------



| | · | Internal costs associated with the development of palifosfamide and indibulin and our ability to secure further financing for
darinaparsin development from a partner;
| | - | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------



| | · | Costs of filing, prosecuting, defending and enforcing any patent claims and any other intellectual property rights, or other
developments; and
| | - | ----------------------------------------------------------------------------------------------------------------------------------------------



| | · | Other matters identified under Part II – Item 1A. “Risk Factors” below.
| | - | -----------------------------------------------------------------------



Working capital as of June 30, 2012 was $101.6 million, consisting
of $119.4 million in current assets and $17.8 million in current liabilities. Working capital as of December 31, 2011 was $92.7
million, consisting of $106.1 million in current assets and $13.4 million in current liabilities.



Contractual obligations



The following table summarizes our outstanding obligations as
of June 30, 2012 and the effect those obligations are expected to have on our liquidity and cash flows in future periods:



|                            |  |       |        |  |           |   |        |             |  |   |             |  |  |           |      
|--------------------------- |  | ----- | ------ |  | --------- | - | ------ | ----------- |  | - | ----------- |  |  | --------- | -----
|                            |  |       |        |  | Less than |   |        |             |  |   |             |  |  | More than |      
|($ in thousands)            |  | Total |        |  | 1 year    |   |        | 2 - 3 years |  |   | 4 - 5 years |  |  | 5 years   |      
|Operating leases            |  | $     | 6,073  |  |           | $ | 1,096  |             |  | $ | 2,432       |  |  | $         | 1,866
|Royalty and license fees    |  |       | 1,650  |  |           |   | 275    |             |  |   | 550         |  |  |           | 550  
|Contract milestone payments |  |       | 25,579 |  |           |   | 15,454 |             |  |   | 10,125      |  |  |           | -    
|Total                       |  | $     | 33,302 |  |           | $ | 16,825 |             |  | $ | 13,107      |  |  | $         | 2,416



Our commitments for operating leases relate to the lease for
our corporate headquarters in New York, New York, our operations center in Boston, Massachusetts and office space in Germantown,
Maryland. Our commitments for royalty and license fees relate to our patent agreement with Baxter Healthcare Corporation and our
royalty agreements with Southern Research Institute and Baxter Healthcare Corporation requiring minimum royalty payments. The contract
milestone payments relate to our CRO agreements with PPD Development, L.P and Pharmaceutical Research Associates, Inc. The timing
of the remaining contract milestone payments are dependent upon factors that are beyond our control, including our ability to recruit
patients, the outcome of future clinical trials and any requirements imposed on our clinical trials by regulatory agencies. However,
for the purpose of the above table, we have assumed that the payment of the milestones will occur within five years of June 30,
2012. On July 16, 2012, we decided to close our Germanton, Maryland office (see Subsequent Events). Our operating lease commitment
for the Germantown, Maryland office included in the above table is $50 thousand – less than 1 year and $39 thousand –
2-3 years.



33







Off-balance sheet arrangements



During the three and six months ended June 30, 2012 and 2011,
we did not engage in any off-balance sheet arrangements.



Critical Accounting Policies and Estimates



In our Annual Report on Form 10-K for the fiscal year ended
December 31, 2011, our most critical accounting policies and estimates upon which our financial status depends were identified
as those relating to stock-based compensation; net operating losses and tax credit carryforwards; and impairment of long-lived
assets. We reviewed our policies and determined that those policies remain our most critical accounting policies for the six months
ended June 30, 2012.



Item 3. Quantitative and Qualitative Disclosures about
Market Risk



Our exposure to market risk is limited to our cash. The goals
of our investment policy are preservation of capital, fulfillment of liquidity needs and fiduciary control of cash. We also seek
to maximize income from our investments without assuming significant risk. To achieve our goals, we maintain our cash in interest-bearing
bank accounts in global banks, U.S. treasuries and other government-backed investments, which are subject to minimal interest rate
risk.



Item 4. Controls and Procedures



Our management, with the participation of our principal executive
officer and principal financial officer, has evaluated the effectiveness of our disclosure controls and procedures (as defined
in Rules 13a-15(e) or 15d-15(e) under the Securities Exchange Act of 1934, as amended, or the Exchange Act) as of
the end of the period covered by this report. Based on such evaluation, our principal executive officer and principal financial
officer have concluded that, as of the end of such period, our disclosure controls and procedures were effective in ensuring that
information required to be disclosed by us in the reports that we file or submit under the Exchange Act is recorded, processed,
summarized and reported, on a timely basis, and is accumulated and communicated to our management, including our principal executive
officer and principal financial officer, as appropriate, to allow timely decisions regarding required disclosure.



No change in our internal control over financial reporting (as
defined in Exchange Act Rules 13a-15(f) and 15d-15(f)) occurred during the period covered by this quarterly report that
has materially affected, or is reasonably likely to materially affect, our internal control over financial reporting.



34







Part II - Other Information



Item 1. Legal Proceedings



In the ordinary course of business, we may periodically become
subject to legal proceedings and claims arising in connection with ongoing business activities. The results of litigation and claims
cannot be predicted with certainty, and unfavorable resolutions are possible and could materially affect our results of operations,
cash flows or financial position. In addition, regardless of the outcome, litigation could have an adverse impact on us because
of defense costs, diversion of management resources and other factors.



While the outcome of these proceedings and claims cannot be
predicted with certainty, there are no matters, as of June 30, 2012, that, in the opinion of management, might have a material
adverse effect on our financial position, results of operations or cash flows.



Item 1A. Risk Factors



The following important factors could cause our actual business
and financial results to differ materially from those contained in forward-looking statements made in this Quarterly Report on
Form 10-Q or elsewhere by management from time to time. The risk factors in this report have been revised to incorporate changes
to our risk factors from those included in our Annual Report on Form 10-K for the fiscal year ended December 31, 2011. The risk
factors set forth below with an asterisk (*) next to the title are new risk factors or risk factors containing changes, which may
be material, from the risk factors previously disclosed in Item 1A of our Annual Report on Form 10-K for the fiscal year ended
December 31, 2011, as filed with the Securities and Exchange Commission.



RISKS RELATED TO OUR BUSINESS



*We will require additional financial resources in order
to continue ongoing development of our product candidates; if we are unable to obtain these additional resources, we may be forced
to delay or discontinue clinical testing of our product candidates.



We have not generated significant revenue and have incurred
significant net losses in each year since our inception. For the six months ended June 30, 2012, we had a net loss of $48.1 million,
and, as of June 30, 2012, we have incurred approximately $235.7 million of cumulative net losses since our inception in 2003. We
expect to continue to incur significant operating expenditures. Further development of our product candidates, including product
candidates that we may develop under our channel partnering arrangement with Intrexon, will likely require substantial increases
in our expenses as we:



| | • | Continue to undertake clinical trials for product candidates;
| | - | -------------------------------------------------------------



| | • | Scale-up the formulation and manufacturing of our product candidates;
| | - | ---------------------------------------------------------------------



| | • | Seek regulatory approvals for product candidates;
| | - | -------------------------------------------------



| | • | Implement additional internal systems and infrastructure; and
| | - | -------------------------------------------------------------



| | • | Hire additional personnel.
| | - | --------------------------



We continue to seek additional financial resources to fund the
further development of our product candidates. If we are unable to obtain sufficient additional capital, one or more of these programs
could be placed on hold. Because we are currently devoting a significant portion of our resources to the development of palifosfamide
and to synthetic biology, further progress with the development of our other candidates may be significantly delayed and may depend
on the success of our ongoing clinical trial involving palifosfamide.



We have no current committed sources of additional capital.
We do not know whether additional financing will be available on terms favorable or acceptable to us when needed, if at all. Our
business is highly cash-intensive and our ability to continue operations after our current cash resources are exhausted depends
on our ability to obtain additional financing and achieve profitable operations, as to which no assurances can be given. If adequate
additional funds are not available when required, or if we are unsuccessful in entering into partnership agreements for the further
development of our products, we will be required to delay, reduce or eliminate planned preclinical and clinical trials and may
be forced to terminate the approval process for our product candidates from the FDA or other regulatory authorities. In addition,
we could be forced to discontinue product development, forego attractive business opportunities or pursue merger or divestiture
strategies. In the event we are unable to obtain additional financing, we may be forced to cease operations altogether.



35







*We need to raise additional capital to fund our operations.  The
manner in which we raise any additional funds may affect the value of your investment in our common stock.



As of June 30, 2012, we had incurred approximately $235.7 million
of cumulative net losses and had approximately $110.4 million of cash and cash equivalents. We anticipate that our cash resources
will be sufficient to fund our operations into the second half of 2013. However, changes may occur that would consume our existing
capital prior to that time, including expansion of the scope, and/or slower than expected progress of, our research and development
efforts and changes in governmental regulation. Actual costs may ultimately vary from our current expectations, which could materially
impact our use of capital and our forecast of the period of time through which our financial resources will be adequate to support
our operations. We have estimated the sufficiency of our cash resources based in part on the trial design for our PICASSO 3 pivotal
trial and our adaptive Phase 3 trial in first-line SCLC for IV palifosfamide and our current timing expectations for enrollment
of the studies, which may change based on the progression of enrollment. We have also assumed responsibility for the advancement
of two product candidates in the clinic under our exclusive channel partnership with Intrexon and we expect that the costs associated
with these and additional product candidates will increase the level of our overall research and development expenses significantly
going forward. Although our forecasts for expenses and the sufficiency of our capital resources takes into account our plans to
develop the Intrexon products, we assumed development responsibility for these products on January 6, 2011 and the actual costs
associated therewith may be significantly in excess of forecasted amounts.



In addition to above factors, our actual cash requirements may
vary materially from our current expectations for a number of other factors that may include, but are not limited to, changes in
the focus and direction of our development programs, competitive and technical advances, costs associated with the development
of our product candidates, our ability to secure partnering arrangements, and costs of filing, prosecuting, defending and enforcing
our intellectual property rights. If we exhaust our capital reserves more quickly than anticipated, regardless of the reason, and
we are unable to obtain additional financing on terms acceptable to us or at all, we will be unable to proceed with development
of some or all of our product candidates on expected timelines and will be forced to prioritize among them.



Recently, capital markets have experienced a period of unprecedented
instability that may severely hinder our ability to raise capital within the time periods needed or on terms we consider acceptable,
if at all. Moreover, if we fail to advance one or more of our current product candidates to later-stage clinical trials, successfully
commercialize one or more of our product candidates, or acquire new product candidates for development, we may have difficulty
attracting investors that might otherwise be a source of additional financing.



In the current economic environment, our need for additional
capital and limited capital resources may force us to accept financing terms that could be significantly more dilutive to existing
stockholders than if we were raising capital when the capital markets were more stable. To the extent that we raise additional
capital by issuing equity securities, our stockholders may experience dilution. In addition, we may grant future investors rights
superior to those of our existing stockholders. If we raise additional funds through collaborations and licensing arrangements,
it may be necessary to relinquish some rights to our technologies, product candidates or products, or grant licenses on terms that
are not favorable to us. If we raise additional funds by incurring debt, we could incur significant interest expense and become
subject to covenants in the related transaction documentation that could affect the manner in which we conduct our business.



*Clinical trials are very expensive, time-consuming, and
difficult to design and implement.



Human clinical trials are very expensive and difficult to design
and implement, in part because they are subject to rigorous regulatory requirements. The clinical trial process itself is also
time-consuming. We estimate that clinical trials of our product candidates will take at least several years to complete. Furthermore,
failure can occur at any stage of the trials, and we could encounter problems that cause us to abandon or repeat clinical trials.
The commencement and completion of clinical trials may be delayed by several factors, including:



| | · | Unforeseen safety issues;
| | - | -------------------------

| | · | Determination of dosing issues;
| | - | -------------------------------

| | · | Lack of effectiveness during clinical trials;
| | - | ---------------------------------------------

| | · | Slower than expected rates of patient recruitment and enrollment;
| | - | -----------------------------------------------------------------

| | · | Inability to monitor patients adequately during or after treatment;
| | - | -------------------------------------------------------------------

| | · | Inability or unwillingness of medical investigators to follow our
clinical protocols; and
| | - | -----------------------------------------------------------------------------------------

| | · | Regulatory determinations to temporarily or permanently cease enrollment
for other reasons not related to patient safety.
| | - | -------------------------------------------------------------------------------------------------------------------------



36







We commenced the PICASSO 3 pivotal trial for IV
palifosfamide early in the third quarter of 2010 in a small number of sites in the United States as we pursued site review
board clearance for trial conduct in the anticipated 150 or more sites expected worldwide. Site opening is a complex and
time-consuming process, often requiring six months to complete outside of the United States. PICASSO 3 has a targeted
enrollment of 424 patients. We experienced slower than anticipated enrollment in the trial at start-up due in part to the
timing of site openings and regulatory approvals. While enrollment is complicated by a number of factors outside of our
control, we completed full enrollment in June 2012. The outcome in progression-free survival, the study’s primary
endpoint for accelerated approval, is anticipated in the fourth quarter of 2012. As an orphan designated indication,
the patient population available for participation in the PICASSO 3 trial is generally limited. If we cannot meet our
forecasted enrollment, or the trial is delayed for other reasons, the delay will postpone our receipt of results from the
trial and, consequently, our ability to submit a corresponding NDA with FDA for regulatory approval in accordance with our
plans. See also “Risk Factors—Our product candidates are in various stages of clinical trials, which are very
expensive and time-consuming. We cannot be certain when we will be able to file an NDA or BLA with the FDA and any failure or
delay in completing clinical trials for our product candidates could harm our business.”



We have received “Orphan Drug” status for palifosfamide
for treatment of soft tissue sarcomas and darinaparsin for treatment of peripheral T-cell lymphoma in both the United States and
Europe, and we may be able to receive additional Orphan Drug status from the FDA, Europe and certain other countries for other
product candidates. Orphan Drug status promotes the development of products that demonstrate the promise for the diagnosis and
treatment of one disease or condition affecting fewer than 200,000 patients in the United States and affords certain financial
and market protection benefits to successful applicants. There is no guarantee that any of our other product candidates will be
granted Orphan Drug status by the FDA or that, even if such product candidate is granted such status, the product candidate’s
clinical development and regulatory approval process will not be delayed or will be successful.



In addition, we or the FDA may suspend our clinical trials at
any time if it appears that we are exposing participants to unacceptable health risks or if the FDA finds deficiencies in our IND
submission or in the conduct of these trials.



We may not be able to commercialize any products, generate
significant revenues, or attain profitability.



To date, none of our product candidates have been approved for
commercial sale in any country. The process to develop, obtain regulatory approval for, and commercialize potential drug candidates
is long, complex, and costly. Unless and until we receive approval from the FDA and/or other regulatory authorities for our product
candidates, we cannot sell our drugs and will not have product revenues. Even if we obtain regulatory approval for one or more
of our product candidates, if we are unable to successfully commercialize our products, we may not be able to generate sufficient
revenues to achieve or maintain profitability, or to continue our business without raising significant additional capital, which
may not be available. Our failure to achieve or maintain profitability could negatively impact the trading price of our common
stock.



The technology on which our Channel Agreement with Intrexon
Corporation is based in part on early stage technology in the field of human oncologic therapeutics.



Our Channel Agreement with Intrexon contemplates our using Intrexon’s
advanced transgene engineering platform for the controlled and precise cellular production of anti-cancer effectors. Thein
vivo effector platform in which we have acquired rights represents early-stage technology in the field of human oncologic biotherapeutics,
with ZIN-CTI-001 which has completed a Phase 1b study and ZIN-ATI-001 currently in a Phase 1b study, both in melanoma. Although
we plan to leverage Intrexon’s synthetic biology platform for additional products targeting key pathways used by cancers
to grow and metastasize, we may not be successful in developing and commercializing these products for a variety of reasons. The
risk factors set forth herein that apply to our small molecule drug candidates, which are in various stages of development, also
apply to product candidates that we seek to develop under our Channel Agreement with Intrexon.



37







We will incur additional expenses in connection with our
Channel Agreement with Intrexon Corporation.



The in vivoeffector platform, in which we have acquired
rights for cancer from Intrexon, includes two existing product candidates, with DC-RTS-IL-12 and Ad-RTS-IL-12. Upon entry into
the Channel Agreement with Intrexon, we assumed responsibility for the clinical development of these product candidates, which
we expect will increase the level of our overall research and development expenses significantly going forward. Although all human
clinical trials are expensive and difficult to design and implement, we believe that due to complexity, costs associated with clinical
trials for synthetic biology products are greater than the corresponding costs associated with clinical trials for small molecule
candidates. In addition to increased research and development costs, we have added, and continue to add, headcount in part to support
our Channel Agreement endeavors, which will add to our general and administrative expenses going forward.



Although our forecasts for expenses and the sufficiency of our
capital resources takes into account our plans to develop the Intrexon products, we assumed development responsibility for these
products on January 6, 2011 and the actual costs associated therewith may be significantly in excess of forecasted amounts. In
addition to the amount and timing of expenses related to the clinical trials, our actual cash requirements may vary materially
from our current expectations for a number of other factors that may include, but are not limited to, changes in the focus and
direction of our development programs, competitive and technical advances, costs associated with the development of our product
candidates and costs of filing, prosecuting, defending and enforcing our intellectual property rights. If we exhaust our capital
reserves more quickly than anticipated, regardless of the reason, and we are unable to obtain additional financing on terms acceptable
to us or at all, we will be unable to proceed with development of some or all of our product candidates on expected timelines and
will be forced to prioritize among them.



We have a limited operating history upon which to base
an investment decision.



We are a development-stage company that was incorporated in
September 2003. To date, we have not demonstrated an ability to perform the functions necessary for the successful commercialization
of any product candidates. The successful commercialization of any product candidates will require us to perform a variety of functions,
including:



| | · | Continuing to undertake preclinical development and clinical trials;
| | - | --------------------------------------------------------------------

| | · | Participating in regulatory approval process;
| | - | ---------------------------------------------

| | · | Formulating and manufacturing products; and
| | - | -------------------------------------------

| | · | Conducting sales and marketing activities.
| | - | ------------------------------------------



Our operations have been limited to organizing and staffing
our company, acquiring, developing and securing our proprietary product candidates, and undertaking preclinical and clinical trials
of our product candidates. These operations provide a limited basis for you to assess our ability to commercialize our product
candidates and the advisability of investing in our securities.



Because we currently neither have nor intend to establish
internal research capabilities, we are dependent upon pharmaceutical and biotechnology companies and academic and other researchers
to sell or license us their product candidates and technology.



Proposing, negotiating, and implementing an economically viable
product acquisition or license is a lengthy and complex process. We compete for partnering arrangements and license agreements
with pharmaceutical, biopharmaceutical, and biotechnology companies, many of which have significantly more experience than we do,
and have significantly more financial resources. Our competitors may have stronger relationships with certain third parties including
academic research institutions, with whom we are interested in collaborating and may have, therefore, a competitive advantage in
entering into partnering arrangements with those third parties. We may not be able to acquire rights to additional product candidates
on terms that we find acceptable, or at all.



We expect that any product candidate to which we acquire rights
will require significant additional development and other efforts prior to commercial sale, including extensive clinical testing
and approval by the FDA and applicable foreign regulatory authorities. All drug product candidates are subject to the risks of
failure inherent in pharmaceutical product development, including the possibility that the product candidate will not be shown
to be sufficiently safe or effective for approval by regulatory authorities. Even if our product candidates are approved, they
may not be economically manufactured or produced, or be successfully commercialized.



38







We actively evaluate additional product candidates to acquire
for development. Such additional product candidates, if any, could significantly increase our capital requirements and place further
strain on the time of our existing personnel, which may delay or otherwise adversely affect the development of our existing product
candidates. We must manage our development efforts and clinical trials effectively, and hire, train and integrate additional management,
administrative, and sales and marketing personnel. We may not be able to accomplish these tasks, and our failure to accomplish
any of them could prevent us from successfully growing.



We may not be able to successfully manage our growth.



In the future, if we are able to advance our product candidates
to the point of, and thereafter through, clinical trials, we will need to expand our development, regulatory, manufacturing, marketing
and sales capabilities or contract with third parties to provide for these capabilities. Any future growth will place a significant
strain on our management and on our administrative, operational, and financial resources. Therefore, our future financial performance
and our ability to commercialize our product candidates and to compete effectively will depend, in part, on our ability to manage
any future growth effectively. To manage this growth, we must expand our facilities, augment our operational, financial and management
systems, and hire and train additional qualified personnel. If we are unable to manage our growth effectively, our business may
be harmed.



Our business will subject us to the risk of liability
claims associated with the use of hazardous materials and chemicals.



Our contract research and development activities may involve
the controlled use of hazardous materials and chemicals. Although we believe that our safety procedures for using, storing, handling
and disposing of these materials comply with federal, state and local laws and regulations, we cannot completely eliminate the
risk of accidental injury or contamination from these materials. In the event of such an accident, we could be held liable for
any resulting damages and any liability could have a materially adverse effect on our business, financial condition, and results
of operations. In addition, the federal, state and local laws and regulations governing the use, manufacture, storage, handling
and disposal of hazardous or radioactive materials and waste products may require our contractors to incur substantial compliance
costs that could materially adversely affect our business, financial condition, and results of operations.



*We rely on key executive officers and scientific and
medical advisors, and their knowledge of our business and technical expertise would be difficult to replace.



We are highly dependent on Dr. Jonathan Lewis, our Chief Executive
Officer, Dr. Hagop Youssoufian, our President of Research & Development and Chief Medical Officer, Caesar J. Belbel, our Executive
Vice President and Chief Legal Officer, Jason A. Amello, our Executive Vice President and Chief Financial Officer and our principal
scientific, regulatory, and medical advisors. Dr. Lewis’, Dr. Youssoufian’s, Mr. Belbel’s and Mr. Amello’s
employment are governed by written employment agreements. The employment agreement with Dr. Lewis provides for terms that expire
in January 2013. Drs. Lewis and Youssoufian, and Messrs. Belbel and Amello may terminate their employment with us at any time,
subject, however, to certain non-compete and non-solicitation covenants. The loss of the technical knowledge and management and
industry expertise of Drs. Lewis and Youssoufian and Messrs. Belbel and Amello, or any of our other key personnel, could result
in delays in product development, loss of customers and sales, and diversion of management resources, which could adversely affect
our operating results. We do not carry “key person” life insurance policies on any of our officers or key employees.



If we are unable to hire additional qualified personnel,
our ability to grow our business may be harmed.



We will need to hire additional qualified personnel with expertise
in preclinical and clinical research and testing, government regulation, formulation and manufacturing, and eventually, sales and
marketing. We compete for qualified individuals with numerous biopharmaceutical companies, universities, and other research institutions.
Competition for such individuals is intense and we cannot be certain that our search for such personnel will be successful. Attracting
and retaining qualified personnel will be critical to our success. If we are unable to hire additional qualified personnel, our
ability to grow our business may be harmed.



39







We may incur substantial liabilities and may be required
to limit commercialization of our products in response to product liability lawsuits.



The testing and marketing of medical products entail an inherent
risk of product liability. If we cannot successfully defend ourselves against product liability claims, we may incur substantial
liabilities or be required to limit commercialization of our products, if approved. Even a successful defense would require significant
financial and management resources. Regardless of the merit or eventual outcome, liability claims may result in:



| | • | Decreased demand for our product candidates;
| | - | --------------------------------------------



| | • | Injury to our reputation;
| | - | -------------------------



| | • | Withdrawal of clinical trial participants;
| | - | ------------------------------------------



| | • | Withdrawal of prior governmental approvals;
| | - | -------------------------------------------



| | • | Costs of related litigation;
| | - | ----------------------------



| | • | Substantial monetary awards to patients;
| | - | ----------------------------------------



| | • | Product recalls;
| | - | ----------------



| | • | Loss of revenue; and
| | - | --------------------



| | • | The inability to commercialize our product candidates.
| | - | ------------------------------------------------------



We currently carry clinical trial insurance and product liability
insurance. However, an inability to renew our policies or to obtain sufficient insurance at an acceptable cost could prevent or
inhibit the commercialization of pharmaceutical products that we develop, alone or with collaborators.



RISKS RELATED TO THE CLINICAL TESTING, REGULATORY APPROVAL
AND MANUFACTURING OF OUR PRODUCT CANDIDATES



If we are unable to obtain the necessary U.S. or worldwide
regulatory approvals to commercialize any product candidate, our business will suffer.



We may not be able to obtain the approvals necessary to commercialize
our product candidates, or any product candidate that we may acquire or develop in the future for commercial sale. We will need
FDA approval to commercialize our product candidates in the United States and approvals from regulatory authorities in foreign
jurisdictions equivalent to the FDA to commercialize our product candidates in those jurisdictions. In order to obtain FDA approval
of any product candidate, we must submit to the FDA an NDA or biologic license application, or BLA, demonstrating that the product
candidate is safe for humans and effective for its intended use. This demonstration requires significant research and animal tests,
which are referred to as preclinical studies, as well as human tests, which are referred to as clinical trials. Satisfaction of
the FDA’s regulatory requirements typically takes many years, depending upon the type, complexity, and novelty of the product
candidate, and will require substantial resources for research, development, and testing. We cannot predict whether our research,
development, and clinical approaches will result in drugs that the FDA will consider safe for humans and effective for their intended
uses. The FDA has substantial discretion in the drug approval process and may require us to conduct additional preclinical and
clinical testing or to perform post-marketing studies. The approval process may also be delayed by changes in government regulation,
future legislation, or administrative action or changes in FDA policy that occur prior to or during our regulatory review. Delays
in obtaining regulatory approvals may:



| | • | Delay commercialization of, and our ability to derive product revenues from, our product candidates;
| | - | ----------------------------------------------------------------------------------------------------



| | • | Impose costly procedures on us; and
| | - | -----------------------------------



| | • | Diminish any competitive advantages that we may otherwise enjoy.
| | - | ----------------------------------------------------------------



40







Even if we comply with all FDA requests, the FDA may ultimately
reject one or more of our NDAs or BLAs. We cannot be sure that we will ever obtain regulatory clearance for any of our product
candidates. Failure to obtain FDA approval for our product candidates will severely undermine our business by leaving us without
a saleable product, and therefore without any potential revenue source, until another product candidate can be developed. There
is no guarantee that we will ever be able to develop or acquire another product candidate or that we will obtain FDA approval if
we are able to do so.



In foreign jurisdictions, we similarly must receive approval
from applicable regulatory authorities before we can commercialize any drugs. Foreign regulatory approval processes generally include
all of the risks associated with the FDA approval procedures described above.



Our product candidates are in various stages of clinical
trials, which are very expensive and time-consuming. We cannot be certain when we will be able to file an NDA or BLA with the FDA
and any failure or delay in completing clinical trials for our product candidates could harm our business.



Our product candidates are in various stages of development
and require extensive clinical testing. Notwithstanding our current clinical trial plans for each of our existing product candidates,
we may not be able to commence additional trials or see results from these trials within our anticipated timelines. As such, we
cannot predict with any certainty if or when we might submit an NDA or BLA for regulatory approval of our product candidates or
whether such an NDA or BLA will be accepted. Because we do not anticipate generating revenues unless and until we submit one or
more NDAs or BLAs and thereafter obtain requisite FDA approvals, the timing of our NDA or BLA submissions and FDA determinations
regarding approval thereof, will directly affect if and when we are able to generate revenues.



The results of our clinical trials may not support our
product candidate claims.



Even if our clinical trials are completed as planned, we cannot
be certain that their results will support approval of our product candidates. The FDA normally expects two randomized, well-controlled
Phase 3 pivotal studies in support of approval of an NDA or BLA. Our PICASSO 3 trial, even if successful, may not be sufficient
to support approval and we may be required to conduct additional pivotal trials of palifosfamide in metastatic soft tissue sarcoma
in order to obtain NDA approval. Success in preclinical testing and early clinical trials does not ensure that later clinical trials
will be successful, and we cannot be certain that the results of later clinical trials will replicate the results of prior clinical
trials and preclinical testing. The clinical trial process may fail to demonstrate that our product candidates are safe for humans
and effective for the indicated uses. This failure would cause us to abandon a product candidate and may delay development of other
product candidates. Any delay in, or termination of, our clinical trials will delay the submission of our NDAs or BLAs with the
FDA and, ultimately, our ability to commercialize our product candidates and generate product revenues. In addition, our clinical
trials involve small patient populations. Because of the small sample size, the results of these clinical trials may not be indicative
of future results.



Because we are dependent upon clinical research institutions
and other contractors for clinical testing and for research and development activities, the results of our clinical trials and
such research activities are, to a certain extent, beyond our control.



We materially rely upon independent investigators and collaborators,
such as universities and medical institutions, to conduct our preclinical and clinical trials under agreements with us. These collaborators
are not our employees and we cannot control the amount or timing of resources that they devote to our programs. These investigators
may not assign as great a priority to our programs or pursue them as diligently as we would if we were undertaking such programs
ourselves. If outside collaborators fail to devote sufficient time and resources to our drug development programs, or if their
performance is substandard, the approval of our FDA applications, if any, and our introduction of new products, if any, will be
delayed. These collaborators may also have relationships with other commercial entities, some of whom may compete with us. If our
collaborators assist our competitors to our detriment, our competitive position would be harmed.



41







Our reliance on third parties to formulate and manufacture
our product candidates exposes us to a number of risks that may delay the development, regulatory approval and commercialization
of our products or result in higher product costs.



We do not have experience in drug formulation or manufacturing
of drugs or biologics and do not intend to establish our own manufacturing facilities. Although we will work closely with and rely
upon Intrexon on the manufacturing and scale-up of Intrexon product candidates, we lack the resources and expertise to formulate
or manufacture our own product candidates. We currently are contracting for the manufacture of our product candidates. We intend
to contract with one or more manufacturers to manufacture, supply, store, and distribute drug supplies for our clinical trials.
If a product candidate we develop or acquire in the future receives FDA approval, we will rely on one or more third-party contractors
or Intrexon to manufacture our products. Our anticipated future reliance on a limited number of third-party manufacturers exposes
us to the following risks:



| | • | We may be unable to identify manufacturers on acceptable terms or at all because the number of potential manufacturers is limited
and the FDA must approve any replacement contractor. This approval would require new testing and compliance inspections. In addition,
a new manufacturer would have to be educated in, or develop substantially equivalent processes for, production of our products
after receipt of FDA approval, if any.
| | - | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------



| | • | Our third-party manufacturers might be unable to formulate and manufacture our products in the volume and of the quality required
to meet our clinical needs and commercial needs, if any.
| | - | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------



| | • | Our future contract manufacturers may not perform as agreed or may not remain in the contract manufacturing business for the
time required to supply our clinical trials or to successfully produce, store, and distribute our products.
| | - | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------



| | • | Drug manufacturers are subject to ongoing periodic unannounced inspection by the FDA, the Drug Enforcement Administration and
corresponding state agencies to ensure strict compliance with good manufacturing practices and other government regulations and
corresponding foreign standards. We do not have control over third-party manufacturers’ compliance with these regulations
and standards.
| | - | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------



| | • | If any third-party manufacturer makes improvements in the manufacturing process for our products, we may not own, or may have
to share, the intellectual property rights to the innovation.
| | - | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------



Each of these risks could delay our clinical trials, the approval,
if any, of our product candidates by the FDA or the commercialization of our product candidates or result in higher costs or deprive
us of potential product revenues.



42







RISKS RELATED TO OUR ABILITY TO COMMERCIALIZE OUR PRODUCT
CANDIDATES



If we are unable either to create sales, marketing and
distribution capabilities or enter into agreements with third parties to perform these functions, we will be unable to commercialize
our product candidates successfully.



We currently have no marketing, sales, or distribution capabilities.
If and when we become reasonably certain that we will be able to commercialize our current or future products, we anticipate allocating
resources to the marketing, sales and distribution of our proposed products in North America and in certain other countries; however,
we cannot assure that we will be able to market, sell, and distribute our products successfully. Our future success also may depend,
in part, on our ability to enter into and maintain collaborative relationships for such capabilities and to encourage the collaborator’s
strategic interest in the products under development, and such collaborator’s ability to successfully market and sell any
such products. Although we intend to pursue certain collaborative arrangements regarding the sale and marketing of certain of our
products, there are no assurances that we will be able to establish or maintain collaborative arrangements or, if we are able to
do so, whether we would be able to conduct our own sales efforts. There can also be no assurance that we will be able to establish
or maintain relationships with third-party collaborators or develop in-house sales and distribution capabilities. To the extent
that we depend on third parties for marketing and distribution, any revenues we receive will depend upon the efforts of such third
parties, and there can be no assurance that such efforts will be successful. In addition, there can also be no assurance that we
will be able to market and sell our products in the United States or overseas.



If we are not able to partner with a third party and are not
successful in recruiting sales and marketing personnel or in building a sales and marketing infrastructure, we will have difficulty
commercializing our product candidates, which would harm our business. If we rely on pharmaceutical or biotechnology companies
with established distribution systems to market our products, we will need to establish and maintain partnership arrangements,
and we may not be able to enter into these arrangements on acceptable terms or at all. To the extent that we enter into co-promotion
or other arrangements, any revenues we receive will depend upon the efforts of third parties that may not be successful and that
will be only partially in our control.



If we cannot compete successfully for market share against
other drug companies, we may not achieve sufficient product revenues and our business will suffer.



The market for our product candidates is characterized by intense
competition and rapid technological advances. If a product candidate receives FDA approval, it will compete with a number of existing
and future drugs and therapies developed, manufactured and marketed by others. Existing or future competing products may provide
greater therapeutic convenience or clinical or other benefits for a specific indication than our products, or may offer comparable
performance at a lower cost. If our products fail to capture and maintain market share, we may not achieve sufficient product revenues
and our business will suffer.



We will compete against fully integrated pharmaceutical companies
and smaller companies that are collaborating with larger pharmaceutical companies, academic institutions, government agencies and
other public and private research organizations. Many of these competitors have products already approved or in development. In
addition, many of these competitors, either alone or together with their collaborative partners, operate larger research and development
programs or have substantially greater financial resources than we do, as well as significantly greater experience in:



| | • | Developing drugs and biopharmaceuticals;
| | - | ----------------------------------------



| | • | Undertaking preclinical testing and human clinical trials;
| | - | ----------------------------------------------------------



| | • | Obtaining FDA and other regulatory approvals of drugs and biopharmaceuticals;
| | - | -----------------------------------------------------------------------------



| | • | Formulating and manufacturing drugs and biopharmaceuticals; and
| | - | ---------------------------------------------------------------



| | • | Launching, marketing, and selling drugs and biopharmaceuticals.
| | - | ---------------------------------------------------------------



43







If physicians and patients do not accept and use our product
candidates, our ability to generate revenue from sales of our products will be materially impaired.



Even if the FDA approves our product candidates, physicians
and patients may not accept and use them. Acceptance and use of our products will depend upon a number of factors including:



| | • | Perceptions by members of the health care community, including physicians, about the safety and effectiveness of our drugs;
| | - | ---------------------------------------------------------------------------------------------------------------------------



| | • | Pharmacological benefit and cost-effectiveness of our products relative to competing products;
| | - | ----------------------------------------------------------------------------------------------



| | • | Availability of reimbursement for our products from government or other healthcare payors;
| | - | ------------------------------------------------------------------------------------------



| | • | Effectiveness of marketing and distribution efforts by us and our licensees and distributors, if any; and
| | - | ---------------------------------------------------------------------------------------------------------



| | • | The price at which we sell our products.
| | - | ----------------------------------------



Because we expect sales of our current product candidates, if
approved, to generate substantially all of our product revenues for the foreseeable future, the failure of a drug to find market
acceptance would harm our business and could require us to seek additional financing in order to fund the development of future
product candidates.



Our ability to generate product revenues will be diminished
if our drugs sell for inadequate prices or patients are unable to obtain adequate levels of reimbursement.



Our ability to commercialize our drugs, alone or with collaborators,
will depend in part on the extent to which reimbursement will be available from:



| | • | Government and health administration authorities;
| | - | -------------------------------------------------



| | • | Private health maintenance organizations and health insurers; and
| | - | -----------------------------------------------------------------



| | • | Other healthcare payers.
| | - | ------------------------



Government and other healthcare payers increasingly attempt
to contain healthcare costs by limiting both coverage and the level of reimbursement for drugs. As a result, we cannot provide
any assurances that third-party payors will provide adequate coverage of and reimbursement for any of our product candidates. If
we are unable to obtain adequate coverage of and payment levels for our product candidates from third-party payors, physicians
may limit how much or under what circumstances they will prescribe or administer them and patients may decline to purchase them.
This in turn could affect our ability to successfully commercialize our products and impact our profitability and future success.



In both the United States and certain foreign jurisdictions,
there have been a number of legislative and regulatory proposals in recent years to change the healthcare system in ways that could
impact our ability to sell our products profitably.



We cannot predict the impact on our business of any legislation
or regulations that may be adopted in the future. The implementation of cost containment measures or other healthcare reforms may
prevent us from being able to generate revenue, attain profitability, or commercialize our products.



In addition, in many foreign countries, particularly the countries
of the European Union, the pricing of prescription drugs is subject to government control. We may face competition for our product
candidates from lower-priced products in foreign countries that have placed price controls on pharmaceutical products. In addition,
there may be importation of foreign products that compete with our own products, which could negatively impact our profitability.



44







Our ability to use net operating loss carryforwards to
reduce future tax payments may be limited or restricted.



We have generated significant net operating loss carryforwards,
or NOLs, as a result of our incurrence of losses since inception. We generally are able to carry NOLs forward to reduce taxable
income in future years. However, our ability to utilize the NOLs is subject to the rules of Section 382 of the Internal Revenue
Code. Section 382 generally restricts the use of NOLs after an “ownership change.” An ownership change occurs if, among
other things, the stockholders (or specified groups of stockholders) who own or have owned, directly or indirectly, 5% or more
of a corporation's common stock or are otherwise treated as 5% stockholders under Section 382 and the U.S. Treasury Department
regulations promulgated thereunder increase their aggregate percentage ownership of that corporation's stock by more than 50 percentage
points over the lowest percentage of the stock owned by these stockholders over a three-year rolling period. In the event of an
ownership change, Section 382 imposes an annual limitation on the amount of taxable income a corporation may offset with NOL carry
forwards. This annual limitation is generally equal to the product of the value of the corporation's stock on the date of the ownership
change, multiplied by the long-term tax-exempt rate published monthly by the Internal Revenue Service. Any unused annual limitation
may be carried over to later years until the applicable expiration date for the respective NOL carry forwards. We may have experienced
an “ownership change” within the meaning of Section 382 in the past. As a result, our NOLs may be subject to limitations
and we may be required to pay taxes earlier and in larger amounts than would be the case if our NOLs were freely usable.



RISKS RELATED TO OUR INTELLECTUAL PROPERTY



If we fail to adequately protect or enforce our intellectual
property rights or secure rights to patents of others, the value of our intellectual property rights would diminish.



Our success, competitive position, and future revenues will
depend in part on our ability and the abilities of our licensors to obtain and maintain patent protection for our products, methods,
processes and other technologies, to preserve our trade secrets, to prevent third parties from infringing on our proprietary rights,
and to operate without infringing the proprietary rights of third parties.



To date, we have exclusive rights to certain U.S. and foreign
intellectual property with respect to our small molecule product candidates and with respect to the Intrexon technology, including
the existing Intrexon product candidates. Under our Channel Agreement with Intrexon, Intrexon has the sole right to conduct and
control the filings, prosecution and maintenance of the patents and patent applications licensed to us. Although under the agreement
Intrexon has agreed to consider in good faith and consult with us regarding any comments we may have regarding these patents and
patent applications, we cannot guarantee that our comments will be solicited or followed. Without direct control of the channel
program patents and patent applications, we are dependent on Intrexon to keep us advised of prosecution, particularly in foreign
jurisdictions where prosecution information may not be publicly available. We anticipate that we and Intrexon will file additional
patent applications both in the United States and in other countries. However, we cannot predict or guarantee:



| | • | The degree and range of protection any patents will afford us against competitors, including whether third parties will find
ways to invalidate or otherwise circumvent our patents;
| | - | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------



| | • | If and when patents will be issued;
| | - | -----------------------------------



| | · | Whether or not others will obtain patents claiming aspects similar to those covered by our patents and patent applications;
or
| | - | ------------------------------------------------------------------------------------------------------------------------------



| | • | Whether we will need to initiate litigation or administrative proceedings that may be costly whether we win or lose.
| | - | --------------------------------------------------------------------------------------------------------------------



45







Changes in patent laws or in interpretations of patent laws
in the United States and other countries may diminish the value of our intellectual property or narrow the scope of our patent
protection. In September 2011, the Leahy-Smith America Invents Act, or the Leahy-Smith Act, was signed into law, resulting in a
number of significant changes to U.S. patent law. These changes include provisions that affect the way patent applications will
be prosecuted and may also affect patent litigation. In addition, the U.S. Supreme Court has ruled on several patent cases in recent
years, either narrowing the scope of patent protection available in certain circumstances or weakening the rights of patent owners
in certain situations. This combination of events has created uncertainty with respect to the value of patents, once obtained,
and with regard to our ability to obtain patents in the future. Depending on decisions by the U.S. Patent and Trademark Office,
which is developing regulations and procedures to implement the Leahy-Smith Act, and federal courts, the laws and regulations governing
patents could change in unpredictable ways that would weaken our ability to obtain new patents or to enforce our existing patents
and patents that we might obtain in the future.



Certain technologies utilized in our research and development
programs are already in the public domain. Moreover, a number of our competitors have developed technologies, filed patent applications
or obtained patents on technologies, compositions and methods of use that are related to our business and may cover or conflict
with our owned or licensed patent applications, technologies or product candidates. Such conflicts could limit the scope of the
patents that we may be able to obtain or may result in the rejection of claims in our patent applications. Because patent applications
in the United States and many foreign jurisdictions are typically not published until eighteen months after filing, or in some
cases not at all, and because publications of discoveries in the scientific literature often lag behind actual discoveries, neither
we nor our licensors can be certain that others have not filed or maintained patent applications for technology used by us or covered
by our pending patent applications without our being aware of these applications. In addition, our own earlier filed patents and
applications or those of Intrexon may limit the scope of later patents we obtain or may result in the rejection of claims in our
later filed patent applications. If third parties filed patent applications or obtained patents on technologies, compositions and
methods of use that are related to our business and that cover or conflict with our owned or licensed patent applications, technologies
or product candidates, we may be required to challenge such protection, terminate or modify our programs impacted by such protection
or obtain licenses from such third parties, which might not be available on acceptable terms, or at all.



Our success also depends upon the skills, knowledge, and experience
of our scientific and technical personnel, our consultants and advisors, as well as our licensors and contractors. To help protect
our proprietary know-how and our inventions for which patents may be unobtainable or difficult to obtain, we rely on trade secret
protection and confidentiality agreements. To this end, it is our general policy to require our employees, consultants, advisors,
and contractors to enter into agreements that prohibit the disclosure of confidential information and, where applicable, require
disclosure and assignment to us of the ideas, developments, discoveries, and inventions important to our business. These agreements
may not provide adequate protection for our trade secrets, know-how or other proprietary information in the event of any unauthorized
use or disclosure or the lawful development by others of such information. If any of our trade secrets, know-how or other proprietary
information is disclosed, the value of our trade secrets, know-how and other proprietary rights would be significantly impaired
and our business and competitive position would suffer.



Third-party claims of intellectual property infringement
would require us to spend significant time and money and could prevent us from developing or commercializing our products.



In order to protect or enforce patent rights, we, or Intrexon,
may initiate patent infringement litigation against third parties. Similarly, we may be sued by others for patent infringement.
We also may become subject to proceedings conducted in the U.S. Patent and Trademark Office, including interference proceedings
to determine the priority of inventions, or reexamination proceedings. In addition, any foreign patents that are granted may become
subject to opposition, nullity, or revocation proceedings in foreign jurisdictions having such proceedings. The defense and prosecution,
if necessary, of intellectual property actions are costly and divert technical and management personnel away from their normal
responsibilities.



46







Our research, development and commercialization activities,
as well as any product candidates or products resulting from these activities, may infringe or be claimed to infringe patents or
patent applications under which we do not hold licenses or other rights. Patents do not protect its owner from a claim of infringement
of another owner’s patent. Therefore, our patent position cannot and does not provide any assurance that we are not infringing
the patent rights of another.



The patent landscape in the field of novel DNA biotherapeutics,
which we are pursuing under our exclusive channel partnership with Intrexon, is particularly complex. We are aware of numerous
U.S. and foreign patents and pending patent applications of third parties that cover compositions, methods of use and methods of
manufacture of novel DNA biotherapeutics, including biotherapeutics involving the in vivo expression of human IL-12. In
addition, there may be patents and patent applications in the field of which we are not aware. The technology we license from Intrexon
is early-stage technology and we are just beginning the process of designing and developing products using this technology. Although
we will seek to avoid pursuing the development of products that may infringe any patent claims that we believe to be valid and
enforceable, we may fail to do so. Moreover, given the breadth and number of claims in patents and pending patent applications
in the field of novel DNA biotherapeutics and the complexities and uncertainties associated with them, third parties may allege
that we are infringing upon patent claims even if we do not believe such claims to be valid and enforceable.



If a claim for patent infringement is asserted, there can be
no assurance that the resolution of the claim would permit us to continue marketing the relevant product on commercially reasonable
terms, if at all. We may not have sufficient resources to bring these actions to a successful conclusion. If we do not successfully
defend any infringement actions to which we become a party or are unable to have infringed patents declared invalid or unenforceable,
we may have to pay substantial monetary damages, which can be tripled if the infringement is deemed willful, or be required to
discontinue or significantly delay commercialization and development of the affected products.



Any legal action against us or our collaborators claiming damages
and seeking to enjoin developmental or marketing activities relating to affected products could, in addition to subjecting us to
potential liability for damages, require us or our collaborators to obtain licenses to continue to develop, manufacture, or market
the affected products. Such a license may not be available to us on commercially reasonable terms, if at all.



An adverse determination in a proceeding involving our owned
or licensed intellectual property may allow entry of generic substitutes for our products.



If we breach any of the agreements under which we license
rights to products or technology from others, we could lose license rights that are material to our business or be subject to claims
by our licensors.



We license rights to products and technology that are important
to our business, and we expect to enter into additional licenses in the future. For instance, we have exclusively licensed patents
and patent applications under our agreement with Intrexon. Under these agreements, we are subject to a range of commercialization
and development, sublicensing, royalty, patent prosecution and maintenance, insurance and other obligations.



Any failure by us to comply with any of these obligations or
any other breach by us of our license agreements could give the licensor the right to terminate the license in whole, terminate
the exclusive nature of the license or bring a claim against us for damages. Any such termination or claim could have a material
adverse effect on our financial condition, results of operations, liquidity or business. Even if we contest any such termination
or claim and are ultimately successful, such dispute could lead to delays in the development or commercialization of potential
products and result in time-consuming and expensive litigation or arbitration. On termination we may be required to license to
the licensor any related intellectual property that we developed.



In addition, in certain cases, the rights licensed to us are
rights of a third party licensed to our licensor. In such instances, if our licensors do not comply with their obligations under
such licenses, our rights under our license agreements with our licensor may be adversely affected.



47







OTHER RISKS RELATED TO OUR COMPANY



We are subject to Sarbanes-Oxley and the reporting requirements
of federal securities laws, which can be expensive.



As a public reporting company, we are subject to the Sarbanes-Oxley
Act of 2002, as well as to the information and reporting requirements of the Securities Exchange Act of 1934, as amended, or the
Exchange Act, and other federal securities laws. As a result, we incur significant legal, accounting, and other expenses that we
would not incur as a private company, including costs associated with our public company reporting requirements and corporate governance
requirements. As an example of public reporting company requirements, we evaluate the effectiveness of disclosure controls and
procedures and of our internal control over financing reporting in order to allow management to report on such controls. Sarbanes-Oxley
generally requires that a public reporting company’s independent registered public accounting firm attest to the effectiveness
of the company’s internal control over financial reporting as of the end of each fiscal year in the company’s annual
report on Form 10-K. In addition, any updates to our finance and accounting systems, procedures and controls, which may be required
as a result of our ongoing analysis of internal controls, or results of testing by our independent auditor, may require significant
time and expense. As a company with limited accounting resources, a significant amount of management’s time and attention
has been and will continue to be diverted from our business to ensure compliance with these regulatory requirements. This diversion
of management’s time and attention may have a material adverse effect on our business, financial condition and results of
operations.



Management is working to continuously monitor and improve internal
controls and has set in place controls to mitigate the potential segregation of duties risk. In the event significant deficiencies
or material weaknesses are indentified in our internal control over financial reporting that we cannot remediate in a timely manner,
or if we are unable to receive a positive attestation from our independent registered public accounting firm with respect to our
internal controls over financial reporting, investors and others may lose confidence in the reliability of our financial statements
and the trading price of our common stock and ability to obtain any necessary equity or debt financing could suffer. In addition,
in the event that our independent registered public accounting firm is unable to rely on our internal controls over financial reporting
in connection with its audit of our financial statements, and in the further event that it is unable to devise alternative procedures
in order to satisfy itself as to the material accuracy of our financial statements and related disclosures, we may be unable to
file our periodic reports with the SEC. This would likely have an adverse affect on the trading price of our common stock and our
ability to secure any necessary additional equity or debt financing, and could result in the delisting of our common stock from
the NASDAQ Capital Market, which would severely limit the liquidity of our common stock.



Anti-takeover provisions in our charter documents and
under Delaware law may make an acquisition of us, which may be beneficial to our stockholders, more difficult.



Provisions of our amended and restated certificate of incorporation
and bylaws, as well as provisions of Delaware law, could make it more difficult for a third party to acquire us, even if doing
so would benefit our stockholders. These provisions authorize the issuance of “blank check” preferred stock that could
be issued by our board of directors to increase the number of outstanding shares and hinder a takeover attempt, and limit who may
call a special meeting of stockholders. In addition, Section 203 of the Delaware General Corporation Law generally prohibits a
publicly-held Delaware corporation from engaging in a business combination with a party that owns at least 15% of its common stock
unless the business combination is approved by the company’s board of directors before the person acquires the 15% ownership
stake or later by its board of directors and two-thirds of its stockholders. In connection with our January 2011 issuance of shares
of common stock to Intrexon in a private placement transaction, our board of directors waived the Section 203 prohibition with
respect to a future business combination with Intrexon. However, the Stock Purchase Agreement governing such issuance contains
a standstill provision that generally prohibits Intrexon from seeking, initiating, offering or proposing to effect such a transaction
with our inviting them to do so. Section 203 and this standstill provision could have the effect of delaying, deferring or preventing
a change in control that our stockholders might consider to be in their best interests.



Because we do not expect to pay dividends, you will not
realize any income from an investment in our common stock unless and until you sell your shares at profit.



We have never paid dividends on our capital stock and we do
not anticipate that we will pay any dividends for the foreseeable future. Accordingly, any return on an investment in us will be
realized, if at all, only when you sell shares of our common stock.



48







Item 2. Unregistered Sale of Equity Securities and Use
of Proceeds



None.



Item 3. Defaults upon Senior Securities



Not applicable.



Item 4. Mine Safety Disclosures



Not applicable.



Item 5. Other Information



Not applicable.



Item 6. Exhibits



The exhibits listed in the Exhibit Index immediately preceding
such exhibits are filed as part of this report and such Exhibit Index is incorporated herein by reference.



49







SIGNATURES



Pursuant to the requirements of the Securities Exchange Act
of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned thereunto duly authorized.



|/s/ Jonathan Lewis                                         
|-----------------------------------------------------------
|Jonathan Lewis, M.D., Ph.D.
        Chief Executive Officer
|(Principal Executive Officer)                              

Dated: August 2, 2012



|/s/ Jason A. Amello                                                         
|----------------------------------------------------------------------------
|Jason A. Amello
        Executive Vice President and Chief Financial Officer
|(Principal Financial and Accounting Officer)                                

Dated: August 2, 2012



50







EXHIBIT INDEX



| | 10.1 | Employment Agreement, dated May 8, 2012 by and between the Company and Jason Amello (incorporated
by reference to Exhibit 10.1 to the Company’s Current Report on Form 8-K filed May 10, 2012)
| | ---- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

| | 10.2 | ZIOPHARM Oncology, Inc. 2012 Equity Incentive Plan (incorporated by reference to Exhibit 10.1 to
the Company’s Current Report on Form 8-K filed June 26, 2012)
| | ---- | --------------------------------------------------------------------------------------------------------------------------------------------------------------

| | 10.3 | Form of Restricted Stock Agreement granted under the ZIOPHARM Oncology, Inc. 2012 Equity Incentive
Plan (incorporated by reference to Exhibit 10.2 to the Company’s Current Report on Form 8-K filed June 26, 2012)
| | ---- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

| | 10.4 | Form of Option Agreement Granted under the ZIOPHARM Oncology, Inc. 2012 Equity Incentive Plan (incorporated
by reference to Exhibit 10.3 to the Company’s Current Report on Form 8-K filed June 26, 2012)
| | ---- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

| | 31.1* | Certification pursuant to Section 302 of the Sarbanes-Oxley Act of 2002
| | ----- | -----------------------------------------------------------------------

| | 31.2* | Certification pursuant to Section 302 of the Sarbanes-Oxley Act of 2002
| | ----- | -----------------------------------------------------------------------

| | 32.1* | Certifications pursuant to 18 U.S.C. Section 1350
| | ----- | -------------------------------------------------

| | 101.INS** | XBRL Instance Document
| | --------- | ----------------------

| | 101.SCH** | XBRL Taxonomy Extension Schema Document
| | --------- | ---------------------------------------

| | 101.CAL** | XBRL Taxonomy Extension Calculation Linkbase Document
| | --------- | -----------------------------------------------------

| | 101.DEF** | XBRL Taxonomy Definition Linkbase Document
| | --------- | ------------------------------------------

| | 101.LAB** | XBRL Taxonomy Extension Label Linkbase Document
| | --------- | -----------------------------------------------

| | 101.PRE** | XBRL Taxonomy Extension Presentation Linkbase Document
| | --------- | ------------------------------------------------------



| | * | Filed herewith.
| | - | ---------------

| | ** | To be furnished in an amendment to this Form 10-Q to be filed no later than 30 days after the filing date of this Form 10-Q, as permitted by Rule 405 of Regulation S-T.
| | -- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------



51