10-Q

UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

FORM 10-Q

(Mark One)

x 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

For the transition period from              to             

Commission file number: 000-51531

SUNESIS PHARMACEUTICALS, INC.

(Exact Name of Registrant as Specified in its Charter)

Delaware	94-3295878
(State or Other Jurisdiction of Incorporation or Organization)	(I.R.S. Employer Identification Number)

395 Oyster Point Boulevard, Suite 400

South San Francisco, California 94080

(Address of Principal Executive Offices including Zip Code)

(650) 266-3500

(Registrant’s Telephone Number, Including Area Code)

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 that the registrant was required to file reports), and (2) has been subject to such filing requirements for the past 90 days.     Yes  x    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  x    No  ¨

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer or a 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	¨
Non-accelerated filer	¨  (Do not check if a smaller reporting company)	Smaller reporting company	x

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

The registrant had 47,104,974 shares of common stock, $0.0001 par value per share, outstanding as of July 31, 2012.

SUNESIS PHARMACEUTICALS, INC.

TABLE OF CONTENTS

		Page No.
PART I. FINANCIAL INFORMATION			3
Item 1.	Financial Statements:		3
	Condensed Consolidated Balance Sheets as of June 30, 2012 and December 31, 2011		3
	Condensed Consolidated Statements of Operations and Comprehensive Income (Loss) for the Three and Six Months Ended June 30, 2012 and 2011		4
	Condensed Consolidated Statements of Cash Flows for the Six Months Ended June 30, 2012 and 2011		5
	Notes to Condensed Consolidated Financial Statements		6
Item 2.	Management’s Discussion and Analysis of Financial Condition and Results of Operations		11
Item 3.	Quantitative and Qualitative Disclosures About Market Risk		15
Item 4.	Controls and Procedures		15
PART II. OTHER INFORMATION			16
Item 1.	Legal Proceedings		16
Item 1A.	Risk Factors		16
Item 2.	Unregistered Sales of Equity Securities and Use of Proceeds		26
Item 3.	Defaults Upon Senior Securities		26
Item 4.	Mine Safety Disclosures		26
Item 5.	Other Information		26
Item 6.	Exhibits		26
	Signatures		27

PART I—FINANCIAL INFORMATION

Item 1. Financial Statements

SUNESIS PHARMACEUTICALS, INC.

CONDENSED CONSOLIDATED BALANCE SHEETS

(In thousands)

	June 30, 2012			December 31, 2011
	(Unaudited)			(1)
ASSETS
Current assets:
Cash and cash equivalents	$	11,743		$	9,311
Marketable securities		17,531			34,804
Prepaids and other current assets		1,602			1,550
Total current assets		30,876			45,665
Property and equipment, net		58			74
Deposits and other assets		108			130
Total assets	$	31,042		$	45,869
LIABILITIES AND STOCKHOLDERS’ EQUITY
Current liabilities:
Accounts payable	$	393		$	658
Accrued clinical expense		3,982			2,370
Accrued compensation		780			1,274
Other accrued liabilities		2,749			1,805
Current portion of notes payable		900			—
Warrant liability		6,402			2,276
Total current liabilities		15,206			8,383
Non-current portion of notes payable		8,737			9,453
Non-current portion of deferred rent		—			13
Commitments
Stockholders’ equity:
Common stock		5			5
Additional paid-in capital		430,748			429,142
Accumulated other comprehensive income (loss)		(5	)		19
Accumulated deficit		(423,649	)		(401,146	)
Total stockholders’ equity		7,099			28,020
Total liabilities and stockholders’ equity	$	31,042		$	45,869

(1) The condensed consolidated balance sheet as of December 31, 2011 has been derived from the audited financial statements as of that date included in the Company’s Annual Report on Form 10-K for the year ended December 31, 2011.

See accompanying notes to condensed consolidated financial statements.

3

SUNESIS PHARMACEUTICALS, INC.

CONDENSED CONSOLIDATED STATEMENTS OF OPERATIONS AND COMPREHENSIVE INCOME (LOSS)

(In thousands, except per share amounts)

	Three months ended June 30,						Six months ended June 30,
	2012			2011			2012			2011
	(Unaudited)						(Unaudited)
Revenue:
License and other revenue	$	1,500		$	—		$	1,500		$	4,000
Total revenues		1,500			—			1,500			4,000
Operating expenses:
Research and development		8,072			5,950			14,718			10,020
General and administrative		2,182			1,975			4,371			3,989
Total operating expenses		10,254			7,925			19,089			14,009
Loss from operations		(8,754	)		(7,925	)		(17,589	)		(10,009	)
Interest expense		(316	)		—			(631	)		—
Other income (expense), net		491			(302	)		(4,283	)		3,622
Net loss		(8,579	)		(8,227	)		(22,503	)		(6,387	)
Unrealized gain (loss) on available-for-sale securities		(13	)		21			(24	)		33
Comprehensive loss	$	(8,592	)	$	(8,206	)	$	(22,527	)	$	(6,354	)
Shares used in computing net loss per common share:
Basic		46,953			46,295			46,873			46,095
Diluted		47,286			46,295			46,873			46,095
Net loss per common share:
Basic	$	(0.18	)	$	(0.18	)	$	(0.48	)	$	(0.14	)
Diluted	$	(0.20	)	$	(0.18	)	$	(0.48	)	$	(0.14	)

See accompanying notes to condensed consolidated financial statements.

4

SUNESIS PHARMACEUTICALS, INC.

CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS

(In thousands)

	Six months ended June 30,
	2012			2011
	(Unaudited)
Cash flows from operating activities
Net loss	$	(22,503	)	$	(6,387	)
Adjustments to reconcile loss to net cash used in operating activities:
Stock-based compensation expense		1,145			344
Depreciation and amortization		16			38
Amortization of debt discount and debt issuance costs		138			—
Change in fair value of warrant liability		4,126			(3,241	)
Foreign exchange loss (gain) on marketable securities		151			(240	)
Changes in operating assets and liabilities:
Prepaids and other assets		(53	)		(154	)
Accounts payable		(265	)		(87	)
Accrued clinical expense		1,612			827
Accrued compensation		(494	)		(255	)
Other accrued liabilities		1,000			277
Net cash used in operating activities		(15,127	)		(8,878	)
Cash flows from investing activities
Purchases of property and equipment		—			(16	)
Purchases of marketable securities		(9,325	)		(28,168	)
Proceeds from maturities of marketable securities		26,423			26,356
Net cash provided by (used in) investing activities		17,098			(1,828	)
Cash flows from financing activities
Proceeds from issuance of common stock through controlled equity offering facilities, net		272			4,053
Proceeds from exercise of warrants, stock options and stock purchase rights		189			4
Net cash provided by financing activities		461			4,057
Net increase (decrease) in cash and cash equivalents		2,432			(6,649	)
Cash and cash equivalents at beginning of period		9,311			14,223
Cash and cash equivalents at end of period	$	11,743		$	7,574

See accompanying notes to condensed consolidated financial statements.

5

SUNESIS PHARMACEUTICALS, INC.

NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

JUNE 30, 2012

(Unaudited)

1. Company Overview

Description of Business

Sunesis Pharmaceuticals, Inc. (the “Company” or “Sunesis”) was incorporated in the state of Delaware on February 10, 1998, and its facilities are located in South San Francisco, California. Sunesis is a biopharmaceutical company focused on the development and commercialization of new oncology therapeutics for the treatment of solid and hematologic cancers. The Company’s primary activities since incorporation have been conducting research and development internally and through corporate collaborators, in-licensing and out-licensing pharmaceutical compounds and technology, conducting clinical trials and raising capital.

In December 2010, the Company commenced enrollment of a Phase 3, multi-national, randomized, double-blind, placebo-controlled, pivotal clinical trial of vosaroxin in combination with cytarabine in patients with relapsed or refractory acute myeloid leukemia (the “VALOR trial”).

Significant Risks and Uncertainties

The Company has incurred significant losses and negative cash flows from operations since its inception, and as of June 30, 2012, had cash, cash equivalents and marketable securities totaling $29.3 million and an accumulated deficit of $423.6 million.

While the Company believes that it currently has access to resources to fund its operations until the unblinding of the VALOR trial, including if a sample size adjustment occurs, the Company may need to raise additional capital if the costs of the trial exceed the Company’s current estimates or unblinding does not occur within the currently anticipated timeframe. The Company will need to raise substantial additional capital to complete development and the potential commercialization of vosaroxin.

The Company expects to finance its future cash needs primarily through equity issuances, the potential sale of revenue participation rights, debt arrangements, a possible license, collaboration or other similar arrangement with respect to development and/or commercialization rights to vosaroxin, or a combination of the above.

Concentrations of Credit Risk

In accordance with its investment policy, the Company invests cash that is not currently being used for operational purposes. The policy allows for the purchase of low risk debt securities issued by: (a) the United States and certain European governments and government agencies, and (b) highly rated banks and corporations, denominated in U.S. dollars, Euros or British pounds, subject to certain concentration limits. The policy limits maturities of securities purchased to no longer than 18 months and the weighted average maturity of the portfolio to nine months. Management believes these guidelines ensure both the safety and liquidity of any investment portfolio the Company may hold.

Financial instruments that potentially subject the Company to concentrations of credit risk generally consist of cash, cash equivalents and marketable securities. The Company is exposed to credit risk in the event of default by the institutions holding its cash, cash equivalents and any marketable securities to the extent of the amounts recorded in the balance sheets.

2. Summary of Significant Accounting Policies

Basis of Presentation

The accompanying unaudited condensed consolidated financial statements have been prepared in accordance with U.S. generally accepted accounting principles (“GAAP”) for interim financial information and with the instructions to Form 10-Q and Rule 10-01 of Regulation S-X. Accordingly, they do not include all of the information and notes required by GAAP for complete financial statements. The financial statements include a wholly owned subsidiary, Sunesis Europe Limited, a United Kingdom corporation. Management has determined that the Company operates as a single reportable segment. The financial statements include all adjustments (consisting only of normal recurring adjustments) that management believes are necessary for a fair presentation of the periods presented. The balance sheet as of December 31, 2011 was derived from the audited financial statements as of that date. These interim financial results are not necessarily indicative of results to be expected for the full year or any other period. These unaudited condensed consolidated financial statements and the notes accompanying them should be read in conjunction with the Company’s Annual Report on Form 10-K for the year ended December 31, 2011.

Reverse Stock Split

On February 14, 2011, the Company effected a one-for-six reverse split of its capital stock (the “Reverse Split”), as previously authorized and approved at the annual meeting of stockholders on June 2, 2010. As a result of the Reverse Split, every six shares of capital stock were combined into one share of capital stock. The Reverse Split affected the shares of Company’s common stock: (a) outstanding immediately prior to the effective time of the Reverse Split, (b) available for issuance under the Company’s equity incentive plans, and (c) issuable upon the exercise of outstanding stock options and warrants. The accompanying financial statements and notes thereto give retroactive effect to the Reverse Split for all periods presented.

Significant Estimates and Judgments

The preparation of financial statements in conformity with GAAP requires management to make estimates and assumptions that affect the amounts reported in the Company’s condensed consolidated financial statements and accompanying notes. Actual results could differ materially from these estimates. Significant estimates, assumptions and judgments made by management include those related to the valuation of equity and related instruments, revenue recognition, stock-based compensation and clinical trial accounting.

6

Cash Equivalents and Marketable Securities

Invoices for certain services provided to the Company are denominated in foreign currencies. To manage the risk of future movements in foreign exchange rates that would affect such amounts, the Company may purchase certain European currencies or highly-rated investments denominated in those currencies, subject to similar criteria as for other investments defined in the Company’s investment policy. There is no guarantee that the related gains and losses will substantially offset each other, and the Company may be subject to significant exchange gains or losses as currencies fluctuate from quarter to quarter. To date, the Company has purchased Euros and Euro-denominated obligations of foreign governments and corporate debt, and as of June 30, 2012, held investments denominated in Euros with an aggregate fair value of $3.9 million. These cash, cash equivalent and short-term investment balances are recorded at their fair value based on the current exchange rate as of each balance sheet date. The resulting exchange gains or losses and those from amounts payable for services originally denominated in foreign currencies are both recorded in other income (expense) in the statements of operations and comprehensive income (loss).

Fair Value Measurements

The Company measures cash equivalents, marketable securities and warrant liabilities at fair value on a recurring basis using the following hierarchy to prioritize valuation inputs, in accordance with applicable GAAP:

Level 1 — quoted prices (unadjusted) in active markets for identical assets and liabilities that can be accessed at the measurement date.

Level 2 — inputs other than quoted prices included within Level 1 that are observable, either directly or indirectly.

Level 3 — unobservable inputs.

The Company’s Level 2 valuations of marketable securities are generally based upon quoted prices in active markets for similar securities, with prices adjusted for yield and number of days to maturity.

The fair value of the Company’s liability for warrants issued in connection with an underwritten offering completed in October 2010 is determined using the Black-Scholes model, which requires inputs such as the expected term of the warrants, share price volatility, expected dividend yield and risk-free interest rate. As some of these inputs are unobservable, and require significant analysis and judgment to measure, these variables are classified as Level 3.

The Company does not measure cash, prepayments, accounts payable, accrued liabilities and notes payable at fair value, as their carrying amounts approximated their fair value as of June 30, 2012 and December 31, 2011.

3. Loss per Common Share

Basic loss per common share is calculated by dividing net loss by the weighted-average number of common shares outstanding for the period. Diluted net loss per common share is computed by dividing (a) net loss, less any anti-dilutive amounts recorded during the period for the change in the fair value of warrant liabilities, by (b) the weighted-average number of common shares outstanding for the period plus dilutive potential common shares as determined using the treasury stock method for options and warrants to purchase common stock.

The following table sets forth the computation of basic and diluted loss per common share for the periods presented (in thousands, except per share amounts):

	Three months ended June 30,						Six months ended June 30,
	2012			2011			2012			2011
Numerator:
Net loss—basic	$	(8,579	)	$	(8,227	)	$	(22,503	)	$	(6,387	)
Adjustment for change in fair value of warrant liability		(753	)		—			—			—
Net loss—diluted	$	(9,332	)	$	(8,227	)	$	(22,503	)	$	(6,387	)
Denominator:
Weighted-average common shares outstanding—basic		46,953			46,295			46,873			46,095
Dilutive effect of warrants		333			—			—			—
Weighted-average common shares outstanding—diluted		47,286			46,295			46,873			46,095
Net loss per common share:
Basic	$	(0.18	)	$	(0.18	)	$	(0.48	)	$	(0.14	)
Diluted	$	(0.20	)	$	(0.18	)	$	(0.48	)	$	(0.14	)

The following table represents the potential common shares issuable pursuant to outstanding securities as of the related period end dates that were excluded from the computation of diluted loss per common share because their inclusion would have had an anti-dilutive effect (in thousands):

	Three months ended June 30,				Six months ended June 30,
	2012		2011		2012		2011
Warrants to purchase shares of common stock		7,355		8,648		11,025		8,648
Options to purchase shares of common stock		6,303		4,897		6,303		4,897
Outstanding securities not included in calculations		13,658		13,545		17,328		13,545

7

4. Royalty Agreement

On March 29, 2012, the Company entered into a Revenue Participation Agreement (the “Royalty Agreement”), with RPI Finance Trust (“RPI”), an entity related to Royalty Pharma, under which RPI may acquire a revenue participation right (the “Revenue Participation Right”), for $25.0 million. RPI will be obligated to purchase the Revenue Participation Right if, following the interim efficacy analysis of data from the VALOR trial, the independent Data and Safety Monitoring Board (“DSMB”), recommends that the Company undertake a one-time 225 patient increase in sample size for the VALOR trial, or terminates the VALOR trial for efficacy, and the Company follows such recommendation. If the DSMB recommends that the Company continue the VALOR trial with the planned sample size of 450 patients, RPI will have the option to purchase the Revenue Participation Right following unblinding of the VALOR trial.

The applicable Revenue Participation Right payments are determined as follows: (a) if the DSMB recommends a stop for efficacy at the interim analysis, 3.6% of net sales; (b) if RPI exercises its option following continuation of the VALOR trial as planned, 3.6% of net sales; or (c) if the DSMB recommends a one-time increase in enrollment of the VALOR trial at the interim analysis, 6.75% of net sales. Revenue Participation Right payments will be made to RPI on a product-by-product and country-by-country basis world-wide through the later of: (i) the expiration of the last to expire of certain specifically identified patents, (ii) 10 years from the date of first commercial sale of such product in such country; or (iii) the expiration of all applicable periods of data, market or other regulatory exclusivity in such country with respect to such product.

In conjunction with entering into the Royalty Agreement, the Company issued two five-year warrants to RPI, each to purchase 1,000,000 shares of the Company’s common stock, at exercise prices of $3.48 and $4.64 per share, respectively. RPI has the right to exercise the warrants only if the DSMB recommends that the Company expand enrollment of the VALOR trial, and the Company follows such recommendation. If the DSMB issues any other recommendation, the warrants will terminate.

If, following the purchase of the Revenue Participation Right by RPI, the Company fails to make payments due to RPI under the Royalty Agreement in a timely manner, RPI may require the Company to repurchase the Revenue Participation Right. Additionally, as collateral for these payments, the Company agreed to grant RPI a security interest in certain of the Company’s assets, including the Company’s intellectual property related to vosaroxin. The security interest will be granted at the time of any purchase of the Revenue Participation Right but may only be perfected following first product approval in any country or territory. The security interest will be released upon the satisfaction of certain conditions specified in the Agreement. In connection with entering into the Royalty Agreement, the Company amended its Loan and Security Agreement, dated October 18, 2011 (the “Loan Agreement”), with Oxford Finance LLC, Silicon Valley Bank and Horizon Technology Finance Corporation (collectively, the “Lenders”) (see Note 5), to permit the grant of the security interest to RPI, and to concurrently grant to the Lenders a security interest in the same assets, which may also be perfected following the first product approval in any country or territory, to secure the Company’s obligations under the Loan Agreement. The Lenders will retain a senior position to the RPI security interest for so long as any indebtedness under the Loan Agreement remains outstanding.

RPI may terminate the Royalty Agreement without purchasing the Revenue Participation Right if the interim analysis of the VALOR trial is not completed by the end of 2012 or if the DSMB does not issue its recommendation by such date. In addition, the Royalty Agreement will terminate automatically if the DSMB recommends that the Company terminate the VALOR trial for futility. If RPI purchases the Revenue Participation Right, the Royalty Agreement will automatically terminate after all payment obligations to RPI have been satisfied.

5. Notes Payable

On October 18, 2011, the Company entered into the Loan Agreement with the Lenders, under which the Company may borrow up to $25.0 million in two tranches (the “Loan Facility”). The first tranche of $10.0 million was funded upon closing of the transaction on October 18, 2011. Subject to the Company’s continued compliance with the terms and conditions of the Loan Facility, the second tranche of $15.0 million may be drawn at the Company’s option between June 30, 2012 and September 30, 2012, contingent upon the recommendation by the DSMB following the interim analysis of the VALOR trial to either: (a) discontinue the trial due to positive efficacy, or (b) continue the trial.

The interest rate for the first tranche is 8.95% per annum, and the interest rate for the second tranche will be fixed upon drawdown at a per annum rate equal to the greater of: (a) 8.95%, or (b) 8.61% plus the then effective three-month U.S. LIBOR rate. Payments under the Loan Agreement are monthly in arrears and interest-only until February 1, 2013, followed by 32 equal monthly payments of principal and interest through the scheduled maturity date of October 1, 2015. In addition, a final payment equal to 3.75% of the aggregate amount drawn will be due on October 1, 2015, or such earlier date specified in the Loan Agreement. If the Company repays all or a portion of the loans prior to maturity, it will pay the Lenders a prepayment fee of between 1-3% of the principal amount prepaid.

In accordance with the terms of the Loan Agreement, the Company agreed to issue five-year warrants to the Lenders upon each drawdown to purchase shares of common stock in an amount equal to 5.0% of the amount drawn at such tranche, divided by the exercise price per share, which is determined in each case to be the lower of: (a) the 10-day average closing share price prior to the drawdown, or (b) the closing price per share the day prior to the drawdown. As a result of the drawdown of the first tranche of $10.0 million, the Company issued warrants to purchase 386,100 shares of its common stock at an exercise price of $1.30 per share. The warrants may be exercised on a cashless basis, and will expire on October 18, 2016. As of June 30, 2012, the warrants remained outstanding and exercisable.

Future minimum payments under the Loan agreement as of June 30, 2012 were as follows (in thousands):

Period ending December 31,
2012	$	447
2013		3,674
2014		4,229
2015		3,524
Total minimum payments		11,874
Less: amount representing interest		(1,874	)
Notes payable, gross		10,000
Unamortized discount on notes payable		(460	)
Accretion of the final payment		97
Notes payable, balance		9,637
Current portion of notes payable		(900	)
Non-current portion of notes payable	$	8,737

The Company recorded interest expense related to the loan of $0.3 million and $0.6 million for the three and six months ended June 30, 2012, respectively. The annual effective interest rate on the note payable, including the amortization of the debt discounts and accretion of the final payments, is 13.1%.

8

6. Financial Instruments

Financial Assets

The following tables summarize the estimated fair value of the Company’s financial assets measured on a recurring basis as of the dates indicated, which were comprised solely of available-for-sale securities with remaining contractual maturities of one year or less (in thousands):

June 30, 2012	Input Level		Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Estimated Fair Value
Money market funds		Level 1	$	8,848	$	—	$	—		$	8,848
U.S. corporate debt obligations		Level 2		7,587		—		—			7,587
U.S. commercial paper		Level 2		8,745		3		—			8,748
Foreign corporate debt obligations		Level 2		3,954		—		(8	)		3,946
Total available-for-sale securities				29,134		3		(8	)		29,129
Less: amounts classified as cash equivalents				11,597		1		—			11,598
Amounts classified as marketable securities			$	17,537	$	2	$	(8	)	$	17,531

December 31, 2011	Input Level		Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Estimated Fair Value
Money market funds		Level 1	$	7,156	$	—	$	—		$	7,156
U.S. corporate debt obligations		Level 2		16,619		5		(1	)		16,623
U.S. commercial paper		Level 2		14,556		18		—			14,574
Foreign government obligations		Level 2		3,607		1		—			3,608
Foreign corporate debt obligations		Level 2		1,476		—		(3	)		1,473
Total available-for-sale securities				43,414		24		(4	)		43,434
Less: amounts classified as cash equivalents				8,632		—		(2	)		8,630
Amounts classified as marketable securities			$	34,782	$	24	$	(2	)	$	34,804

The following table summarizes the available-for-sale securities that were in an unrealized loss position as of June 30, 2012, each having been in such a position for less than 12 months, and none deemed to be other-than-temporarily impaired (in thousands):

June 30, 2012	Gross Unrealized Losses		Estimated Fair Value
Corporate debt obligations	$	8	$	3,946

No significant facts or circumstances have arisen to indicate that there has been any deterioration in the creditworthiness of the issuers of these securities. The gross unrealized losses are not considered to be significant and have been for relatively short durations. The Company does not intend to sell these securities and it is not more likely than not that they will need to be sold prior to the recovery of their amortized cost basis. There were no sales of available-for-sale securities in the six months ended June 30, 2012 and 2011.

Financial Liabilities

The following table summarizes the inputs and assumptions and estimated fair value of the Company’s financial liabilities measured on a recurring basis as of the dates indicated, which were comprised solely of a liability for warrants issued in connection with an underwritten offering completed in October 2010:

	June 30, 2012			December 31, 2011
Inputs and assumptions:
Fair market value of Company’s common stock	$	2.87		$	1.17
Exercise price	$	2.52		$	2.52
Expected term (years)		3.3			3.8
Expected volatility		88.7	%		98.9	%
Risk-free interest rate		0.5	%		0.5	%
Expected dividend yield		0.0	%		0.0	%
Fair value:
Estimated fair value per warrant share	$	1.74		$	0.62
Shares underlying outstanding warrants classified as liabilities (in thousands)		3,671			3,679
Total estimated fair value of outstanding warrants (in thousands)	$	6,402		$	2,276

9

The warrants have been classified as a derivative liability on the Company’s balance sheet due to the potential for the warrants to be settled in cash upon the occurrence of certain transactions specified in the warrant agreements. The warrants were initially recorded at their fair value of $4.5 million, which was estimated using the Black-Scholes model. At each subsequent balance sheet date, the estimated fair value of the outstanding warrants is determined using the Black-Scholes model and recorded to the balance sheet, with the change in fair value recorded to other income (expense) in the statements operations and of comprehensive income (loss).

The Black-Scholes model requires Level 3 inputs such as the expected term of the warrants and share price volatility. These inputs are subjective and generally require significant analysis and judgment to develop. Any changes in these inputs could result in a significantly higher or lower fair value measurement. The following table summarizes the changes in the fair value of the Company’s Level 3 financial liabilities for the periods indicated (in thousands):

	Warrant Liability
Balance as of December 31, 2010	$	8,154
Change in fair value of warrant liability		(5,878	)
Balance as of December 31, 2011		2,276
Change in fair value of warrant liability		4,126
Balance as of June 30, 2012	$	6,402

7. Stockholders’ Equity

Controlled Equity Offerings

In April 2010, the Company entered into a controlled equity offering sales agreement with Cantor Fitzgerald & Co. (“Cantor”), pursuant to which the Company could issue and sell shares of its common stock having an aggregate offering price of up to $20.0 million from time to time through Cantor acting as agent and/or principal. The Company agreed to pay Cantor a commission of 3.0% of the gross proceeds from each sale. In the six months ended June 30, 2012, the Company sold an aggregate of 88,500 shares of common stock at an average price of approximately $3.08 per share for gross and net proceeds of $0.3 million, after deducting Cantor’s commission. Through June 30, 2012, the Company had sold an aggregate of 4,471,783 shares of common stock under this facility at an average price of approximately $4.08 per share for gross proceeds of $18.3 million and net proceeds of $17.7 million, after deducting Cantor’s commission. As of June 30, 2012, $1.7 million of common stock remained available to be sold under this facility, subject to certain conditions as specified in the agreement.

In August 2011, the Company entered into an additional controlled equity offering sales agreement with Cantor, pursuant to which the Company may issue and sell shares of its common stock having an aggregate offering price of up to $20.0 million from time to time through Cantor acting as agent and/or principal. The Company agreed to pay Cantor a commission of 3.0% of the gross proceeds from each sale. As of June 30, 2012, no sales had been made under this facility, and $20.0 million of common stock remained available to be sold under this facility, subject to certain conditions as specified in the agreement.

8. Stock-Based Compensation

Employee stock-based compensation expense is calculated based on the grant-date fair value of awards ultimately expected to vest, reduced for estimated forfeitures, and is recorded on a straight-line basis over the vesting period of the awards. Forfeitures are estimated at the time of grant, based on historical option cancellation information, and revised in subsequent periods if actual forfeitures differ from those estimates.

The following table summarizes stock-based compensation expense related to the Company’s stock-based awards for the periods indicated (in thousands):

	Three months ended June 30,				Six months ended June 30,
	2012		2011		2012		2011
Research and development	$	207	$	65	$	433	$	139
General and administrative		353		67		670		198
Employee stock-based compensation expense		560		132		1,103		337
Non-employee stock-based compensation expense		17		3		42		7
Total stock-based compensation expense	$	577	$	135	$	1,145	$	344

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

The following discussion and analysis of our financial condition as of June 30, 2012 and results of operations for the three and six months ended June 30, 2012 and 2011 should be read together with our condensed consolidated financial statements and related notes included elsewhere in this Quarterly Report on Form 10-Q and in our other Securities and Exchange Commission, or SEC, filings, including our Annual Report on Form 10-K for the year ended December 31, 2011, filed with the SEC on March 14, 2012.

This discussion and analysis 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, or the Exchange Act, which involve risks, uncertainties and assumptions. All statements, other than statements of historical facts, are “forward-looking statements” for purposes of these provisions, including without limitation any statements relating to our strategy, including our plans with respect to unblinding the VALOR trial, the planned interim analysis of the VALOR trial, presenting clinical data and initiating clinical trials, our future research and development activities, including clinical testing and the costs and timing thereof, sufficiency of our cash resources, our ability to raise additional funding when needed, any statements concerning anticipated regulatory activities or licensing or collaborative arrangements, our research and development and other expenses, our operations and legal risks, and any statement of assumptions underlying any of the foregoing. In some cases, forward-looking statements can be identified by the use of terminology such as “anticipates,” “believe,” “continue,” “estimates,” “expects,” “intend,” “look forward,” “may,” “could,” “seeks,” “plans,” “potential,” or “will” or the negative thereof or other comparable terminology. Although we believe that the expectations reflected in the forward-looking statements contained herein are reasonable, there can be no assurance that such expectations or any of the forward-looking statements will prove to be correct, and actual results could differ materially from those projected or assumed in the forward-looking statements. Our actual results may differ materially from those anticipated in these forward-looking statements as a result of many factors, including but not limited to those set forth under “Risk Factors,” and elsewhere in this report. We urge you not to place undue reliance on these forward-looking statements, which speak only as of the date of this report. All forward-looking statements included in this report are based on information available to us on the date of this report, and we assume no obligation to update any forward-looking statements contained in this report.

In this report, “Sunesis,” the “Company,” “we,” “us,” and “our” refer to Sunesis Pharmaceuticals, Inc. and its wholly-owned subsidiary, except where it is made clear that the term means only the parent company.

Overview

We are a biopharmaceutical company focused on the development and commercialization of new oncology therapeutics for the treatment of solid and hematologic cancers. Our efforts are currently focused primarily on the development of vosaroxin for the treatment of acute myeloid leukemia, or AML. In December 2010, we commenced enrollment of a Phase 3, multi-national, randomized, double-blind, placebo-controlled, pivotal trial of vosaroxin in combination with cytarabine in patients with relapsed or refractory AML, or the VALOR trial.

The VALOR trial is designed to evaluate the effect of vosaroxin in combination with cytarabine, a widely used chemotherapy in AML, on overall survival as compared to placebo in combination with cytarabine. We expect to enroll 450 evaluable patients in the VALOR trial at more than 110 study sites in the U.S., Canada, Europe, Australia and New Zealand. The trial is designed to have a 90% probability of detecting a 40% difference in overall survival, and includes a single pre-specified interim analysis by the independent Data and Safety Monitoring Board, or DSMB, which is expected to occur in September 2012. The DSMB will examine pre-specified efficacy and safety data sets and decide whether to: (i) stop the trial early for efficacy or for futility; (ii) continue the study to its planned unblinding, which is expected in mid-2013; or (iii) recommend a one-time sample size adjustment of 225 additional evaluable patients if deemed beneficial by the DSMB to maintain adequate statistical power across a range of clinically meaningful and statistically significant outcomes. In this event, trial unblinding would be expected in early 2014. In June 2012, we announced that the DSMB had completed a planned periodic safety review and recommended that the trial continue as planned without changes to study conduct.

We are also completing data analysis in preparation for database lock for two fully-enrolled clinical trials of vosaroxin: (a) the Phase 2 portion of a Phase 1b/2 trial of vosaroxin in combination with cytarabine for the treatment of patients with relapsed or refractory AML, and (b) a Phase 2 trial in previously untreated patients age 60 years or older with AML, or REVEAL-1, which explored three dose schedules of vosaroxin.

In March 2012, patient dosing commenced in the LI-1 Trial, a Phase 2/3 randomized, controlled, multi-center trial evaluating novel treatment regimens against low-dose cytarabine, or LD Ara-C, in patients older than 60 years with AML or high-risk myelodysplastic syndrome, or MDS. In this Cardiff University sponsored trial, several treatments, including two regimens containing vosaroxin, will be evaluated in a randomized Phase 2 design with key endpoints including complete remission, 12-month survival, and overall survival. Treatment arms exhibiting promising results on the basis of these endpoints may continue to enroll in a Phase 3 portion of the trial with a primary endpoint of overall survival.

In June 2012, we received a pre-commercialization event-based payment of $1.5 million from Biogen Idec for the advancement of pre-clinical work under the Restated Biogen Idec Agreement.

We own worldwide development and commercialization rights to vosaroxin. In April 2012, the European Commission granted orphan drug designation to vosaroxin for the treatment of AML, which provides for 10 years of marketing exclusivity in all member countries of the European Union following product approval in Europe. In 2009, vosaroxin received orphan drug designation for the treatment of AML from the U.S. Food and Drug Administration, or FDA. In February 2011, the FDA granted fast track designation to vosaroxin for the potential treatment of relapsed or refractory AML in combination with cytarabine. During the first half of 2012, we were granted the following key patents for vosaroxin:

• In February 2012, the U.S. Patent and Trademark Office, or USPTO, granted us a patent covering certain vosaroxin hydrate forms, which is due to expire in 2028. Corresponding applications are pending in other major markets, including Europe, Japan, Australia and Canada.

• In March 2012, the USPTO granted us a patent covering certain compositions related to vosaroxin, which is due to expire in 2030. Corresponding patent applications are pending internationally.

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Recent Financial History

Royalty Agreement

On March 29, 2012, we entered into a Revenue Participation Agreement, or the Royalty Agreement, with RPI Finance Trust, or RPI, an entity related to Royalty Pharma, under which RPI may acquire a revenue participation right, or the Revenue Participation Right, for $25.0 million. RPI will be obligated to purchase the Revenue Participation Right if, following the interim efficacy analysis of data from the VALOR trial, the DSMB recommends that we undertake a one-time 225 patient increase in sample size for the VALOR trial or terminate the VALOR trial for efficacy, and we follow such recommendation. If the DSMB recommends that we continue the VALOR trial with the planned sample size of 450 patients, RPI will have the option to purchase the Revenue Participation Right following unblinding of the VALOR trial. The applicable Revenue Participation Right payments are determined as follows: (a) if the DSMB recommends a stop for efficacy at the interim analysis, 3.6% of net sales; (b) if RPI exercises its option following continuation of the VALOR trial as planned, 3.6% of net sales; or (c) if the DSMB recommends a one-time increase in enrollment of the VALOR trial at the interim analysis, 6.75% of net sales. Revenue Participation Right payments will be made to RPI on a product-by-product and country-by-country basis world-wide through the later of: (i) the expiration of the last to expire of certain specifically identified patents, (ii) 10 years from the date of first commercial sale of such product in such country; or (iii) the expiration of all applicable periods of data, market or other regulatory exclusivity in such country with respect to such product.

In conjunction with the Royalty Agreement, we issued two five-year warrants to RPI, each to purchase 1,000,000 shares of our common stock, at exercise prices of $3.48 and $4.64 per share, respectively. RPI has the right to exercise the warrants only if the DSMB recommends that we expand enrollment of the VALOR trial, and we follow such recommendation. If the DSMB issues any other recommendation, the warrants will terminate.

If, following the purchase of the Revenue Participation Right by RPI, we fail to make payments due to RPI under the Royalty Agreement in a timely manner, RPI may require us to repurchase the Revenue Participation Right. Additionally, as collateral for these payments, we agreed to grant RPI a security interest in certain of our assets, including our intellectual property related to vosaroxin. The security interest will be granted at the time of any purchase of the Revenue Participation Right but may only be perfected following first product approval in any country or territory. The security interest will be released upon the satisfaction of certain conditions specified in the Agreement. In connection with entering into the Royalty Agreement, we amended our Loan and Security Agreement, dated October 18, 2011, or the Loan Agreement, with Oxford Finance LLC, Silicon Valley Bank and Horizon Technology Finance Corporation, or, collectively, the Lenders, to permit the grant of the security interest to RPI, and to concurrently grant to the Lenders a security interest in the same assets, which may also be perfected following the first product approval in any country or territory, to secure our obligations under the Loan Agreement. The Lenders will retain a senior position to the RPI security interest for so long as any indebtedness under the Loan Agreement remains outstanding.

RPI may terminate the Royalty Agreement without purchasing the Revenue Participation Right if the interim analysis of the VALOR trial is not completed by the end of 2012 or if the DSMB does not issue its recommendation by such date. In addition, the Royalty Agreement will terminate automatically if the DSMB recommends that we terminate the VALOR trial for futility. If RPI purchases the Revenue Participation Right, the Royalty Agreement will automatically terminate after all payment obligations to RPI have been satisfied.

Capital Requirements

We have incurred significant losses in each year since our inception. As of June 30, 2012, we had cash, cash equivalents and marketable securities of $29.3 million and an accumulated deficit of $423.6 million. We expect to continue to incur significant losses for the foreseeable future as we continue the development process and seek regulatory approvals for vosaroxin.

While we believe that we currently have access to resources to fund our operations until the unblinding of the VALOR trial, including if a sample size adjustment occurs, we may need to raise additional capital if the costs of the trial exceed our current estimates or unblinding does not occur within the currently anticipated timeframe. We will need to raise substantial additional capital to complete development and the potential commercialization of vosaroxin.

We expect to finance our future cash needs primarily through equity issuances, the potential sale of revenue participation rights, debt arrangements, a possible license, collaboration or other similar arrangement with respect to development and/or commercialization rights to vosaroxin, or a combination of the above. However, we do not know whether additional funding will be available on acceptable terms, or at all. If we are unable to raise required funding on acceptable terms or at all, we will need to reduce operating expenses, enter into a collaboration or other similar arrangement with respect to development and/or commercialization rights to vosaroxin, outlicense intellectual property rights to vosaroxin, sell unsecured assets, or a combination of the above, or be forced to delay or reduce the scope of our vosaroxin development program, potentially including the VALOR trial, and/or limit or cease our operations.

Critical Accounting Policies and Significant Judgments and Estimates

There have been no significant changes during the six months ended June 30, 2012 to our critical accounting policies and significant judgments and estimates as disclosed in our management’s discussion and analysis of financial condition and results of operations included in our Annual Report on Form 10-K for the year ended December 31, 2011.

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Overview of Revenues

We have not generated, and do not expect to generate in the foreseeable future, any revenue from sales of commercial products.

License and other revenue

In March 2011, we entered into three agreements as part of a series of agreements among Biogen Idec MA Inc., or Biogen Idec, Millennium Pharmaceuticals, Inc., a wholly-owned subsidiary of Takeda Pharmaceutical Company Limited, or Millennium, and ourselves:

• A license agreement with Millennium, or the Millennium Agreement, pursuant to which we granted Millennium exclusive licenses for the development of our oral, selective pan-Raf kinase inhibitor and one additional undisclosed kinase inhibitor program in oncology that were previously a part of our August 2004 collaboration agreement with Biogen Idec, or the Original Biogen Idec Agreement. Under this agreement, we may in the future receive up to $59.3 million in pre-commercialization event-based payments related to the development of the first two indications for each of the licensed products directed against the two exclusively licensed targets, and royalty payments depending on future product sales. The Millennium Agreement also provides us with future co-development and co-promotion rights. In September 2011, we announced that Millennium had initiated a Phase 1 clinical study of an oral investigative drug selective for pan-Raf kinase inhibition, MLN2480, which was licensed to them under the Millennium Agreement.

• An amendment and restatement of the Original Biogen Idec Agreement, or the Restated Biogen Idec Agreement, to provide for the discovery, development and commercialization of small molecule inhibitors of a unique preclinical kinase inhibitor program involved in immunology. In June 2012, we announced that we had received a pre-commercialization event-based payment of $1.5 million from Biogen Idec for the advancement of pre-clinical work under this agreement. We are eligible to receive up to an additional $58.5 million in pre-commercialization event-based payments related to the development of the first two indications for licensed products against the specified immunology target under the Restated Biogen Idec Agreement, and royalty payments depending on future product sales. We also retain future co-development and co-promotion rights.

• A termination and transition agreement with Biogen Idec and Millennium, which included a provision for an upfront, non-refundable payment of $4.0 million to us, which we received in April 2011.

We cannot predict whether we will receive any additional pre-commercialization event-based or royalty payments from these agreements in the foreseeable future, or at all.

Overview of Operating Expenses

Research and Development expense. Research and development expense consists primarily of clinical trial costs, which include payments for work performed by our contract research organizations, clinical trial sites, labs and other clinical service providers and for drug packaging, storage and distribution; drug manufacturing costs, which include costs for producing drug substance and drug product, and for stability and other testing; personnel costs for related permanent and temporary employees; other outside services and consulting costs; and payments under license agreements. We expense all research and development costs as they are incurred.

We are currently focused on the development of vosaroxin for the treatment of AML. Based on results of translational research, our own and investigator-sponsored trials, regulatory and competitive concerns and our overall financial resources, we anticipate that we will make determinations as to which indications to pursue and patient populations to treat in the future, and how much funding to direct to each indication, which will affect our research and development expense.

If we engage a development or commercialization partner for our vosaroxin program, or if, in the future, we acquire additional product candidates, our research and development expenses could be significantly affected. We cannot predict whether future licensing or collaborative arrangements will be secured, if at all, and to what degree such arrangements would affect our development plans and capital requirements.

Under the Restated Biogen Idec Agreement and the Millennium Agreement, we have the right to participate in co-development and co-promotion activities for the related product candidates. If we were to exercise our option on one or more product candidates, our research and development expense would increase significantly.

General and Administrative expense. General and administrative expense consists primarily of personnel costs for the related employees, including non-cash stock-based compensation; professional service costs, including fees paid to outside legal advisors, marketing consultants and our independent registered public accounting firm; facilities expenses; and other administrative costs.

Results of Operations

Revenue

Total revenue was $1.5 million for the three and six months ended June 30, 2012, as compared to nil and $4.0 million for the same periods in 2011. Revenue in the six months ended June 30, 2012 was due the receipt of a payment of $1.5 million from Biogen Idec in June 2012 for the advancement of pre-clinical work under the Restated Biogen Idec Agreement. Revenue in the six months ended June 30, 2011 was due to the upfront payment of $4.0 million to us for the termination of the Original Biogen Idec Agreement and the permitted assignment of assets and rights to Millennium as provided in the Millennium Agreement, which occurred in March 2011. We expect revenue to be lower in 2012 than in 2011.

Research and Development Expense

Research and development expense was $8.1 million and $14.7 million for the three and six months ended June 30, 2012, as compared to $6.0 million and $10.0 million for the same periods in 2011, substantially all relating to the vosaroxin development program. The increase of $2.1 million between the comparable three month periods was primarily due to increases of $1.0 million in clinical trial expenses, $0.8 million in outside services and consulting costs, and $0.3 million in personnel costs, as a result of the ramp-up of the VALOR trial. The increase of $4.7 million between the comparable six month periods was primarily due to increases of $2.2 million in clinical trial expenses, $1.6 million in outside services and consulting costs, and $0.9 million in personnel costs. We expect research and development expense to be higher in 2012 than in 2011 as we continue the development of vosaroxin.

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General and Administrative Expense

General and administrative expense was $2.2 million and $4.4 million for the three and six months ended June 30, 2012, as compared to $2.0 million and $4.0 million for the same periods in 2011. The increases of $0.2 million and $0.4 million between the comparable three and six month periods were primarily due to higher non-cash stock-based compensation expenses.

Interest Expense

Interest expense was $0.3 million and $0.6 million for the three and six months ended June 30, 2012, as compared to nil for the same periods in 2011. The interest expense in the 2012 periods was due to our entering into the Loan Agreement with the Lenders in October 2011.

Other Income (Expense), Net

Net other income was $0.5 million for the three months ended June 30, 2012, as compared to net other expense of $0.3 million for the same period in 2011. Net other income for the 2012 period was primarily comprised of a non-cash credit of $0.7 million for the revaluation of warrants issued in the October 2010 underwritten offering, or the 2010 Offering, to their fair value as of June 30, 2012, partially offset by foreign exchange losses of $0.3 million. Net other expense for the comparable period in 2011 was primarily comprised of a non-cash expense of $0.4 million for the revaluation of these warrants.

Net other expense was $4.3 million for the six months ended June 30, 2012, as compared to net other income of $3.6 million for the same period in 2011. Net other expense for the six months ended June 30, 2012 was primarily comprised of non-cash expenses of $4.1 million for the revaluation of the warrants issued in the 2010 Offering to their fair value as of June 30, 2012 and foreign exchange losses of $0.2 million. Net other income for the comparable period in 2011 was primarily comprised of a non-cash credit of $3.2 million for the revaluation of these warrants and foreign exchange gains of $0.3 million.

Liquidity and Capital Resources

Sources of Liquidity

Since our inception, we have funded our operations primarily through the issuance of common and preferred stock, debt financings, the receipt of funds from our collaboration partners, and from research grants.

Our cash, cash equivalents and marketable securities totaled $29.3 million as of June 30, 2012, as compared to $44.1 million as of December 31, 2011. The decrease of $14.8 million was primarily due to net cash used in operating activities.

On March 29, 2012, we entered into a Royalty Agreement with RPI, under which RPI may acquire a Revenue Participation Right for $25.0 million. RPI will be obligated to purchase the Revenue Participation Right if, following the interim efficacy analysis of data from the VALOR trial, the DSMB recommends that we undertake a one-time 225 patient increase in sample size for the VALOR trial or terminate the VALOR trial for efficacy. If the DSMB recommends that we continue the VALOR trial with the planned sample size of 450 patients, RPI will have the option to purchase the Revenue Participation Right following unblinding of the VALOR trial.

On October 18, 2011, we entered into the Loan Agreement with the Lenders, under which we may borrow up to $25.0 million in two tranches. The first tranche of $10.0 million was funded at closing. The second tranche of $15.0 million may be drawn at our option on or before September 30, 2012, subject to our continued compliance with the Loan Agreement and contingent upon recommendation by the DSMB following the interim analysis of the VALOR trial to either: (a) discontinue the trial due to positive efficacy, or (b) continue the trial.

In April 2010, we entered into a controlled equity offering sales agreement with Cantor, pursuant to which we may issue and sell shares of our common stock having an aggregate offering price of up to $20.0 million from time to time through Cantor acting as agent and/or principal. Cantor is entitled to a 3.0% commission rate of the gross sales price per share of any common stock sold through Cantor as agent under the sales agreement. In the six months ended June 30, 2012, we sold an aggregate of 88,500 shares of common stock at an average price of approximately $3.08 per share for gross and net proceeds of $0.3 million, after deducting Cantor’s commission. As of June 30, 2012, $1.7 million of common stock remained available to be sold under this facility, subject to certain conditions as specified in the agreement.

In August 2011, we entered into an additional controlled equity offering sales agreement with Cantor, pursuant to which we may issue and sell shares of our common stock having an aggregate offering price of up to $20.0 million from time to time through Cantor acting as agent and/or principal. As of June 30, 2012, no sales had been made under this facility, and $20.0 million of common stock remained available to be sold, subject to certain conditions as specified in the agreement.

Cash Flows

Net cash used in operating activities was $15.1 million for the six months ended June 30, 2012, as compared to $8.9 million for the same period in 2011. Net cash used in the 2012 period resulted primarily from the net loss of $22.5 million, partially offset by net adjustments for non-cash items of $5.6 million (including expenses of $4.1 million for the revaluation of warrants issued in the 2010 Offering and $1.1 million of stock-based compensation), and changes in operating assets and liabilities of $1.8 million, primarily as a result of an increase in accrued clinical expenses related to the VALOR trial. Net cash used in the 2011 period resulted primarily from the net loss of $6.4 million and net adjustments for non-cash items of $3.1 million (including a net credit of $3.2 million related to the revaluation of warrants issued in the 2010 Offering), partially offset by changes in operating assets and liabilities of $0.6 million, primarily as a result of an increase in accrued clinical expenses.

Net cash provided by investing activities was $17.1 million for the six months ended June 30, 2012, as compared to $1.8 million used in investing activities in the same period in 2011. Net cash provided in the 2012 period consisted primarily of proceeds from maturities of marketable securities, partially offset by purchases of marketable securities. Net cash used in the 2011 period consisted primarily of purchases of marketable securities, partially offset by proceeds from maturities of marketable securities.

Net cash provided by financing activities was $0.5 million for the six months ended June 30, 2012, as compared to $4.1 million for the same period in 2011. Net cash provided in both periods was primarily from sales of our common stock through Cantor.

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Operating Capital Requirements

We expect to continue to incur substantial operating losses in the future. We will not receive any product revenue until a product candidate has been approved by the FDA or similar regulatory agencies in other countries, and has been successfully commercialized, if at all. We will need to raise substantial additional funding to complete the development and potential commercialization of vosaroxin. Additionally, we may evaluate in-licensing and acquisition opportunities to gain access to new drugs or drug targets that would fit with our strategy. Any such transaction would likely increase our funding needs in the future.

Our future funding requirements will depend on many factors, including but not limited to:

• the rate of progress and cost of our clinical trials, including the VALOR trial in particular;

• the need for additional or expanded clinical trials (including in particular potential expansion of the number of patients included in the VALOR trial based on the pre-specified interim analysis of data from the trial by the DSMB);

• the timing, economic and other terms of any licensing, collaboration or other similar arrangement into which we may enter;

• the costs and timing of seeking and obtaining FDA and other regulatory approvals;

• the extent of our other development activities;

• the costs associated with building or accessing commercialization and additional manufacturing capabilities and supplies;

• the costs of acquiring or investing in businesses, product candidates and technologies, if any;

• the costs of filing, prosecuting, defending and enforcing any patent claims and other intellectual property rights;

• the effect of competing technological and market developments; and

• the costs, if any, of supporting our arrangements with Biogen Idec and Millennium.

While we believe that we currently have access to resources to fund our operations until the unblinding of the VALOR trial, including if a sample size adjustment occurs, we may need to raise additional capital if the costs of the trial exceed our current estimates or unblinding does not occur within the currently anticipated timeframe.

Until we can generate a sufficient amount of licensing or collaboration or product revenue to finance our cash requirements, which we may never do, we expect to finance our future cash needs primarily through equity issuances, the potential sale of revenue participation rights, debt arrangements, a possible license, collaboration or other similar arrangement with respect to development and/or commercialization rights to vosaroxin, or a combination of the above.

Our failure to raise significant additional capital in the future would force us to delay or reduce the scope of our vosaroxin development program, potentially including the VALOR trial, and/or limit or cease our operations. Any one of the foregoing would have a material adverse effect on our business, financial condition and results of operations.

Contractual Obligations

There were no material changes in our contractual obligations in the six months ended June 30, 2012 from those disclosed in our Annual Report on Form 10-K for the year ended December 31, 2011 other than scheduled payments through June 30, 2012. Please see Item 7, Management’s Discussion and Analysis of Financial Condition and Results of Operations—Contractual Obligations in our Form 10-K for a description of contractual obligations as of December 31, 2011.

Off-Balance Sheet Arrangements

Since our inception, we have not had any off-balance sheet arrangements or relationships with unconsolidated entities or financial partnerships, such as entities often referred to as structured finance or variable interest entities, which are typically established for the purpose of facilitating off-balance sheet arrangements or other contractually narrow or limited purposes.

Item 3. Quantitative and Qualitative Disclosures About Market Risk

This item is not applicable to us as a smaller reporting company.

Item 4. Controls and Procedures

Evaluation of Disclosure Controls and Procedures

We maintain disclosure controls and procedures, as such term is defined in SEC Exchange Act Rule 13a-15(e), that are designed to ensure that information required to be disclosed in our reports under the Exchange Act is recorded, processed, summarized and reported within the time periods specified in the SEC’s rules and forms and that such information is accumulated and communicated to our management, including our Chief Executive Officer and Chief Financial Officer, as appropriate, to allow for timely decisions regarding required disclosure. In designing and evaluating the disclosure controls and procedures, management recognizes that any controls and procedures, no matter how well designed and operated, can provide only reasonable assurance of achieving the desired control objectives, and management is required to apply its judgment in evaluating the cost-benefit relationship of possible controls and procedures.

As required by SEC Exchange Act Rule 13a-15(b), we carried out an evaluation, under the supervision and with the participation of our management, including our Chief Executive Officer and Chief Financial Officer, of the effectiveness of the design and operation of our disclosure controls and procedures as of the end of the period covered by this Quarterly Report on Form 10-Q. Based on the foregoing, our Chief Executive Officer and Chief Financial Officer concluded that our disclosure controls and procedures were effective at the reasonable assurance level as of the end of the period covered by this Quarterly Report on Form 10-Q.

Changes in Internal Control over Financial Reporting

There were no changes in our internal control over financial reporting during the quarter ended June 30, 2012 that have materially affected, or are reasonably likely to materially affect, our internal control over financial reporting.

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PART II. OTHER INFORMATION

Item 1. Legal Proceedings

From time to time, we may be involved in routine legal proceedings, as well as demands, claims and threatened litigation, which arise in the normal course of our business. The ultimate outcome of any litigation is uncertain and unfavorable outcomes could have a negative impact on our results of operations and financial condition. Regardless of outcome, litigation can have an adverse impact on us because of the defense costs, diversion of management resources and other factors.

We believe there is no litigation pending that could, individually or in the aggregate, have a material adverse effect on our results of operations or financial condition.

Item 1A. Risk Factors

Investing in our common stock involves a high degree of risk. You should carefully consider the risks and uncertainties described below and all information contained in this Quarterly Report on Form 10-Q, as each of these risks could adversely affect our business, operating results and financial condition. If any of the possible adverse events described below actually occurs, we may be unable to conduct our business as currently planned and our financial condition and operating results could be harmed. In addition, the trading price of our common stock could decline due to the occurrence of any of these risks, and you may lose all or part of your investment.

Please see the language regarding forward-looking statements in “Management’s Discussion and Analysis of Financial Condition and Results of Operations.”

We have marked with an asterisk (*) those risk factors below that reflect substantive changes from the risk factors included in our Annual Report on Form 10-K filed with the Securities and Exchange Commission on March 14, 2012.

Risks Related to Our Business

We need to raise substantial additional funding to complete the development and potential commercialization of vosaroxin.*

We believe that with $29.3 million in cash and investments as of June 30, 2012, we currently have access to resources to fund our operations until the unblinding of the VALOR trial, including if a sample size adjustment occurs. To the extent that the costs of the VALOR trial exceed our current estimates or unblinding does not occur within the currently anticipated timeframe and we are unable to raise sufficient additional capital to cover such additional costs, we will need to reduce operating expenses, enter into a collaboration or other similar arrangement with respect to development and/or commercialization rights to vosaroxin, outlicense intellectual property rights to vosaroxin, sell assets, or a combination of the above.

In addition, we will need to raise substantial additional capital to:

• complete the development and potential commercialization of vosaroxin;

• fund additional clinical trials of vosaroxin and seek regulatory approvals;

• expand our development activities;

• implement additional internal systems and infrastructure; and

• build or access commercialization and additional manufacturing capabilities and supplies.

Our future funding requirements and sources will depend on many factors, including but not limited to:

• the rate of progress and cost of our clinical trials, including the VALOR trial in particular;

• the need for additional or expanded clinical trials (including in particular the potential expansion of the number of patients included in the VALOR trial based on the pre-specified interim analysis of data from the trial by the DSMB);

• the timing, economic and other terms of any licensing, collaboration or other similar arrangement into which we may enter;

• the costs and timing of seeking and obtaining FDA and other regulatory approvals;

• the extent of our other development activities;

• the costs associated with building or accessing commercialization and additional manufacturing capabilities and supplies;

• the costs of acquiring or investing in businesses, product candidates and technologies, if any;

• the costs of filing, prosecuting, defending and enforcing any patent claims and other intellectual property rights;

• the effect of competing technological and market developments, and;

• the costs, if any, of supporting our arrangements with Biogen Idec and Millennium or any potential future licensees or partners.

Until we can generate a sufficient amount of licensing, collaboration or product revenue to finance our cash requirements, which we may never do, we expect to finance future cash needs primarily through equity issuances, the potential sale of revenue participation rights, debt arrangements, a possible license, collaboration or other similar arrangement with respect to development and/or commercialization rights to vosaroxin, or a combination of the above. Any issuance of convertible debt securities, preferred stock or common stock may be at a discount from the then-current trading price of our common stock. If we issue additional common or preferred stock or securities convertible into common stock, our stockholders will experience additional dilution, which may be significant. Further, we do not know whether additional funding will be available on acceptable terms, or at all. If we are unable to raise substantial additional funding on acceptable terms or at all, we will be forced to delay or reduce the scope of our vosaroxin development program, potentially including the VALOR trial, and/or limit or cease our operations.

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We have incurred losses since inception and anticipate that we will continue to incur losses for the foreseeable future. We may not ever achieve or sustain profitability.*

We are not profitable and have incurred losses in each year since our inception in 1998. Our net losses for the six months ended June 30, 2012 and the years ended December 31, 2011 and 2010 were $22.5 million, $20.1 million and $24.6 million, respectively. As of June 30, 2012, we had an accumulated deficit of $423.6 million. We do not currently have any products that have been approved for marketing, and we continue to incur substantial development and general and administrative expenses related to our operations. We expect to continue to incur losses for the foreseeable future, and we expect these losses to increase significantly as the VALOR trial progresses, as we seek regulatory approvals for vosaroxin, and as we commercialize vosaroxin, if approved. Our losses, among other things, have caused and will continue to cause our stockholders’ equity and working capital to decrease.

To date, we have derived substantially all of our revenue from license and collaboration agreements. On March 31, 2011, the only remaining collaboration agreement, which was with Biogen Idec, was amended and restated to provide for the discovery, development and commercialization of small molecule inhibitors of a unique preclinical kinase inhibitor program involved in immunology. Concurrently, we entered into a license agreement with Millennium, under which we granted Millennium exclusive licenses for the development of our oral, selective pan-Raf kinase inhibitor and one additional undisclosed kinase inhibitor program in oncology. While we are entitled to certain pre-commercialization event-based and royalty payments under each of the Restated Biogen Idec Agreement and Millennium Agreement, we cannot predict whether we will receive any such payments under these agreements in the foreseeable future, or at all. Similarly, although we entered into the Royalty Agreement to sell the Revenue Participation Right to RPI for $25.0 million, RPI will be obligated to purchase the Revenue Participation Right only if, following the interim efficacy analysis of data from the VALOR trial, the DSMB recommends that we undertake a one-time 225 patient increase in sample size for the VALOR trial or terminate the VALOR trial for efficacy, and we follow such recommendation. We do not know whether the DSMB will make such recommendations, and we may elect not to follow such recommendations if they are made. If the DSMB recommends that we continue the VALOR trial with the planned sample size of 450 patients, RPI will have the option to purchase the Revenue Participation Right following the unblinding of the VALOR trial, which RPI may elect not to exercise even if the DSMB makes such recommendation. Accordingly, we cannot predict whether we will receive any payment under the Royalty Agreement.

We also do not anticipate that we will generate revenue from the sale of products for the foreseeable future. In the absence of additional sources of capital, which may not be available to us on acceptable terms, or at all, the development of vosaroxin or future product candidates, if any, may be reduced in scope, delayed or terminated. If our product candidates or those of our collaborators fail in clinical trials or do not gain regulatory approval, or if our future products do not achieve market acceptance, we may never become profitable. Even if we achieve profitability in the future, we may not be able to sustain profitability in subsequent periods.

The development of vosaroxin could be halted or significantly delayed for various reasons; our clinical trials for vosaroxin may not demonstrate safety or efficacy or lead to regulatory approval.

Vosaroxin is vulnerable to the risks of failure inherent in the drug development process. We may need to conduct significant additional preclinical studies and clinical trials before we can attempt to demonstrate that vosaroxin is safe and effective to the satisfaction of the FDA and other regulatory authorities. Failure can occur at any stage of the development process, and successful preclinical studies and early clinical trials do not ensure that later clinical trials will be successful. A number of companies in the pharmaceutical industry have suffered significant setbacks in advanced clinical trials, even after obtaining promising results in earlier trials.

For example, we terminated two Phase 2 clinical trials of vosaroxin in small cell and non-small cell lung cancer. If our clinical trials result in unacceptable toxicity or lack of efficacy, we may have to terminate them. If clinical trials are halted, or if they do not show that vosaroxin is safe and effective in the indications for which we are seeking regulatory approval, our future growth will be limited and we may not have any other product candidates to develop.

We do not know whether our ongoing clinical trials or any other future clinical trials with vosaroxin or any of our product candidates, including the VALOR trial in particular, will be completed on schedule, or at all, or whether our ongoing or planned clinical trials will begin or progress on the time schedule we anticipate. The commencement of future clinical trials could be substantially delayed or prevented by several factors, including:

• delays or failures to raise additional funding;

• results of meetings with the FDA and/or other regulatory bodies;

• a limited number of, and competition for, suitable patients with particular types of cancer for enrollment in our clinical trials;

• delays or failures in obtaining regulatory approval to commence a clinical trial;

• delays or failures in obtaining sufficient clinical materials;

• delays or failures in obtaining approval from independent institutional review boards to conduct a clinical trial at prospective sites; or

• delays or failures in reaching acceptable clinical trial agreement terms or clinical trial protocols with prospective sites.

The completion of our clinical trials, including the VALOR trial, could be substantially delayed or prevented by several factors, including:

• delays or failures to raise additional funding;

• slower than expected rates of patient recruitment and enrollment;

• failure of patients to complete the clinical trial;

• delays or failures in reaching the number of events pre-specified in the trial design;

• the need to expand the clinical trial (including, in particular, potential expansion of the number of patients included in our VALOR trial based on the pre-specified interim analysis of data by the DSMB);

• delays or failures in obtaining sufficient clinical materials, including vosaroxin, its matching placebo and cytarabine;

• unforeseen safety issues;

• lack of efficacy during clinical trials;

• inability or unwillingness of patients or clinical investigators to follow our clinical trial protocols; and

• inability to monitor patients adequately during or after treatment.

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Additionally, our clinical trials may be suspended or terminated at any time by the FDA, other regulatory authorities, or ourselves. Any failure to complete or significant delay in completing clinical trials for our product candidates could harm our financial results and the commercial prospects for our product candidates.

We rely on a limited number of third-party manufacturers that are capable of manufacturing the vosaroxin active pharmaceutical ingredient, or API, and finished drug product, or FDP, to supply us with our vosaroxin API and FDP and the placebo used in the VALOR trial. If we fail to obtain sufficient quantities of these materials, the VALOR trial and the development of vosaroxin could be halted or significantly delayed. In addition, we have previously identified product impurities in the vosaroxin API that negatively impact FDP quality. Process improvements have been implemented to minimize these impurities, however there is no assurance they will not occur in the future.

We do not currently own or operate manufacturing facilities and lack the capability to manufacture vosaroxin on a clinical or commercial scale. As a result, we rely on third parties to manufacture vosaroxin API and FDP and the placebo product used in the VALOR trial. The vosaroxin API is classified as a cytotoxic substance, limiting the number of available manufacturers for both API and FDP.

We currently rely on two contract manufacturers for the vosaroxin API. We also currently rely on a single contract manufacturer to formulate the vosaroxin API and fill and finish vials of the vosaroxin FDP. If our third-party vosaroxin API or FDP manufacturers are unable or unwilling to produce the vosaroxin API or FDP or placebo we require, we would need to establish arrangements with one or more alternative suppliers. However, establishing a relationship with an alternative supplier would likely delay our ability to produce vosaroxin API or FDP by six to nine months. Our ability to replace an existing manufacturer would also be difficult and time consuming because the number of potential manufacturers is limited and the FDA must approve any replacement manufacturer before it can be an approved commercial supplier. Such approval would require new testing, stability programs and compliance inspections. It may be difficult or impossible for us to identify and engage a replacement manufacturer on acceptable terms in a timely manner, or at all. We expect to continue to depend on third-party contract manufacturers for all our vosaroxin API, FDP and placebo needs for the foreseeable future.

Vosaroxin requires precise, high quality manufacturing. We have observed visible particles during stability studies of two vosaroxin FDP lots. We have since identified a process impurity in the vosaroxin API that, when formulated into the packaged vial of the vosaroxin FDP, can result in the formation of particles over time. As a response to these findings, we implemented a revised manufacturing process to seek to control the impurity and thereby prevent particle formation. Two lots of vosaroxin API manufactured using a revised manufacturing process were formulated into FDP lots that have both completed up to 24 months of stability testing at room temperature without formation of particles. Three additional lots of API have been manufactured using this improved process, and four lots of FDP have been successfully manufactured using the API resulting from the improved process. All FDP lots made with the new API have passed quality testing and have been released for use in the VALOR trial. All lots have been placed on an International Committee on Harmonization, or ICH, compliant stability program. It will take time to evaluate whether or not our revised manufacturing process for vosaroxin API will be successful in stopping the formation of particles in FDP lots over the longer term, and to evaluate whether or not such control of particle formation can also be reliably and consistently achieved in subsequent lots over the shorter or longer term. If our changes in the manufacturing process do not adequately control the formation of visible particles, we will need to discuss other possibilities with the FDA and/or other regulatory bodies, which could include a temporary clinical hold of the VALOR trial until the issue has been resolved to their satisfaction.

In addition to process impurities, the failure of our contract manufacturers to achieve and maintain high manufacturing standards in compliance with current Good Manufacturing Practice, or cGMP, regulations could result in other manufacturing errors leading to patient injury or death, product recalls or withdrawals, delays or interruptions of production or failures in product testing or delivery. Although contract manufacturers are subject to ongoing periodic unannounced inspection by the FDA and corresponding state agencies to ensure strict compliance with cGMP and other applicable government regulations and corresponding foreign standards, any such performance failures on the part of a contract manufacturer could result in the delay or prevention of filing or approval of marketing applications for vosaroxin, cost overruns or other problems that could seriously harm our business. This would deprive us of potential product revenue and result in additional losses.

To date, vosaroxin has been manufactured in quantities appropriate for preclinical studies and clinical trials. New lots of API and FDP may need to be manufactured and released to support our VALOR trial, and for stability assessments required for regulatory approval. There can be no assurance that we will be able to obtain a sufficient supply of vosaroxin API and FDP to supply our VALOR trial at the anticipated rate of enrollment or to continue the trial without interruption. Prior to approval for commercial sale, we will need to manufacture registration batches of API and FDP, which will be accompanied by process validation studies. Process validation studies are conducted at risk prior to FDA review and approval. If the results of these process validation studies do not meet preset criteria, the regulatory approval or commercial launch of vosaroxin may be delayed.

We rely on third-party distributors for the supply of cytarabine for our VALOR trial. Cytarabine has until recently been in short supply throughout the world, and there is no guarantee we can procure sufficient quantities to supply our VALOR trial.

The cytarabine used in our VALOR trial is procured from third-party distributors. Cytarabine has until recently been in short supply throughout the world. Additional procurement of cytarabine will be necessary to complete the VALOR trial if there is a sample size adjustment based on the pre-specified interim analysis by the DSMB. If we are unable to procure the necessary supplies to support our VALOR trial in a timely manner, the trial will be delayed. Any significant delay could seriously harm our business.

The failure to enroll patients for clinical trials may cause delays in developing vosaroxin.

We may encounter delays if we are unable to enroll enough patients to complete clinical trials of vosaroxin, including the VALOR trial. Patient enrollment depends on many factors, including the size of the patient population, the nature of the protocol, the proximity of patients to clinical sites, the number and nature of competing treatments and ongoing clinical trials of competing drugs for the same indication, and the eligibility criteria for the trial. Patients participating in our trials may elect to leave our trials and switch to alternative treatments that are available to them, either commercially or on an expanded access basis, or in other clinical trials. Competing treatments include nucleoside analogs, anthracyclines and hypomethylating agents. Moreover, when one product candidate is evaluated in multiple clinical trials simultaneously, patient enrollment in ongoing trials can be adversely affected by negative results from completed trials. In the VALOR trial, vosaroxin is being tested in patients with AML, which can be a difficult patient population to recruit.

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The results of preclinical studies and clinical trials may not satisfy the requirements of the FDA or other regulatory agencies.

Prior to receiving approval to commercialize vosaroxin or future product candidates, if any, in the United States or abroad, we must demonstrate with substantial evidence from well-controlled clinical trials, to the satisfaction of the FDA and other regulatory authorities, that such product candidates are safe and effective for their intended uses. The results from preclinical studies and clinical trials can be interpreted in different ways, and the favorable results from previous trials of vosaroxin may not be experienced in the VALOR trial. Even if we believe the preclinical or clinical data are promising, such data may not be sufficient to support approval by the FDA and other regulatory authorities. In addition, although we believe that our discussions with the FDA support the potential approval of vosaroxin for the treatment of AML based on positive results from the VALOR trial without the need to conduct additional clinical trials, the FDA has substantial discretion in the approval process and may not grant approval based on data from this trial.

We rely on third parties to conduct our clinical trials. If these third parties do not successfully carry out their contractual duties or meet expected deadlines, we may be unable to obtain regulatory approval for, or commercialize vosaroxin.

We rely on third parties, such as contract research organizations, medical institutions, clinical investigators and contract laboratories, to conduct our planned and existing clinical trials for vosaroxin. If the third parties conducting our clinical trials do not perform their contractual duties or obligations, do not meet expected deadlines or need to be replaced, or if the quality or accuracy of the clinical data they obtain is compromised due to the failure to adhere to our clinical trial protocols or for any other reason, we may need to enter into new arrangements with alternative third parties and our clinical trials may be extended, delayed or terminated or may need to be repeated, and we may not be able to obtain regulatory approval for or commercialize the product candidate being tested in such trials.

We expect to expand our development capabilities, and any difficulties hiring or retaining key personnel or managing this growth could disrupt our operations.

We are highly dependent on the principal members of our development staff. We expect to expand our development capabilities by increasing expenditures in these areas, hiring additional employees and potentially expanding the scope of our current operations. Future growth will require us to continue to implement and improve our managerial, operational and financial systems and continue to retain, recruit and train additional qualified personnel, which may impose a strain on our administrative and operational infrastructure. The competition for qualified personnel in the biopharmaceutical field is intense. We are highly dependent on our continued ability to attract, retain and motivate highly qualified management and specialized personnel required for clinical development. Due to our limited resources, we may not be able to effectively manage any expansion of our operations or recruit and train additional qualified personnel. If we are unable to retain key personnel or manage our growth effectively, we may not be able to implement our business plan.

If we are sued for infringing intellectual property rights of third parties, litigation will be costly and time consuming and could prevent us from developing or commercializing vosaroxin.

Our commercial success depends on not infringing the patents and other proprietary rights of third parties and not breaching any collaboration or other agreements we have entered into with regard to our technologies and product candidates. If a third party asserts that we are using technology or compounds claimed in issued and unexpired patents owned or controlled by the third party, we may need to obtain a license, enter into litigation to challenge the validity of the patents or incur the risk of litigation in the event that a third party asserts that we infringe its patents.

If a third party asserts that we infringe its patents or other proprietary rights, we could face a number of challenges that could seriously harm our competitive position, including:

• infringement and other intellectual property claims, which would be costly and time consuming to litigate, whether or not the claims have merit, and which could delay the regulatory approval process and divert management’s attention from our business;

• substantial damages for past infringement, which we may have to pay if a court determines that vosaroxin or any future product candidates infringe a third party’s patent or other proprietary rights;

• a court order prohibiting us from selling or licensing vosaroxin or any future product candidates unless a third party licenses relevant patent or other proprietary rights to us, which it is not required to do; and

• if a license is available from a third party, we may have to pay substantial royalties or grant cross-licenses to our patents or other proprietary rights.

If our competitors develop and market products that are more effective, safer or less expensive than vosaroxin, our commercial opportunities will be negatively impacted.

The life sciences industry is highly competitive, and we face significant competition from many pharmaceutical, biopharmaceutical and biotechnology companies that are researching, developing and marketing products designed to address the treatment of cancer, including AML. Many of our competitors have significantly greater financial, manufacturing, marketing and drug development resources than we do. Large pharmaceutical companies in particular have extensive experience in the clinical testing of, obtaining regulatory approvals for, and marketing drugs.

We believe that our ability to successfully compete in the marketplace with vosaroxin and any future product candidates, if any, will depend on, among other things:

• our ability to develop novel compounds with attractive pharmaceutical properties and to secure, protect and maintain intellectual property rights based on our innovations;

• the efficacy, safety and reliability of our product candidates;

• the speed at which we develop our product candidates;

• our ability to design and successfully execute appropriate clinical trials;

• our ability to maintain a good relationship with regulatory authorities;

• our ability to obtain, and the timing and scope of, regulatory approvals;

• our ability to manufacture and sell commercial quantities of future products to the market; and

• acceptance of future products by physicians and other healthcare providers.

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Vosaroxin is a small molecule therapeutic that will compete with other drugs and therapies currently used for AML, such as nucleoside analogs, anthracyclines, hypomethylating agents, Flt-3 inhibitors, other inhibitors of topoisomerase II, and other novel agents. Additionally, other compounds currently in development could become potential competitors of vosaroxin, if approved for marketing.

We expect competition for vosaroxin for the treatment of AML to increase as additional products are developed and approved in various patient populations. If our competitors market products that are more effective, safer or less expensive than vosaroxin or our other future products, if any, or that reach the market sooner we may not achieve commercial success or substantial market penetration. In addition, the biopharmaceutical industry is characterized by rapid change. Products developed by our competitors may render vosaroxin or any future product candidates obsolete.

Our proprietary rights may not adequately protect vosaroxin or future product candidates, if any.

Our commercial success will depend on our ability to obtain patents and maintain adequate protection for vosaroxin and any future product candidates in the United States and other countries. We own, co-own or have rights to a significant number of issued U.S. and foreign patents and pending U.S. and foreign patent applications. We will be able to protect our proprietary rights from unauthorized use by third parties only to the extent that our proprietary technologies and future products are covered by valid and enforceable patents or are effectively maintained as trade secrets.

We apply for patents covering both our technologies and product candidates, as we deem appropriate. However, we may fail to apply for patents on important technologies or product candidates in a timely fashion, or at all. Our existing patents and any future patents we obtain may not be sufficiently broad to prevent others from practicing our technologies or from developing competing products and technologies. In addition, we generally do not exclusively control the patent prosecution of subject matter that we license to or from others. Accordingly, in such cases we are unable to exercise the same degree of control over this intellectual property as we would over our own. Moreover, the patent positions of biopharmaceutical companies are highly uncertain and involve complex legal and factual questions for which important legal principles remain unresolved. As a result, the validity and enforceability of patents cannot be predicted with certainty. In addition, we do not know whether:

• we, our licensors or our collaboration partners were the first to make the inventions covered by each of our issued patents and pending patent applications;

• we, our licensors or our collaboration partners were the first to file patent applications for these inventions;

• others will independently develop similar or alternative technologies or duplicate any of our technologies;

• any of our or our licensors’ or our collaboration partners’ pending patent applications will result in issued patents;

• any of our, our licensors’ or our collaboration partners’ patents will be valid or enforceable;

• any patents issued to us, our licensors or our collaboration partners will provide us with any competitive advantages, or will be challenged by third parties;

• we will develop additional proprietary technologies that are patentable; or

• the patents of others will have an adverse effect on our business.

We also rely on trade secrets to protect some of our technology, especially where we do not believe patent protection is appropriate or obtainable. However, trade secrets are difficult to maintain. While we use reasonable efforts to protect our trade secrets, our or our collaboration partners’ employees, consultants, contractors or scientific and other advisors, or those of our licensors, may unintentionally or willfully disclose our proprietary information to competitors. Enforcement of claims that a third party has illegally obtained and is using trade secrets is expensive, time consuming and uncertain. In addition, foreign courts are sometimes less willing than U.S. courts to protect trade secrets. If our competitors independently develop equivalent knowledge, methods and know-how, we would not be able to assert our trade secret protection against them and our business could be harmed.

The initial composition of matter patents covering vosaroxin are due to expire in 2015. Even if vosaroxin is approved by the FDA and foreign equivalents thereof, we may not be able to recover our development costs prior to the expiration of these patents.*

The vosaroxin composition of matter is covered by U.S. Patent No. 5,817,669 and its counterpart patents in 43 foreign jurisdictions. This patent is due to expire in October 2015, and most of its foreign counterparts are due to expire in June 2015. In November 2010, the USPTO granted us a patent covering pharmaceutical compositions of vosaroxin, including the formulation used in our VALOR trial. In January 2011, the European Patent Office, or EPO, granted us a similar patent, which has been validated in multiple EPC member states. These patents are due to expire in 2025. In December 2009, the EPO granted us a patent covering combinations of vosaroxin with cytarabine, which is due to expire in 2025 in multiple European Patent Convention, or EPC, member states. In June 2011, the USPTO granted us a similar patent, which is due to expire in 2026. In August 2011, the USPTO granted us a patent covering methods of use for vosaroxin at clinically relevant dose ranges and schedules for the treatment of leukemia. This patent has been granted a two year patent term adjustment, which extends its term through 2026. In February 2012, the USPTO granted us a patent covering certain vosaroxin hydrate forms, which is due to expire in 2028. In March 2012, the USPTO granted us a patent covering certain compositions related to vosaroxin, which is due to expire in 2030. Vosaroxin must undergo extensive clinical trials before it can be approved by the FDA. We do not know when, if ever, vosaroxin will be approved by the FDA. Even if vosaroxin is approved by the FDA in the future, we may not have sufficient time to commercialize our vosaroxin product to enable us to recover our development costs prior to the expiration of the U.S. and foreign patents covering vosaroxin. We do not know whether patent term extensions and data exclusivity periods will be available in the future for any or all of the patents we own or have licensed. Our obligation to pay royalties to Dainippon, the company from which we licensed vosaroxin, may extend beyond the patent expiration, which would further erode the profitability of this product. In addition, our potential obligation to pay RPI royalties pursuant to the Royalty Agreement could also further erode the profitability of this product.

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Any future workforce and expense reductions may have an adverse impact on our internal programs, our ability to hire and retain key personnel and may be distracting to management.

We have, in the past, implemented a number of workforce reductions. Depending on our need for additional funding and expense control, we may be required to implement further workforce and expense reductions in the future. Further workforce and expense reductions could result in reduced progress on our internal programs. In addition, employees, whether or not directly affected by a reduction, may seek future employment with our business partners or competitors. Although our employees are required to sign a confidentiality agreement at the time of hire, the confidential nature of certain proprietary information may not be maintained in the course of any such future employment. Further, we believe that our future success will depend in large part upon our ability to attract and retain highly skilled personnel. We may have difficulty retaining and attracting such personnel as a result of a perceived risk of future workforce and expense reductions. In addition, the implementation of expense reduction programs may result in the diversion of efforts of our executive management team and other key employees, which could adversely affect our business.

We may be subject to damages resulting from claims that we or our employees have wrongfully used or disclosed alleged trade secrets of our employees’ former employers.

Many of our employees were previously employed at biotechnology or pharmaceutical companies, including our competitors or potential competitors. We may be subject to claims that we or our employees have inadvertently or otherwise used or disclosed trade secrets or other proprietary information of their former employers. Litigation may be necessary to defend against these claims. If we fail in defending such claims, in addition to paying monetary damages, we may lose valuable intellectual property rights or personnel. A loss of key personnel or the work product of current or former personnel could hamper or prevent our ability to commercialize vosaroxin, which could severely harm our business. Even if we are successful in defending against these claims, litigation could result in substantial costs and be a distraction to management.

We currently have limited marketing staff and no sales or distribution organization. If we are unable to develop a sales and marketing and distribution capability on our own or through collaborations with marketing partners, we will not be successful in commercializing vosaroxin.

We currently have no sales or distribution capabilities and limited marketing staff. We intend to establish our own sales and marketing organization with technical expertise and supporting distribution capabilities to commercialize vosaroxin in North America, which will be expensive and time consuming. Any failure or delay in the development of our internal sales, marketing and distribution capabilities would adversely impact the commercialization of these products. We plan to collaborate with third parties that have direct sales forces and established distribution systems to commercialize vosaroxin. To the extent that we enter into co-promotion or other licensing arrangements, our product revenue is likely to be lower than if we marketed or sold vosaroxin directly. In addition, any revenue we receive will depend upon the efforts of third parties, which may not be successful and are only partially within our control. If we are unable to enter into such arrangements on acceptable terms or at all, we may not be able to successfully commercialize vosaroxin. If we are not successful in commercializing vosaroxin or our future product candidates, if any, either on our own or through collaborations with one or more third parties, our future product revenue will suffer and we may incur significant additional losses.

We depend on various consultants and advisors for the success and continuation of our development efforts.

We work extensively with various consultants and advisors, who provide advice and or services in various business and development functions, including clinical development, operations and strategy, regulatory matters, accounting and finance. The potential success of our drug development programs depends, in part, on continued collaborations with certain of these consultants and advisors. Our consultants and advisors are not our employees and may have commitments and obligations to other entities that may limit their availability to us. We do not know if we will be able to maintain such relationships or that such consultants and advisors will not enter into other arrangements with competitors, any of which could have a detrimental impact on our development objectives and our business.

If conflicts of interest arise between our current or future licensees or collaboration partners, if any, and us, any of them may act in their self-interest, which may be adverse to our interests.

If a conflict of interest arises between us and one or more of our current or potential future licensees or collaboration partners, if any, they may act in their own self-interest or otherwise in a way that is not in the interest of our company or our stockholders. Biogen Idec, Millennium, or potential future licensees or collaboration partners, if any, are conducting or may conduct product development efforts within the disease area that is the subject of a license or collaboration with our company. In current or potential future licenses or collaborations, if any, we have agreed or may agree not to conduct, independently or with any third party, any research that is competitive with the research conducted under our licenses or collaborations. Our licensees or collaboration partners, however, may develop, either alone or with others, products in related fields that are competitive with the product candidates that are the subject of these licenses or collaborations. Competing products, either developed by our licensees or collaboration partners or to which our licensees or collaboration partners have rights, may result in their withdrawal of support for a product candidate covered by the license or collaboration agreement.

If one or more of our current or potential future licensees or collaboration partners, if any, were to breach or terminate their license or collaboration agreements with us or otherwise fail to perform their obligations thereunder in a timely manner, the preclinical or clinical development or commercialization of the affected product candidates could be delayed or terminated. We do not know whether our licensees or collaboration partners will pursue alternative technologies or develop alternative product candidates, either on their own or in collaboration with others, including our competitors, as a means for developing treatments for the diseases targeted by licenses or collaboration agreements with our company.

Compliance with changing regulation of corporate governance and public disclosure may result in additional expenses.

Changing laws, regulations and standards relating to corporate governance and public disclosure may create uncertainty regarding compliance matters. New or changed laws, regulations and standards are subject to varying interpretations in many cases. As a result, their application in practice may evolve over time. We are committed to maintaining high standards of corporate governance and public disclosure. Complying with evolving interpretations of new or changed legal requirements may cause us to incur higher costs as we revise current practices, policies and procedures, and may divert management time and attention from potential revenue-generating activities to compliance matters. If our efforts to comply with new or changed laws, regulations and standards differ from the activities intended by regulatory or governing bodies due to ambiguities related to practice, our reputation may also be harmed. Further, our board members, chief executive officer and chief financial officer could face an increased risk of personal liability in connection with the performance of their duties. As a result, we may have difficulty attracting and retaining qualified board members and executive officers, which could harm our business.

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Raising funds through lending arrangements or revenue participation agreements may restrict our operations or produce other adverse results.*

Our Loan Agreement with the Lenders contains a variety of affirmative and negative covenants, including required financial reporting, limitations on certain dispositions of assets, limitations on the incurrence of additional debt and other requirements. To secure our performance of our obligations under this loan and security agreement, we granted a perfected first priority security interest in substantially all of our assets, other than intellectual property assets, to the Lenders. Our failure to comply with the covenants in the Loan Agreement, the occurrence of a material impairment in our prospect of repayment or in the perfection or priority of the Lender’s lien on our assets, as determined by the lenders, or the occurrence of certain other specified events could result in an event of default that, if not cured or waived, could result in the acceleration of all or a substantial portion of our debt, potential foreclosure on our assets and other adverse results.

In addition if RPI purchases the Revenue Participation Right, we would be required to pay RPI a specified percentage of any net sales of vosaroxin. If we fail to make payments due to RPI under the Royalty Agreement in a timely manner, RPI may require us to repurchase the Revenue Participation Right. As collateral for these payments, we agreed to grant RPI a security interest in certain of our assets, including our intellectual property related to vosaroxin, at the time of the purchase of the Revenue Participation Right. If granted, the security interest would be granted at the time of RPI’s purchase of the Revenue Participation Right, but could only be perfected following the first product approval in any country or territory. The security interest could later be released upon the satisfaction of certain conditions. The Lenders under the Loan Agreement also have a security interest in the same assets in which RPI may be granted a security interest, which may also be perfected following the first product approval in any country or territory. The security interest to the Lenders would be senior to RPI for so long as any indebtedness under the Loan Agreement remains outstanding.

Economic conditions may make it costly and difficult to raise additional capital.

There has been turmoil in the world economy, which has led to volatility on the U.S. stock market and reduced credit availability. Investors have been unwilling to buy certain corporate stocks and bonds. If economic conditions continue to affect the capital markets, our ability to raise capital, via our existing controlled equity facilities, debt facility or otherwise, may be adversely affected.

We are exposed to risks related to foreign currency exchange rates and European sovereign debt.*

Some of our costs and expenses are denominated in foreign currencies. Most of our foreign expenses are associated with activities related to the VALOR trial that are occurring outside of the United States, and in particular in Western Europe. When the U.S. dollar weakens against the Euro or British pound, the U.S. dollar value of the foreign currency denominated expense increases, and when the U.S. dollar strengthens against the Euro or British pound, the U.S. dollar value of the foreign currency denominated expense decreases. Consequently, changes in exchange rates, and in particular a weakening of the U.S. dollar, may adversely affect our results of operations. We have and may continue to purchase certain European currencies or highly-rated investments denominated in such currencies to manage the risk of future movements in foreign exchange rates that would affect such payables, in accordance with our investment policy. However, there is no guarantee that the related gains and losses will substantially offset each other, and we may be subject to significant exchange gains or losses as currencies fluctuate from quarter to quarter.

In addition, the current sovereign debt crisis concerning certain European countries, including Greece, Italy, Ireland, Portugal and Spain, and related European financial restructuring efforts, may cause the value of European currencies, including the Euro, to deteriorate. Such deterioration could adversely impact our investments denominated in Euros, which had an aggregate fair value of $3.9 million as of June 30, 2012, all of which was invested in corporate debt securities. Recent rating agency downgrades on European sovereign debt and growing concern over the potential default of European government issuers has further contributed to this uncertainty. Should governments default on their obligations, we may experience loss of principal on our investments in European sovereign debt.

Our facilities are located near known earthquake fault zones, and the occurrence of an earthquake or other catastrophic disaster could cause damage to our facilities and equipment, which could require us to cease or curtail operations.

Our facilities are located in the San Francisco Bay Area near known earthquake fault zones and are vulnerable to significant damage from earthquakes. We are also vulnerable to damage from other types of disasters, including fires, floods, power loss, communications failures and similar events. If any disaster were to occur, our ability to operate our business at our facilities may be seriously or completely impaired and our data could be lost or destroyed.

Risks Related to Our Industry

The regulatory approval process is expensive, time consuming and uncertain and may prevent us from obtaining approval for the commercialization of vosaroxin.

The research, testing, manufacturing, selling and marketing of product candidates are subject to extensive regulation by the FDA and other regulatory authorities in the United States and other countries, which regulations differ from country to country. Neither we nor our present or potential future collaboration or licensing partners, if any, are permitted to market our product candidates in the United States until we receive approval of a new drug application, or NDA, from the FDA, or in any other country without the equivalent marketing approval from such country. We have not received marketing approval for vosaroxin in any jurisdiction. None of our collaboration or licensing partners have had a product resulting from our collaboration enter clinical trials. In addition, failure to comply with FDA and other applicable U.S. and foreign regulatory requirements may subject us to administrative or judicially imposed sanctions, including warning letters, civil and criminal penalties, injunctions, product seizure or detention, product recalls, total or partial suspension of production, and refusal to approve pending NDAs, supplements to approved NDAs or their foreign equivalents.

Regulatory approval of an NDA or NDA supplement or a foreign equivalent is not guaranteed, and the approval process is expensive, uncertain and may take several years. Furthermore, the development process for oncology products may take longer than in other therapeutic areas. Regulatory authorities have substantial discretion in the drug approval process. Despite the time and expense exerted, failure can occur at any stage, and we could encounter problems that cause us to abandon clinical trials or to repeat or perform additional preclinical studies and clinical trials. The number of preclinical studies and clinical trials that will be required for marketing approval varies depending on the drug candidate, the disease or condition that the drug candidate is designed to address, and the regulations applicable to any particular drug candidate. In particular, although we believe that our discussions with the FDA support the potential approval of vosaroxin for the treatment of AML based on positive results from the VALOR trial without the need to conduct additional clinical trials, the FDA has substantial discretion in the approval process and may not grant approval based on data from this trial.

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The FDA or a foreign regulatory authority can delay, limit or deny approval of a drug candidate for many reasons, including:

• the drug candidate may not be deemed safe or effective;

• regulatory officials may not find the data from preclinical studies and clinical trials sufficient;

• the FDA or foreign regulatory authority might not approve our or our third-party manufacturers’ processes or facilities; or

• the FDA or foreign regulatory authority may change its approval policies or adopt new regulations.

We may be subject to costly claims related to our clinical trials and may not be able to obtain adequate insurance.

Because we conduct clinical trials in humans, we face the risk that the use of vosaroxin or future product candidates, if any, will result in adverse side effects. We cannot predict the possible harms or side effects that may result from our clinical trials. Although we have clinical trial liability insurance for up to $10.0 million in aggregate, our insurance may be insufficient to cover any such events. We do not know whether we will be able to continue to obtain clinical trial coverage on acceptable terms, or at all. We may not have sufficient resources to pay for any liabilities resulting from a claim excluded from, or beyond the limit of, our insurance coverage. There is also a risk that third parties that we have agreed to indemnify could incur liability. Any litigation arising from our clinical trials, even if we were ultimately successful, would consume substantial amounts of our financial and managerial resources and may create adverse publicity.

Even if we receive regulatory approval to sell vosaroxin, the market may not be receptive to vosaroxin.

Even if vosaroxin obtains regulatory approval, it may not gain market acceptance among physicians, patients, healthcare payors and/or the medical community. We believe that the degree of market acceptance will depend on a number of factors, including:

• timing of market introduction of competitive products;

• efficacy of our product;

• prevalence and severity of any side effects;

• potential advantages or disadvantages over alternative treatments;

• strength of marketing and distribution support;

• price of vosaroxin, both in absolute terms and relative to alternative treatments; and

• availability of reimbursement from health maintenance organizations and other third-party payors.

For example, the potential toxicity of single and repeated doses of vosaroxin has been explored in a number of animal studies that suggest the dose-limiting toxicities in humans receiving vosaroxin may be similar to some of those observed with approved cytotoxic agents, including reversible toxicity to bone marrow cells, the gastrointestinal system and other systems with rapidly dividing cells. In our Phase 1 and Phase 2 clinical trials of vosaroxin, we have witnessed the following side effects, irrespective of causality, ranging from mild to more severe: lowered white blood cell count that may lead to a serious or possibly life-threatening infection, hair loss, mouth sores, fatigue, nausea with or without vomiting, lowered platelet count, which may lead to an increase in bruising or bleeding, lowered red blood cell count (anemia), weakness, tiredness, shortness of breath, diarrhea and intestinal blockage.

If vosaroxin fails to achieve market acceptance, due to unacceptable side effects or any other reasons, we may not be able to generate significant revenue or to achieve or sustain profitability.

Even if we receive regulatory approval for vosaroxin, we will be subject to ongoing FDA and other regulatory obligations and continued regulatory review, which may result in significant additional expense and limit our ability to commercialize vosaroxin.

Any regulatory approvals that we or our potential future collaboration partners receive for vosaroxin or our future product candidates, if any, may also be subject to limitations on the indicated uses for which the product may be marketed or contain requirements for potentially costly post-marketing trials. In addition, even if approved, the labeling, packaging, adverse event reporting, storage, advertising, promotion and recordkeeping for any product will be subject to extensive and ongoing regulatory requirements. The subsequent discovery of previously unknown problems with a product, including adverse events of unanticipated severity or frequency, may result in restrictions on the marketing of the product, and could include withdrawal of the product from the market.

Regulatory policies may change and additional government regulations may be enacted that could prevent or delay regulatory approval of our product candidates. We cannot predict the likelihood, nature or extent of government regulation that may arise from future legislation or administrative action, either in the United States or abroad. If we are not able to maintain regulatory compliance, we might not be permitted to market vosaroxin or our future products and we may not achieve or sustain profitability.

The coverage and reimbursement status of newly approved drugs is uncertain, and failure to obtain adequate coverage and reimbursement could limit our ability to market vosaroxin and decrease our ability to generate revenue.

There is significant uncertainty related to the third party coverage and reimbursement of newly approved drugs both nationally and internationally. The commercial success of vosaroxin and our future products, if any, in both domestic and international markets depends on whether third-party coverage and reimbursement is available for the ordering of our future products by the medical profession for use by their patients. Medicare, Medicaid, health maintenance organizations and other third-party payors are increasingly attempting to manage healthcare costs by limiting both coverage and the level of reimbursement of new drugs and, as a result, they may not cover or provide adequate payment for our future products. These payors may not view our future products as cost-effective, and reimbursement may not be available to consumers or may not be sufficient to allow our future products to be marketed on a competitive basis. Likewise, legislative or regulatory efforts to control or reduce healthcare costs or reform government healthcare programs could result in lower prices or rejection of our future products. Changes in coverage and reimbursement policies or healthcare cost containment initiatives that limit or restrict reimbursement for our future products may reduce any future product revenue.

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Failure to obtain regulatory approval in foreign jurisdictions will prevent us from marketing vosaroxin abroad.

We intend to market vosaroxin in international markets either directly or through a potential future collaboration partner, if any. In order to market vosaroxin in the European Union, Canada and many other foreign jurisdictions, we or a potential future collaboration partner must obtain separate regulatory approvals. We have, and potential future collaboration partners may have, had limited interactions with foreign regulatory authorities, and the approval procedures vary among countries and can involve additional testing at significant cost. The time required to obtain approval may differ from that required to obtain FDA approval. Approval by the FDA does not ensure approval by regulatory authorities in other countries, and approval by one foreign regulatory authority does not ensure approval by regulatory authorities in other foreign countries or by the FDA. The foreign regulatory approval processes may include all of the risks associated with obtaining FDA approval. We or a potential future collaboration partner may not obtain foreign regulatory approvals on a timely basis, if at all. We or a potential future collaboration partner may not be able to file for regulatory approvals and may not receive necessary approvals to commercialize vosaroxin or any other future products in any market.

Foreign governments often impose strict price controls, which may adversely affect our future profitability.

We intend to seek approval to market vosaroxin in both the United States and foreign jurisdictions either directly or through a potential future collaboration partner. If we or a potential future collaboration partner obtain approval in one or more foreign jurisdictions, we or a potential future collaboration partner will be subject to rules and regulations in those jurisdictions relating to vosaroxin. In some foreign countries, particularly in the European Union, prescription drug pricing is subject to governmental control. In these countries, pricing negotiations with governmental authorities can take considerable time after the receipt of marketing approval for a drug candidate. To obtain reimbursement or pricing approval in some countries, we or a potential future collaboration partner may be required to conduct a clinical trial that compares the cost-effectiveness of vosaroxin to other available therapies. If reimbursement of vosaroxin is unavailable or limited in scope or amount, or if pricing is set at unsatisfactory levels, we may be unable to achieve or sustain profitability.

We may incur significant costs complying with environmental laws and regulations, and failure to comply with these laws and regulations could expose us to significant liabilities.

We, through third-party contractors, use hazardous chemicals and radioactive and biological materials in our business and are subject to a variety of federal, state, regional and local laws and regulations governing the use, generation, manufacture, storage, handling and disposal of these materials. Although we believe our safety procedures for handling and disposing of these materials and waste products comply with these laws and regulations, we cannot eliminate the risk of accidental injury or contamination from the use, storage, handling or disposal of hazardous materials. In the event of contamination or injury, we could be held liable for any resulting damages, and any liability could significantly exceed our insurance coverage, which is limited for pollution cleanup and contamination.

Risks Related to Our Common Stock

The price of our common stock may continue to be volatile, and the value of an investment in our common stock may decline.*

In the six months ended June 30, 2012, our common stock traded as low as $1.17 and as high as $3.19, and in 2011, traded as low as $1.01 and as high as $3.21. Factors that could cause continued volatility in the market price of our common stock include, but are not limited to:

• our ability to raise additional capital to carry through with our clinical development plans and current and future operations and the terms of any related financing arrangement;

• results from, and any delays in or discontinuance of, ongoing and planned clinical trials for vosaroxin;

• an expansion of the number of patients included in the VALOR trial based on the pre-specified interim analysis by the DSMB;

• announcements of FDA non-approval of vosaroxin, delays in filing regulatory documents with the FDA or other regulatory agencies, or delays in the review process by the FDA or other foreign regulatory agencies;

• announcements relating to restructuring and other operational changes;

• delays in the commercialization of vosaroxin or our future products, if any;

• market conditions in the pharmaceutical, biopharmaceutical and biotechnology sectors;

• issuance of new or changed securities analysts’ reports or recommendations;

• developments or disputes concerning our intellectual property or other proprietary rights;

• clinical and regulatory developments with respect to potential competitive products;

• failure to maintain compliance with the covenants in our Loan Agreement;

• introduction of new products by our competitors;

• issues in manufacturing vosaroxin drug substance or drug product, or future products, if any;

• market acceptance of vosaroxin or our future products, if any;

• announcements relating to our arrangements with Biogen Idec, Millennium or RPI;

• actual and anticipated fluctuations in our quarterly operating results;

• deviations in our operating results from the estimates of analysts;

• third-party healthcare reimbursement policies;

• FDA or other U.S. or foreign regulatory actions affecting us or our industry;

• litigation or public concern about the safety of vosaroxin or future products, if any;

• failure to develop or sustain an active and liquid trading market for our common stock;

• sales of our common stock by our officers, directors or significant stockholders; and

• additions or departures of key personnel.

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If we fail to maintain compliance with the continued listing requirements of The NASDAQ Capital Market, our common stock may be delisted and the price of our common stock and our ability to access the capital markets could be negatively impacted.

Our common stock currently trades on The NASDAQ Capital Market under the symbol “SNSS.” This market has continued listing standards that we must comply with in order to maintain the listing of our common stock. The continued listing standards include, among others, a minimum bid price requirement of $1.00 per share and any of: (i) a minimum stockholders’ equity of $2.5 million; (ii) a market value of listed securities of at least $35.0 million; or (iii) net income from continuing operations of $500,000 in the most recently completed fiscal year or in the two of the last three fiscal years. Our results of operations and fluctuating stock price directly impact our ability to satisfy these continued listing standards. In the event we are unable to maintain these continued listing standards, our common stock may be subject to delisting from The NASDAQ Capital Market.

We have been out of compliance with the minimum bid price requirement in the past, and as mentioned above, the price of our common stock can be volatile; accordingly, there can be no assurance that we will continue to meet the minimum $1.00 bid price requirement or the other NASDAQ continued listing requirements in the future, and we may be subject to delisting as a result. If we are delisted, we would expect our common stock to be traded in the over-the-counter market, which could adversely affect the liquidity of our common stock. Additionally, we could face significant material adverse consequences, including:

• a limited availability of market quotations for our common stock;

• a reduced amount of analyst coverage for us;

• a decreased ability to issue additional securities or obtain additional financing in the future;

• reduced liquidity for our stockholders;

• potential loss of confidence by collaboration partners and employees; and

• loss of institutional investor interest.

Provisions of our charter documents or Delaware law could delay or prevent an acquisition of our company, even if the acquisition would be beneficial to our stockholders, and could make it more difficult to change management.

Provisions of our amended and restated certificate of incorporation and amended and restated bylaws may discourage, delay or prevent a merger, acquisition or other change in control that stockholders might otherwise consider favorable, including transactions in which stockholders might otherwise receive a premium for their shares. In addition, these provisions may frustrate or prevent any attempt by our stockholders to replace or remove our current management by making it more difficult to replace or remove our board of directors. These provisions include:

• a classified board of directors so that not all directors are elected at one time;

• a prohibition on stockholder action through written consent;

• limitations on our stockholders’ ability to call special meetings of stockholders;

• an advance notice requirement for stockholder proposals and nominations; and

• the authority of our board of directors to issue preferred stock with such terms as our board of directors may determine.

In addition, Delaware law prohibits a publicly held Delaware corporation from engaging in a business combination with an interested stockholder, generally a person who, together with its affiliates, owns or within the last three years has owned 15% of our voting stock, for a period of three years after the date of the transaction in which the person became an interested stockholder, unless the business combination is approved in a prescribed manner. Accordingly, Delaware law may discourage, delay or prevent a change in control of our company.

Provisions in our charter documents and provisions of Delaware law could limit the price that investors are willing to pay in the future for shares of our common stock.

The ownership of our capital stock is highly concentrated, and your interests may conflict with the interests of our existing stockholders.

Our executive officers and directors and their affiliates beneficially owned approximately 36.7% of our outstanding capital stock as of June 30, 2012, assuming the exercise in full of the outstanding warrants to purchase common stock held by these stockholders as of such date. Accordingly, these stockholders, acting as a group, could have significant influence over the outcome of corporate actions requiring stockholder approval, including the election of directors, any merger, consolidation or sale of all or substantially all of our assets or any other significant corporate transaction. The significant concentration of stock ownership may adversely affect the trading price of our common stock due to investors’ perception that conflicts of interest may exist or arise.

We have never paid dividends on our capital stock and we do not anticipate paying any cash dividends in the foreseeable future.

We have never declared or paid cash dividends on our capital stock. We do not anticipate paying any cash dividends on our capital stock in the foreseeable future. In addition, under the terms of our Loan Agreement with the Lenders, we are precluded from paying cash dividends without the prior written consent of the lenders. We currently intend to retain all available funds and any future earnings to fund the development and growth of our business. As a result, capital appreciation, if any, of our common stock will be our stockholders’ sole source of gain for the foreseeable future.

We are at risk of securities class action litigation.

In the past, securities class action litigation has often been brought against a company following a decline in the market price of its securities. This risk is especially relevant for us because biotechnology companies have experienced greater than average stock price volatility in recent years. These broad market fluctuations may adversely affect the trading price or liquidity of our common stock. In the past, when the market price of a stock has been volatile, holders of that stock have sometimes instituted securities class action litigation against the issuer. If any of our stockholders were to bring such a lawsuit against us, we could incur substantial costs defending the lawsuit and the attention of our management would be diverted from the operation of our business.

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

None.

Item 3. Defaults Upon Senior Securities

None.

Item 4. Mine Safety Disclosures

Not applicable.

Item 5. Other Information

None.

Item 6. Exhibits

A list of exhibits filed with this report or incorporated herein by reference is found in the Exhibit Index immediately following the signature page of this report.

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SIGNATURE

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.

	SUNESIS PHARMACEUTICALS, INC. (Registrant)
Date: August 9, 2012	/s/    ERIC H. BJERKHOLT
	Eric H. Bjerkholt
	Executive Vice President, Corporate Development and Finance, Chief Financial Officer and Corporate Secretary

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EXHIBIT INDEX

Exhibit Number		Incorporated By Reference							Filed Herewith
	Exhibit Description	Form	File No.		Exhibit		Filing Date
3.1	Amended and Restated Certificate of Incorporation of the Registrant	10-K/A		000-51531		3.1		5/23/2007
3.2	Amended and Restated Bylaws of the Registrant	8-K		000-51531		3.2		12/11/2007
3.3	Certificate of Designation of the Series A Preferred Stock of the Registrant	8-K		000-51531		3.3		4/3/2009
3.4	Certificate of Amendment to the Amended and Restated Certificate of Incorporation of the Registrant	S-8		333-160528		3.4		7/10/2009
3.5	Certificate of Amendment to the Certificate of Designation of the Series A Preferred Stock of the Registrant	8-K		000-51531		3.4		11/2/2009
3.6	Certificate of Amendment to the Certificate of Designation of the Series A Preferred stock of the Registrant	8-K		000-51531		3.5		1/21/2010
3.7	Certificate of Amendment to the Amended and Restated Certificate of Incorporation of the Registrant	8-K		000-51531		3.1		2/14/2011
4.1	Reference is made to Exhibits 3.1, 3.2, 3.3, 3.4, 3.5, 3.6 and 3.7 above.
4.2	Specimen Common Stock certificate of the Registrant	10-K		000-51531		4.2		3/29/2011
4.3	Investor Rights Agreement, dated April 3, 2009, by and among the Registrant and the purchasers identified on the signature pages thereto	8-K		000-51531		4.1		4/3/2009
31.1	Certification of Chief Executive Officer pursuant to Rule 13a-14(a) or Rule 15d-14(a) of the Exchange Act								X
31.2	Certification of Chief Financial Officer pursuant to Rule 13a-14(a) or Rule 15d-14(a) of the Exchange Act								X
32.1#	Certification of Chief Executive Officer and Chief Financial Officer pursuant to 13a-14(b) or 15d-14(b) of the Exchange Act								X
101.INS	XBRL Instance Document								(1)
101.SCH	XBRL Taxonomy Extension Schema Document								(1)
101.CAL	XBRL Taxonomy Extension Calculation Linkbase Document								(1)
101.LAB	XBRL Taxonomy Extension Labels Linkbase Document								(1)
101.PRE	XBRL Taxonomy Extension Presentation Linkbase Document								(1)

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# In accordance with Item 601(b)(32)(ii) of Regulation S-K and SEC Release Nos. 33-8238 and 34-47986, Final Rule; Management’s Reports on Internal Control over Financial Reporting and Certification of Disclosure in Exchange Act Periodic Reports, the Certification furnished in Exhibit 32.1 hereto is deemed to accompany this Form 10-Q and will not be filed for purposes of Section 18 of the Exchange Act. Such certification will not be deemed incorporated by reference into any filing under the Securities Act or the Exchange Act, except to the extent that the registrant specifically incorporates it by reference.

(1) Pursuant to applicable securities laws and regulations, the Registrant is deemed to have complied with the reporting obligation relating to the submission of interactive data files in such exhibits and is not subject to liability under any anti-fraud provisions of the federal securities laws as long as the Registrant has made a good faith attempt to comply with the submission requirements and promptly amends the interactive data files after becoming aware that the interactive data files fails to comply with the submission requirements. These interactive data files are deemed not filed or part of a registration statement or prospectus for purposes of sections 11 or 12 of the Securities Act are deemed not filed for purposes of section 18 of the Exchange Act.

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EX-31.1

Exhibit 31.1

Certification of Chief Executive Officer

I, Daniel N. Swisher, Jr., certify that:

1. I have reviewed this quarterly report on Form 10-Q of Sunesis Pharmaceuticals, Inc.;

2. Based on my knowledge, this report does not contain any untrue statement of a material fact or omit to state a material fact necessary to make the statements made, in light of the circumstances under which such statements were made, not misleading with respect to the period covered by this report;

3. Based on my knowledge, the financial statements, and other financial information included in this report, fairly present in all material respects the financial condition, results of operations and cash flows of the registrant as of, and for, the periods presented in this report;

4. The registrant’s other certifying officer and I are responsible for establishing and maintaining disclosure controls and procedures (as defined in Exchange Act Rules 13a-15(e) and 15d-15(e)) and internal control over financial reporting (as defined in Exchange Act Rules 13a-15(f) and 15d-15(f)) for the registrant and have:

a) designed such disclosure controls and procedures, or caused such disclosure controls and procedures to be designed under our supervision, to ensure that material information relating to the registrant, including its consolidated subsidiaries, is made known to us by others within those entities, particularly during the period in which this report is being prepared;

b) designed such internal control over financial reporting, or caused such internal control over financial reporting to be designed under our supervision, to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles;

c) evaluated the effectiveness of the registrant’s disclosure controls and procedures and presented in this report our conclusions about the effectiveness of the disclosure controls and procedures, as of the end of the period covered by this report based on such evaluation; and

d) disclosed in this report any change in the registrant’s internal control over financial reporting that occurred during the registrant’s most recent fiscal quarter (the registrant’s fourth fiscal quarter in the case of an annual report) that has materially affected, or is reasonably likely to materially affect, the registrant’s internal control over financial reporting; and

5. The registrant’s other certifying officer and I have disclosed, based on our most recent evaluation of internal control over financial reporting, to the registrant’s auditors and the audit committee of the registrant’s board of directors (or persons performing the equivalent functions):

a) all significant deficiencies and material weaknesses in the design or operation of internal control over financial reporting which are reasonably likely to adversely affect the registrant’s ability to record, process, summarize and report financial information; and

b) any fraud, whether or not material, that involves management or other employees who have a significant role in the registrant’s internal control over financial reporting.

Date: August 9, 2012	/s/    DANIEL N. SWISHER, JR.
	Daniel N. Swisher, Jr. President and Chief Executive Officer

EX-31.2

Exhibit 31.2

Certification of Chief Financial Officer

I, Eric H. Bjerkholt, certify that:

1. I have reviewed this quarterly report on Form 10-Q of Sunesis Pharmaceuticals, Inc.;

2. Based on my knowledge, this report does not contain any untrue statement of a material fact or omit to state a material fact necessary to make the statements made, in light of the circumstances under which such statements were made, not misleading with respect to the period covered by this report;

3. Based on my knowledge, the financial statements, and other financial information included in this report, fairly present in all material respects the financial condition, results of operations and cash flows of the registrant as of, and for, the periods presented in this report;

4. The registrant’s other certifying officer and I are responsible for establishing and maintaining disclosure controls and procedures (as defined in Exchange Act Rules 13a-15(e) and 15d-15(e)) and internal control over financial reporting (as defined in Exchange Act Rules 13a-15(f) and 15d-15(f)) for the registrant and have:

a) designed such disclosure controls and procedures, or caused such disclosure controls and procedures to be designed under our supervision, to ensure that material information relating to the registrant, including its consolidated subsidiaries, is made known to us by others within those entities, particularly during the period in which this report is being prepared;

b) designed such internal control over financial reporting, or caused such internal control over financial reporting to be designed under our supervision, to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles;

c) evaluated the effectiveness of the registrant’s disclosure controls and procedures and presented in this report our conclusions about the effectiveness of the disclosure controls and procedures, as of the end of the period covered by this report based on such evaluation; and

d) disclosed in this report any change in the registrant’s internal control over financial reporting that occurred during the registrant’s most recent fiscal quarter (the registrant’s fourth fiscal quarter in the case of an annual report) that has materially affected, or is reasonably likely to materially affect, the registrant’s internal control over financial reporting; and

5. The registrant’s other certifying officer and I have disclosed, based on our most recent evaluation of internal control over financial reporting, to the registrant’s auditors and the audit committee of the registrant’s board of directors (or persons performing the equivalent functions):

a) all significant deficiencies and material weaknesses in the design or operation of internal control over financial reporting which are reasonably likely to adversely affect the registrant’s ability to record, process, summarize and report financial information; and

b) any fraud, whether or not material, that involves management or other employees who have a significant role in the registrant’s internal control over financial reporting.

Date: August 9, 2012	/s/    ERIC H. BJERKHOLT
	Eric H. Bjerkholt
	Executive Vice President, Corporate Development and Finance, Chief Financial Officer and Corporate Secretary

EX-32.1

Exhibit 32.1

Certification

Pursuant to the requirement set forth in Rule 13a-14(b) of the Securities Exchange Act of 1934, as amended, (the “Exchange Act”) and Section 1350 of Chapter 63 of Title 18 of the United States Code (18 U.S.C. §1350), Daniel N. Swisher, Jr., President and Chief Executive Officer and Eric H. Bjerkholt, Executive Vice President, Corporate Development and Finance and Chief Financial Officer, of Sunesis Pharmaceuticals, Inc. (the “Company”), each hereby certifies that, to the best of his knowledge:

1. The Company’s Quarterly Report on Form 10-Q for the period ended June 30, 2012, to which this Certification is attached as Exhibit 32.1 (the “Periodic Report”), fully complies with the requirements of Section 13(a) or Section 15(d) of the Exchange Act; and

2. The information contained in the Periodic Report fairly presents, in all material respects, the financial condition and results of operations of the Company.

Date: August 9, 2012	/s/    DANIEL N. SWISHER, JR.
	Daniel N. Swisher, Jr. President and Chief Executive Officer
Date: August 9, 2012	/s/    ERIC H. BJERKHOLT
	Eric H. Bjerkholt
	Executive Vice President, Corporate Development and Finance, Chief Financial Officer and Corporate Secretary

This certification accompanies the Form 10-Q to which it relates, is not deemed filed with the Securities and Exchange Commission and is not to be incorporated by reference into any filing of Sunesis Pharmaceuticals, Inc. under the Securities Act of 1933, as amended, or the Securities Exchange Act of 1934, as amended (whether made before or after the date of the Form 10-Q), irrespective of any general incorporation language contained in such filing.

XML

Financial Instruments (Details) (USD $) In Thousands, unless otherwise specified	Jun. 30, 2012	Dec. 31, 2011
Fair value of Company's financial assets measured on recurring basis
Available-for-sale securities, Amortized Cost	$ 29,134	$ 43,414
Available-for-sale securities, Gross Unrealized Gains	3	24
Available-for-sale securities, Gross unrealized losses	(8)	(4)
Available-for-sale securities, Estimated Fair Value	29,129	43,434
Less: amounts classified as cash equivalents, Amortized Cost	11,597	8,632
Less: amounts classified as cash equivalents Gross Unrealized Gains	1
Less: amounts classified as cash equivalents, Gross Unrealized Losses		(2)
Less: amounts classified as cash equivalents, Estimated Fair Value	11,598	8,630
Amounts classified as marketable securities, Amortized Cost	17,537	34,782
Amounts classified as marketable securities, Gross Unrealized Gains	2	24
Amounts classified as marketable securities, Gross Unrealized Losses	(8)	(2)
Amounts classified as marketable securities, Estimated Fair Value	17,531	34,804	[1]
Level 1 [Member] | Money market funds [Member]
Fair value of Company's financial assets measured on recurring basis
Available-for-sale securities, Amortized Cost	8,848	7,156
Available-for-sale securities, Gross Unrealized Gains
Available-for-sale securities, Gross unrealized losses
Available-for-sale securities, Estimated Fair Value	8,848	7,156
Level 2 [Member] | Foreign government obligations [Member]
Fair value of Company's financial assets measured on recurring basis
Available-for-sale securities, Amortized Cost		3,607
Available-for-sale securities, Gross Unrealized Gains		1
Available-for-sale securities, Gross unrealized losses
Available-for-sale securities, Estimated Fair Value		3,608
Level 2 [Member] | Foreign corporate debt obligations [Member]
Fair value of Company's financial assets measured on recurring basis
Available-for-sale securities, Amortized Cost	3,954	1,476
Available-for-sale securities, Gross Unrealized Gains
Available-for-sale securities, Gross unrealized losses	(8)	(3)
Available-for-sale securities, Estimated Fair Value	3,946	1,473
Level 2 [Member] | Corporate debt obligations [Member]
Fair value of Company's financial assets measured on recurring basis
Available-for-sale securities, Amortized Cost	7,587	16,619
Available-for-sale securities, Gross Unrealized Gains		5
Available-for-sale securities, Gross unrealized losses		(1)
Available-for-sale securities, Estimated Fair Value	7,587	16,623
Level 2 [Member] | Commercial paper [Member]
Fair value of Company's financial assets measured on recurring basis
Available-for-sale securities, Amortized Cost	8,745	14,556
Available-for-sale securities, Gross Unrealized Gains	3	18
Available-for-sale securities, Gross unrealized losses
Available-for-sale securities, Estimated Fair Value	$ 8,748	$ 14,574

[1] The condensed consolidated balance sheet as of December 31, 2011 has been derived from the audited financial statements as of that date included in the Company's Annual Report on Form 10-K for the year ended December 31, 2011

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Notes Payable

6 Months Ended

Jun. 30, 2012

Notes Payable [Abstract]

Notes Payable

5. Notes Payable

On October 18, 2011, the Company entered into the Loan Agreement with the Lenders, under which the Company may borrow up to $25.0 million in two tranches (the “Loan Facility”). The first tranche of $10.0 million was funded upon closing of the transaction on October 18, 2011. Subject to the Company’s continued compliance with the terms and conditions of the Loan Facility, the second tranche of $15.0 million may be drawn at the Company’s option between June 30, 2012 and September 30, 2012, contingent upon the recommendation by the DSMB following the interim analysis of the VALOR trial to either: (a) discontinue the trial due to positive efficacy, or (b) continue the trial.

The interest rate for the first tranche is 8.95% per annum, and the interest rate for the second tranche will be fixed upon drawdown at a per annum rate equal to the greater of: (a) 8.95%, or (b) 8.61% plus the then effective three-month U.S. LIBOR rate. Payments under the Loan Agreement are monthly in arrears and interest-only until February 1, 2013, followed by 32 equal monthly payments of principal and interest through the scheduled maturity date of October 1, 2015. In addition, a final payment equal to 3.75% of the aggregate amount drawn will be due on October 1, 2015, or such earlier date specified in the Loan Agreement. If the Company repays all or a portion of the loans prior to maturity, it will pay the Lenders a prepayment fee of between 1-3% of the principal amount prepaid.

In accordance with the terms of the Loan Agreement, the Company agreed to issue five-year warrants to the Lenders upon each drawdown to purchase shares of common stock in an amount equal to 5.0% of the amount drawn at such tranche, divided by the exercise price per share, which is determined in each case to be the lower of: (a) the 10-day average closing share price prior to the drawdown, or (b) the closing price per share the day prior to the drawdown. As a result of the drawdown of the first tranche of $10.0 million, the Company issued warrants to purchase 386,100 shares of its common stock at an exercise price of $1.30 per share. The warrants may be exercised on a cashless basis, and will expire on October 18, 2016. As of June 30, 2012, the warrants remained outstanding and exercisable.

Future minimum payments under the Loan agreement as of June 30, 2012 were as follows (in thousands):

Period ending December 31,
2012	$	447
2013		3,674
2014		4,229
2015		3,524
Total minimum payments		11,874
Less: amount representing interest		(1,874	)
Notes payable, gross		10,000
Unamortized discount on notes payable		(460	)
Accretion of the final payment		97
Notes payable, balance		9,637
Current portion of notes payable		(900	)
Non-current portion of notes payable	$	8,737

The Company recorded interest expense related to the loan of $0.3 million and $0.6 million for the three and six months ended June 30, 2012, respectively. The annual effective interest rate on the note payable, including the amortization of the debt discounts and accretion of the final payments, is 13.1%.

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Financial Instruments (Details Textual) (USD $)	6 Months Ended
	Jun. 30, 2012	Jun. 30, 2011
Financial Instruments (Textual) [Abstract]
Realized gain (loss) on sales of available-for-sale securities	$ 0	$ 0
Initial fair value of warrant liability	$ 4,500,000

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Financial Instruments (Details 3) (USD $) In Thousands, unless otherwise specified	6 Months Ended			12 Months Ended
	Jun. 30, 2012		Jun. 30, 2011	Dec. 31, 2011
Summary of the changes in the fair value of the Company's Level 3 financial liabilities
Beginning Balance	$ 2,276	[1]	$ 8,154	$ 8,154
Change in fair value of warrant liability	4,126		(3,241)	(5,878)
Ending Balance	$ 6,402			$ 2,276	[1]

[1] The condensed consolidated balance sheet as of December 31, 2011 has been derived from the audited financial statements as of that date included in the Company's Annual Report on Form 10-K for the year ended December 31, 2011

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Stockholders' Equity (Details) (USD $) In Millions, except Share data, unless otherwise specified	3 Months Ended	6 Months Ended
	Jun. 30, 2011	Jun. 30, 2012	Aug. 11, 2011	Apr. 29, 2010
Stockholders' Equity (Textual) [Abstract]
Issuance of common stock, offering value				$ 20.0
Issuance of common stock, remaining offering value		1.7
Common stock, shares sold		88,500
Stockholders' Equity (Additional Textual) [Abstract]
Issuance of common stock, commission percentage		3.00%	3.00%	3.00%
Common stock, price per share	$ 4.08	$ 3.08
Proceeds from issuance of common stock through controlled equity offering facilities, gross	18.3	0.3
Proceeds from issuance of common stock through controlled equity offering facilities, net	17.7	0.3
Common stock remained available for sale		20
Additional Controlled Equity Offerings Facilities [Member]
Stockholders' Equity (Textual) [Abstract]
Issuance of common stock, offering value			20.0
Issuance of common stock, remaining offering value		$ 20.0
Sales of shares		0
Common stock, shares sold		4,471,783

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Stock-Based Compensation (Details) (USD $) In Thousands, unless otherwise specified	3 Months Ended		6 Months Ended
	Jun. 30, 2012	Jun. 30, 2011	Jun. 30, 2012	Jun. 30, 2011
Summary of stock-based compensation expense related to the Company's stock-based awards
Total stock-based compensation expense	$ 577	$ 135	$ 1,145	$ 344
Employee stock-based compensation expense [Member]
Summary of stock-based compensation expense related to the Company's stock-based awards
Total stock-based compensation expense	560	132	1,103	337
Non-employee stock-based compensation expense [Member]
Summary of stock-based compensation expense related to the Company's stock-based awards
Total stock-based compensation expense	17	3	42	7
Research and development [Member]
Summary of stock-based compensation expense related to the Company's stock-based awards
Total stock-based compensation expense	207	65	433	139
General and administrative [Member]
Summary of stock-based compensation expense related to the Company's stock-based awards
Total stock-based compensation expense	$ 353	$ 67	$ 670	$ 198

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Royalty Agreement

6 Months Ended

Jun. 30, 2012

Royalty Agreement [Abstract]

Royalty Agreement

4. Royalty Agreement

On March 29, 2012, the Company entered into a Revenue Participation Agreement (the “Royalty Agreement”), with RPI Finance Trust (“RPI”), an entity related to Royalty Pharma, under which RPI may acquire a revenue participation right (the “Revenue Participation Right”), for $25.0 million. RPI will be obligated to purchase the Revenue Participation Right if, following the interim efficacy analysis of data from the VALOR trial, the independent Data and Safety Monitoring Board (“DSMB”), recommends that the Company undertake a one-time 225 patient increase in sample size for the VALOR trial, or terminates the VALOR trial for efficacy, and the Company follows such recommendation. If the DSMB recommends that the Company continue the VALOR trial with the planned sample size of 450 patients, RPI will have the option to purchase the Revenue Participation Right following unblinding of the VALOR trial.

The applicable Revenue Participation Right payments are determined as follows: (a) if the DSMB recommends a stop for efficacy at the interim analysis, 3.6% of net sales; (b) if RPI exercises its option following continuation of the VALOR trial as planned, 3.6% of net sales; or (c) if the DSMB recommends a one-time increase in enrollment of the VALOR trial at the interim analysis, 6.75% of net sales. Revenue Participation Right payments will be made to RPI on a product-by-product and country-by-country basis world-wide through the later of: (i) the expiration of the last to expire of certain specifically identified patents, (ii) 10 years from the date of first commercial sale of such product in such country; or (iii) the expiration of all applicable periods of data, market or other regulatory exclusivity in such country with respect to such product.

In conjunction with entering into the Royalty Agreement, the Company issued two five-year warrants to RPI, each to purchase 1,000,000 shares of the Company’s common stock, at exercise prices of $3.48 and $4.64 per share, respectively. RPI has the right to exercise the warrants only if the DSMB recommends that the Company expand enrollment of the VALOR trial, and the Company follows such recommendation. If the DSMB issues any other recommendation, the warrants will terminate.

If, following the purchase of the Revenue Participation Right by RPI, the Company fails to make payments due to RPI under the Royalty Agreement in a timely manner, RPI may require the Company to repurchase the Revenue Participation Right. Additionally, as collateral for these payments, the Company agreed to grant RPI a security interest in certain of the Company’s assets, including the Company’s intellectual property related to vosaroxin. The security interest will be granted at the time of any purchase of the Revenue Participation Right but may only be perfected following first product approval in any country or territory. The security interest will be released upon the satisfaction of certain conditions specified in the Agreement. In connection with entering into the Royalty Agreement, the Company amended its Loan and Security Agreement, dated October 18, 2011 (the “Loan Agreement”), with Oxford Finance LLC, Silicon Valley Bank and Horizon Technology Finance Corporation (collectively, the “Lenders”) (see Note 5), to permit the grant of the security interest to RPI, and to concurrently grant to the Lenders a security interest in the same assets, which may also be perfected following the first product approval in any country or territory, to secure the Company’s obligations under the Loan Agreement. The Lenders will retain a senior position to the RPI security interest for so long as any indebtedness under the Loan Agreement remains outstanding.

RPI may terminate the Royalty Agreement without purchasing the Revenue Participation Right if the interim analysis of the VALOR trial is not completed by the end of 2012 or if the DSMB does not issue its recommendation by such date. In addition, the Royalty Agreement will terminate automatically if the DSMB recommends that the Company terminate the VALOR trial for futility. If RPI purchases the Revenue Participation Right, the Royalty Agreement will automatically terminate after all payment obligations to RPI have been satisfied.

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Condensed Consolidated Balance Sheets (USD $) In Thousands, unless otherwise specified	Jun. 30, 2012	Dec. 31, 2011
Current assets:
Cash and cash equivalents	$ 11,743	$ 9,311	[1]
Marketable securities	17,531	34,804	[1]
Prepaids and other current assets	1,602	1,550	[1]
Total current assets	30,876	45,665	[1]
Property and equipment, net	58	74	[1]
Deposits and other assets	108	130	[1]
Total assets	31,042	45,869	[1]
Current liabilities:
Accounts payable	393	658	[1]
Accrued clinical expense	3,982	2,370	[1]
Accrued compensation	780	1,274	[1]
Other accrued liabilities	2,749	1,805	[1]
Current portion of notes payable	900		[1]
Warrant liability	6,402	2,276	[1]
Total current liabilities	15,206	8,383	[1]
Non-current portion of notes payable	8,737	9,453	[1]
Non-current portion of deferred rent		13	[1]
Commitments			[1]
Stockholders' equity:
Common stock	5	5	[1]
Additional paid-in capital	430,748	429,142	[1]
Accumulated other comprehensive income (loss)	(5)	19	[1]
Accumulated deficit	(423,649)	(401,146)	[1]
Total stockholders' equity	7,099	28,020	[1]
Total liabilities and stockholders' equity	$ 31,042	$ 45,869	[1]

[1] The condensed consolidated balance sheet as of December 31, 2011 has been derived from the audited financial statements as of that date included in the Company's Annual Report on Form 10-K for the year ended December 31, 2011

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Summary of Significant Accounting Policies

6 Months Ended

Jun. 30, 2012

Summary of Significant Accounting Policies [Abstract]

Summary of Significant Accounting Policies

2. Summary of Significant Accounting Policies

Basis of Presentation

The accompanying unaudited condensed consolidated financial statements have been prepared in accordance with U.S. generally accepted accounting principles (“GAAP”) for interim financial information and with the instructions to Form 10-Q and Rule 10-01 of Regulation S-X. Accordingly, they do not include all of the information and notes required by GAAP for complete financial statements. The financial statements include a wholly owned subsidiary, Sunesis Europe Limited, a United Kingdom corporation. Management has determined that the Company operates as a single reportable segment. The financial statements include all adjustments (consisting only of normal recurring adjustments) that management believes are necessary for a fair presentation of the periods presented. The balance sheet as of December 31, 2011 was derived from the audited financial statements as of that date. These interim financial results are not necessarily indicative of results to be expected for the full year or any other period. These unaudited condensed consolidated financial statements and the notes accompanying them should be read in conjunction with the Company’s Annual Report on Form 10-K for the year ended December 31, 2011.

Reverse Stock Split

On February 14, 2011, the Company effected a one-for-six reverse split of its capital stock (the “Reverse Split”), as previously authorized and approved at the annual meeting of stockholders on June 2, 2010. As a result of the Reverse Split, every six shares of capital stock were combined into one share of capital stock. The Reverse Split affected the shares of Company’s common stock: (a) outstanding immediately prior to the effective time of the Reverse Split, (b) available for issuance under the Company’s equity incentive plans, and (c) issuable upon the exercise of outstanding stock options and warrants. The accompanying financial statements and notes thereto give retroactive effect to the Reverse Split for all periods presented.

Significant Estimates and Judgments

The preparation of financial statements in conformity with GAAP requires management to make estimates and assumptions that affect the amounts reported in the Company’s condensed consolidated financial statements and accompanying notes. Actual results could differ materially from these estimates. Significant estimates, assumptions and judgments made by management include those related to the valuation of equity and related instruments, revenue recognition, stock-based compensation and clinical trial accounting.

Cash Equivalents and Marketable Securities

Invoices for certain services provided to the Company are denominated in foreign currencies. To manage the risk of future movements in foreign exchange rates that would affect such amounts, the Company may purchase certain European currencies or highly-rated investments denominated in those currencies, subject to similar criteria as for other investments defined in the Company’s investment policy. There is no guarantee that the related gains and losses will substantially offset each other, and the Company may be subject to significant exchange gains or losses as currencies fluctuate from quarter to quarter. To date, the Company has purchased Euros and Euro-denominated obligations of foreign governments and corporate debt, and as of June 30, 2012, held investments denominated in Euros with an aggregate fair value of $3.9 million. These cash, cash equivalent and short-term investment balances are recorded at their fair value based on the current exchange rate as of each balance sheet date. The resulting exchange gains or losses and those from amounts payable for services originally denominated in foreign currencies are both recorded in other income (expense) in the statements of operations and comprehensive income (loss).

Fair Value Measurements

The Company measures cash equivalents, marketable securities and warrant liabilities at fair value on a recurring basis using the following hierarchy to prioritize valuation inputs, in accordance with applicable GAAP:

Level 1 — quoted prices (unadjusted) in active markets for identical assets and liabilities that can be accessed at the measurement date.

Level 2 — inputs other than quoted prices included within Level 1 that are observable, either directly or indirectly.

Level 3 — unobservable inputs.

The Company’s Level 2 valuations of marketable securities are generally based upon quoted prices in active markets for similar securities, with prices adjusted for yield and number of days to maturity.

The fair value of the Company’s liability for warrants issued in connection with an underwritten offering completed in October 2010 is determined using the Black-Scholes model, which requires inputs such as the expected term of the warrants, share price volatility, expected dividend yield and risk-free interest rate. As some of these inputs are unobservable, and require significant analysis and judgment to measure, these variables are classified as Level 3.

The Company does not measure cash, prepayments, accounts payable, accrued liabilities and notes payable at fair value, as their carrying amounts approximated their fair value as of June 30, 2012 and December 31, 2011.

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Royalty Agreement (Details) (USD $) In Millions, except Share data, unless otherwise specified	6 Months Ended
	Jun. 30, 2012 Warrants Person	Mar. 29, 2012
Royalty Agreement (Textual) [Abstract]
Date of Loan and Security Agreement	Oct. 18, 2011
Warrant one [Member]
Royalty Agreement (Textual) [Abstract]
Warrant exercise prices	3.48
Warrant two [Member]
Royalty Agreement (Textual) [Abstract]
Warrant exercise prices	4.64
Royalty Agreement Terms [Member]
Royalty Agreement (Textual) [Abstract]
Amount for acquisition of Revenue Participation Right		$ 25.0
Potential one-time patient increase in sample size	225
Planned sample size of patients for the VALOR trial	450
Percentage of net sales as planned or stop for efficacy	3.60%
Percentage of net sales increase in sample size	6.75%
Maximum term of Revenue Participation Right Payments	10 years
Number of common shares issuable on exercise of warrants	1,000,000
Maturity of warrants	5 years
Date of Loan and Security Agreement	Oct. 18, 2011
Number of warrants issued	2

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Notes Payable (Details Textual) (USD $) In Millions, except Share data, unless otherwise specified	6 Months Ended	12 Months Ended	6 Months Ended		6 Months Ended			3 Months Ended	6 Months Ended
	Jun. 30, 2012 Installment	Dec. 31, 2011	Jun. 30, 2012 Tranche One [Member]	Oct. 18, 2011 Tranche One [Member]	Jun. 30, 2012 Tranche Two [Member]	Jun. 30, 2012 Maximum [Member]	Jun. 30, 2012 Minimum [Member]	Jun. 30, 2012 Notes Payable [Member]	Jun. 30, 2012 Notes Payable [Member]
Notes Payable (Textual) [Abstract]
Transaction date			Oct. 18, 2011
Line of credit facility remaining amount drawing period					Between June 30, 2012 and September 30, 2012
Line of Credit Facility Prepayment Fee						3.00%	1.00%
Interest rate on the note payable, including amortization of debt discounts and accretion								13.10%	13.10%
Loan Agreement monthly arrears and interest date									Feb. 01, 2013
Interest expense related to the loan								$ 0.3	$ 0.6
Maximum borrowing Capacity	$ 25.0			$ 10.0	$ 15.0
Interest rate				8.95%	8.95%
Interest rate variable basis					8.61%
Debt instrument, interest rate, basis for effective rate	8.61% plus the then effective three-month U.S. LIBOR rate
Debt instrument, description of variable rate basis					effective three-month U.S. LIBOR rate
Expiration date									Oct. 01, 2015
Number of common shares issuable on exercise of warrants			386,100
Line of Credit Facility Warrants Exercise Price	$ 2.52	$ 2.52	$ 1.30
Notes Payable (Additional Textual) [Abstract]
Date of Loan and Security Agreement	Oct. 18, 2011
Line of credit facility, interest rate description	The interest rate for the first tranche is 8.95% per annum, and the interest rate for the second tranche will be fixed upon drawdown at a per annum rate equal to the greater of: (a) 8.95%, or (b) 8.61% plus the then effective three-month U.S. LIBOR rate.
Number of installments	32
Line of Credit Facility Final Payment Percentage	3.75%
Value of Warrants to Purchase Common Stock Issuable as Percentage of Tranche	5.00%
Warrants expiration date	Oct. 18, 2016
Warrants remained outstanding and exercisable date	Jun. 30, 2012
Period of average closing share price	10 days
Debt instrument drawing capacity conditional term	Issue five-year warrants to the Lenders upon each drawdown to purchase shares of common stock in an amount equal to 5.0% of the amount drawn at such tranche, divided by the exercise price per share, which is determined in each case to be the lower of: (a) the 10-day average closing share price prior to the drawdown, or (b) the closing price per share the day prior to the drawdown

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Loss per Common Share

6 Months Ended

Jun. 30, 2012

Loss per Common Share [Abstract]

Loss per Common Share

3. Loss per Common Share

Basic loss per common share is calculated by dividing net loss by the weighted-average number of common shares outstanding for the period. Diluted net loss per common share is computed by dividing (a) net loss, less any anti-dilutive amounts recorded during the period for the change in the fair value of warrant liabilities, by (b) the weighted-average number of common shares outstanding for the period plus dilutive potential common shares as determined using the treasury stock method for options and warrants to purchase common stock.

The following table sets forth the computation of basic and diluted loss per common share for the periods presented (in thousands, except per share amounts):

	Three months ended June 30,						Six months ended June 30,
	2012			2011			2012			2011
Numerator:
Net loss—basic	$	(8,579	)	$	(8,227	)	$	(22,503	)	$	(6,387	)
Adjustment for change in fair value of warrant liability		(753	)		—			—			—
Net loss—diluted	$	(9,332	)	$	(8,227	)	$	(22,503	)	$	(6,387	)
Denominator:
Weighted-average common shares outstanding—basic		46,953			46,295			46,873			46,095
Dilutive effect of warrants		333			—			—			—
Weighted-average common shares outstanding—diluted		47,286			46,295			46,873			46,095
Net loss per common share:
Basic	$	(0.18	)	$	(0.18	)	$	(0.48	)	$	(0.14	)
Diluted	$	(0.20	)	$	(0.18	)	$	(0.48	)	$	(0.14	)

The following table represents the potential common shares issuable pursuant to outstanding securities as of the related period end dates that were excluded from the computation of diluted loss per common share because their inclusion would have had an anti-dilutive effect (in thousands):

	Three months ended June 30,				Six months ended June 30,
	2012		2011		2012		2011
Warrants to purchase shares of common stock		7,355		8,648		11,025		8,648
Options to purchase shares of common stock		6,303		4,897		6,303		4,897
Outstanding securities not included in calculations		13,658		13,545		17,328		13,545

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Condensed Consolidated Statements of Operations and Comprehensive Income (Loss) (Unaudited) (USD $) In Thousands, except Per Share data, unless otherwise specified	3 Months Ended		6 Months Ended
	Jun. 30, 2012	Jun. 30, 2011	Jun. 30, 2012	Jun. 30, 2011
Revenue:
License and other revenue	$ 1,500		$ 1,500	$ 4,000
Total revenues	1,500		1,500	4,000
Operating expenses:
Research and development	8,072	5,950	14,718	10,020
General and administrative	2,182	1,975	4,371	3,989
Total operating expenses	10,254	7,925	19,089	14,009
Loss from operations	(8,754)	(7,925)	(17,589)	(10,009)
Interest expense	(316)		(631)
Other income (expense), net	491	(302)	(4,283)	3,622
Net loss	(8,579)	(8,227)	(22,503)	(6,387)
Unrealized gain (loss) on available-for-sale securities	(13)	21	(24)	33
Comprehensive loss	$ (8,592)	$ (8,206)	$ (22,527)	$ (6,354)
Shares used in computing net loss per common share:
Basic	46,953	46,295	46,873	46,095
Diluted	47,286	46,295	46,873	46,095
Net loss per common share:
Basic	$ (0.18)	$ (0.18)	$ (0.48)	$ (0.14)
Diluted	$ (0.20)	$ (0.18)	$ (0.48)	$ (0.14)

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Stock-Based Compensation (Tables)

6 Months Ended

Jun. 30, 2012

Stock-Based Compensation [Abstract]

Summary of stock-based compensation expense related to the Company's stock-based awards

The following table summarizes stock-based compensation expense related to the Company’s stock-based awards for the periods indicated (in thousands):

	Three months ended June 30,				Six months ended June 30,
	2012		2011		2012		2011
Research and development	$	207	$	65	$	433	$	139
General and administrative		353		67		670		198
Employee stock-based compensation expense		560		132		1,103		337
Non-employee stock-based compensation expense		17		3		42		7
Total stock-based compensation expense	$	577	$	135	$	1,145	$	344

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Document and Entity Information	6 Months Ended
	Jun. 30, 2012	Jul. 31, 2012
Document and Entity Information [Abstract]
Entity Registrant Name	SUNESIS PHARMACEUTICALS INC
Entity Central Index Key	0001061027
Document Type	10-Q
Document Period End Date	Jun. 30, 2012
Amendment Flag	false
Document Fiscal Year Focus	2012
Document Fiscal Period Focus	Q2
Current Fiscal Year End Date	--12-31
Entity Filer Category	Smaller Reporting Company
Entity Common Stock, Shares Outstanding		47,104,974
Trading Symbol	snss

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Company Overview (Details) (USD $)	6 Months Ended
	Jun. 30, 2012	Dec. 31, 2011
Company Overview (Textual) [Abstract]
Date of Incorporation	Feb. 10, 1998
Cash, cash equivalents and marketable securities	$ 29,300,000
Retained earnings (Accumulated deficit)	$ 423,649,000	$ 401,146,000	[1]
Policy maturity limits period	18 months
Dollars weighted average maturity period	9 months

[1] The condensed consolidated balance sheet as of December 31, 2011 has been derived from the audited financial statements as of that date included in the Company's Annual Report on Form 10-K for the year ended December 31, 2011

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Condensed Consolidated Statements of Cash Flows (Unaudited) (USD $) In Thousands, unless otherwise specified	6 Months Ended
	Jun. 30, 2012		Jun. 30, 2011
Cash flows from operating activities
Net loss	$ (22,503)		$ (6,387)
Adjustments to reconcile loss to net cash used in operating activities:
Stock-based compensation expense	1,145		344
Depreciation and amortization	16		38
Amortization of debt discount and debt issuance costs	138
Change in fair value of warrant liability	4,126		(3,241)
Foreign exchange loss (gain) on marketable securities	151		(240)
Changes in operating assets and liabilities:
Prepaids and other assets	(53)		(154)
Accounts payable	(265)		(87)
Accrued clinical expense	1,612		827
Accrued compensation	(494)		(255)
Other accrued liabilities	1,000		277
Net cash used in operating activities	(15,127)		(8,878)
Cash flows from investing activities
Purchases of property and equipment			(16)
Purchases of marketable securities	(9,325)		(28,168)
Proceeds from maturities of marketable securities	26,423		26,356
Net cash provided by (used in) investing activities	17,098		(1,828)
Cash flows from financing activities
Proceeds from issuance of common stock through controlled equity offering facilities, net	272		4,053
Proceeds from exercise of warrants, stock options and stock purchase rights	189		4
Net cash provided by financing activities	461		4,057
Net increase (decrease) in cash and cash equivalents	2,432		(6,649)
Cash and cash equivalents at beginning of period	9,311	[1]	14,223
Cash and cash equivalents at end of period	$ 11,743		$ 7,574

[1] The condensed consolidated balance sheet as of December 31, 2011 has been derived from the audited financial statements as of that date included in the Company's Annual Report on Form 10-K for the year ended December 31, 2011

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Stock-Based Compensation

6 Months Ended

Jun. 30, 2012

Stock-Based Compensation [Abstract]

Stock-Based Compensation

8. Stock-Based Compensation

Employee stock-based compensation expense is calculated based on the grant-date fair value of awards ultimately expected to vest, reduced for estimated forfeitures, and is recorded on a straight-line basis over the vesting period of the awards. Forfeitures are estimated at the time of grant, based on historical option cancellation information, and revised in subsequent periods if actual forfeitures differ from those estimates.

The following table summarizes stock-based compensation expense related to the Company’s stock-based awards for the periods indicated (in thousands):

	Three months ended June 30,				Six months ended June 30,
	2012		2011		2012		2011
Research and development	$	207	$	65	$	433	$	139
General and administrative		353		67		670		198
Employee stock-based compensation expense		560		132		1,103		337
Non-employee stock-based compensation expense		17		3		42		7
Total stock-based compensation expense	$	577	$	135	$	1,145	$	344

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Stockholders' Equity

6 Months Ended

Jun. 30, 2012

Stockholders' Equity [Abstract]

Stockholders' Equity

7. Stockholders’ Equity

Controlled Equity Offerings

In April 2010, the Company entered into a controlled equity offering sales agreement with Cantor Fitzgerald & Co. (“Cantor”), pursuant to which the Company could issue and sell shares of its common stock having an aggregate offering price of up to $20.0 million from time to time through Cantor acting as agent and/or principal. The Company agreed to pay Cantor a commission of 3.0% of the gross proceeds from each sale. In the six months ended June 30, 2012, the Company sold an aggregate of 88,500 shares of common stock at an average price of approximately $3.08 per share for gross and net proceeds of $0.3 million, after deducting Cantor’s commission. Through June 30, 2012, the Company had sold an aggregate of 4,471,783 shares of common stock under this facility at an average price of approximately $4.08 per share for gross proceeds of $18.3 million and net proceeds of $17.7 million, after deducting Cantor’s commission. As of June 30, 2012, $1.7 million of common stock remained available to be sold under this facility, subject to certain conditions as specified in the agreement.

In August 2011, the Company entered into an additional controlled equity offering sales agreement with Cantor, pursuant to which the Company may issue and sell shares of its common stock having an aggregate offering price of up to $20.0 million from time to time through Cantor acting as agent and/or principal. The Company agreed to pay Cantor a commission of 3.0% of the gross proceeds from each sale. As of June 30, 2012, no sales had been made under this facility, and $20.0 million of common stock remained available to be sold under this facility, subject to certain conditions as specified in the agreement.

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Notes Payable (Details) (USD $) In Thousands, unless otherwise specified	Jun. 30, 2012	Dec. 31, 2011
Future minimum payments under the Loan agreement
Notes payable, gross	$ 10,000
Unamortized discount on notes payable	(460)
Accretion of the final payment	97
Notes payable, balance	9,637
Current portion of notes payable	900		[1]
Non-current portion of notes payable	8,737	9,453	[1]
Notes Payable [Member]
Future minimum payments under the Loan agreement
2012	447
2013	3,674
2014	4,229
2015	3,524
Total minimum payments	11,874
Less: amount representing interest	$ (1,874)

[1] The condensed consolidated balance sheet as of December 31, 2011 has been derived from the audited financial statements as of that date included in the Company's Annual Report on Form 10-K for the year ended December 31, 2011

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Summary of Significant Accounting Policies (Details) (USD $) In Millions, unless otherwise specified	Jun. 30, 2012	Feb. 14, 2011
Summary of Significant Accounting Policies (Textual) [Abstract]
Reverse stock split conversion ratio		0.17
Fair value of investments	$ 3.9

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Notes Payable (Tables)

6 Months Ended

Jun. 30, 2012

Notes Payable [Abstract]

Future minimum payments under the Loan agreement

Future minimum payments under the Loan agreement as of June 30, 2012 were as follows (in thousands):

Period ending December 31,
2012	$	447
2013		3,674
2014		4,229
2015		3,524
Total minimum payments		11,874
Less: amount representing interest		(1,874	)
Notes payable, gross		10,000
Unamortized discount on notes payable		(460	)
Accretion of the final payment		97
Notes payable, balance		9,637
Current portion of notes payable		(900	)
Non-current portion of notes payable	$	8,737

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Summary of Significant Accounting Policies (Policies)

6 Months Ended

Jun. 30, 2012

Summary of Significant Accounting Policies [Abstract]

Basis of Presentation

Basis of Presentation

The accompanying unaudited condensed consolidated financial statements have been prepared in accordance with U.S. generally accepted accounting principles (“GAAP”) for interim financial information and with the instructions to Form 10-Q and Rule 10-01 of Regulation S-X. Accordingly, they do not include all of the information and notes required by GAAP for complete financial statements. The financial statements include a wholly owned subsidiary, Sunesis Europe Limited, a United Kingdom corporation. Management has determined that the Company operates as a single reportable segment. The financial statements include all adjustments (consisting only of normal recurring adjustments) that management believes are necessary for a fair presentation of the periods presented. The balance sheet as of December 31, 2011 was derived from the audited financial statements as of that date. These interim financial results are not necessarily indicative of results to be expected for the full year or any other period. These unaudited condensed consolidated financial statements and the notes accompanying them should be read in conjunction with the Company’s Annual Report on Form 10-K for the year ended December 31, 2011.

Reverse Stock Split

Reverse Stock Split

On February 14, 2011, the Company effected a one-for-six reverse split of its capital stock (the “Reverse Split”), as previously authorized and approved at the annual meeting of stockholders on June 2, 2010. As a result of the Reverse Split, every six shares of capital stock were combined into one share of capital stock. The Reverse Split affected the shares of Company’s common stock: (a) outstanding immediately prior to the effective time of the Reverse Split, (b) available for issuance under the Company’s equity incentive plans, and (c) issuable upon the exercise of outstanding stock options and warrants. The accompanying financial statements and notes thereto give retroactive effect to the Reverse Split for all periods presented.

Significant Estimates and Judgments

Significant Estimates and Judgments

The preparation of financial statements in conformity with GAAP requires management to make estimates and assumptions that affect the amounts reported in the Company’s condensed consolidated financial statements and accompanying notes. Actual results could differ materially from these estimates. Significant estimates, assumptions and judgments made by management include those related to the valuation of equity and related instruments, revenue recognition, stock-based compensation and clinical trial accounting.

Cash Equivalents and Marketable Securities

Cash Equivalents and Marketable Securities

Invoices for certain services provided to the Company are denominated in foreign currencies. To manage the risk of future movements in foreign exchange rates that would affect such amounts, the Company may purchase certain European currencies or highly-rated investments denominated in those currencies, subject to similar criteria as for other investments defined in the Company’s investment policy. There is no guarantee that the related gains and losses will substantially offset each other, and the Company may be subject to significant exchange gains or losses as currencies fluctuate from quarter to quarter. To date, the Company has purchased Euros and Euro-denominated obligations of foreign governments and corporate debt, and as of June 30, 2012, held investments denominated in Euros with an aggregate fair value of $3.9 million. These cash, cash equivalent and short-term investment balances are recorded at their fair value based on the current exchange rate as of each balance sheet date. The resulting exchange gains or losses and those from amounts payable for services originally denominated in foreign currencies are both recorded in other income (expense) in the statements of operations and comprehensive income (loss).

Fair Value Measurements

Fair Value Measurements

The Company measures cash equivalents, marketable securities and warrant liabilities at fair value on a recurring basis using the following hierarchy to prioritize valuation inputs, in accordance with applicable GAAP:

Level 1 — quoted prices (unadjusted) in active markets for identical assets and liabilities that can be accessed at the measurement date.

Level 2 — inputs other than quoted prices included within Level 1 that are observable, either directly or indirectly.

Level 3 — unobservable inputs.

The Company’s Level 2 valuations of marketable securities are generally based upon quoted prices in active markets for similar securities, with prices adjusted for yield and number of days to maturity.

The fair value of the Company’s liability for warrants issued in connection with an underwritten offering completed in October 2010 is determined using the Black-Scholes model, which requires inputs such as the expected term of the warrants, share price volatility, expected dividend yield and risk-free interest rate. As some of these inputs are unobservable, and require significant analysis and judgment to measure, these variables are classified as Level 3.

The Company does not measure cash, prepayments, accounts payable, accrued liabilities and notes payable at fair value, as their carrying amounts approximated their fair value as of June 30, 2012 and December 31, 2011.

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Loss Per Common Share (Tables)

6 Months Ended

Jun. 30, 2012

Loss per Common Share [Abstract]

Computation of basic and diluted loss per common share

	Three months ended June 30,				Six months ended June 30,
	2012		2011		2012		2011
Warrants to purchase shares of common stock		7,355		8,648		11,025		8,648
Options to purchase shares of common stock		6,303		4,897		6,303		4,897
Outstanding securities not included in calculations		13,658		13,545		17,328		13,545

Schedule of common shares issuable to outstanding securities excluded from the computation of diluted loss per common share

The following table sets forth the computation of basic and diluted loss per common share for the periods presented (in thousands, except per share amounts):

	Three months ended June 30,						Six months ended June 30,
	2012			2011			2012			2011
Numerator:
Net loss—basic	$	(8,579	)	$	(8,227	)	$	(22,503	)	$	(6,387	)
Adjustment for change in fair value of warrant liability		(753	)		—			—			—
Net loss—diluted	$	(9,332	)	$	(8,227	)	$	(22,503	)	$	(6,387	)
Denominator:
Weighted-average common shares outstanding—basic		46,953			46,295			46,873			46,095
Dilutive effect of warrants		333			—			—			—
Weighted-average common shares outstanding—diluted		47,286			46,295			46,873			46,095
Net loss per common share:
Basic	$	(0.18	)	$	(0.18	)	$	(0.48	)	$	(0.14	)
Diluted	$	(0.20	)	$	(0.18	)	$	(0.48	)	$	(0.14	)

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Financial Instruments (Tables)

6 Months Ended

Jun. 30, 2012

Financial Instruments [Abstract]

Fair value of Company's financial assets measured on recurring basis

The following tables summarize the estimated fair value of the Company’s financial assets measured on a recurring basis as of the dates indicated, which were comprised solely of available-for-sale securities with remaining contractual maturities of one year or less (in thousands):

June 30, 2012	Input Level		Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Estimated Fair Value
Money market funds		Level 1	$	8,848	$	—	$	—		$	8,848
U.S. corporate debt obligations		Level 2		7,587		—		—			7,587
U.S. commercial paper		Level 2		8,745		3		—			8,748
Foreign corporate debt obligations		Level 2		3,954		—		(8	)		3,946
Total available-for-sale securities				29,134		3		(8	)		29,129
Less: amounts classified as cash equivalents				11,597		1		—			11,598
Amounts classified as marketable securities			$	17,537	$	2	$	(8	)	$	17,531

December 31, 2011	Input Level		Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Estimated Fair Value
Money market funds		Level 1	$	7,156	$	—	$	—		$	7,156
U.S. corporate debt obligations		Level 2		16,619		5		(1	)		16,623
U.S. commercial paper		Level 2		14,556		18		—			14,574
Foreign government obligations		Level 2		3,607		1		—			3,608
Foreign corporate debt obligations		Level 2		1,476		—		(3	)		1,473
Total available-for-sale securities				43,414		24		(4	)		43,434
Less: amounts classified as cash equivalents				8,632		—		(2	)		8,630
Amounts classified as marketable securities			$	34,782	$	24	$	(2	)	$	34,804

Summary of available-for-sale securities in unrealized loss position

The following table summarizes the available-for-sale securities that were in an unrealized loss position as of June 30, 2012, each having been in such a position for less than 12 months, and none deemed to be other-than-temporarily impaired (in thousands):

June 30, 2012	Gross Unrealized Losses		Estimated Fair Value
Corporate debt obligations	$	8	$	3,946

Summary of assumptions and estimated fair value of the Company's financial liabilities measured on a recurring basis

The following table summarizes the inputs and assumptions and estimated fair value of the Company’s financial liabilities measured on a recurring basis as of the dates indicated, which were comprised solely of a liability for warrants issued in connection with an underwritten offering completed in October 2010:

	June 30, 2012			December 31, 2011
Inputs and assumptions:
Fair market value of Company’s common stock	$	2.87		$	1.17
Exercise price	$	2.52		$	2.52
Expected term (years)		3.3			3.8
Expected volatility		88.7	%		98.9	%
Risk-free interest rate		0.5	%		0.5	%
Expected dividend yield		0.0	%		0.0	%
Fair value:
Estimated fair value per warrant share	$	1.74		$	0.62
Shares underlying outstanding warrants classified as liabilities (in thousands)		3,671			3,679
Total estimated fair value of outstanding warrants (in thousands)	$	6,402		$	2,276

Summary of the changes in the fair value of the Company's Level 3 financial liabilities

The following table summarizes the changes in the fair value of the Company’s Level 3 financial liabilities for the periods indicated (in thousands):

	Warrant Liability
Balance as of December 31, 2010	$	8,154
Change in fair value of warrant liability		(5,878	)
Balance as of December 31, 2011		2,276
Change in fair value of warrant liability		4,126
Balance as of June 30, 2012	$	6,402

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Loss per Common Share (Details 1) In Thousands, unless otherwise specified	3 Months Ended		6 Months Ended
	Jun. 30, 2012	Jun. 30, 2011	Jun. 30, 2012	Jun. 30, 2011
Schedule of common stock issuable to outstanding securities excluded from the computation of diluted loss per common share
Outstanding securities not included in calculations	13,658	13,545	17,328	13,545
Warrants to purchase shares of common stock [Member]
Schedule of common stock issuable to outstanding securities excluded from the computation of diluted loss per common share
Outstanding securities not included in calculations	7,355	8,648	11,025	8,648
Options to purchase shares of common stock [Member]
Schedule of common stock issuable to outstanding securities excluded from the computation of diluted loss per common share
Outstanding securities not included in calculations	6,303	4,897	6,303	4,897

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Financial Instruments (Details 1) (Corporate debt obligations [Member], USD $) In Thousands, unless otherwise specified	Jun. 30, 2012
Corporate debt obligations [Member]
Summary of available-for-sale securities in unrealized loss position
Gross Unrealized Losses	$ 8
Estimated Fair Value	$ 3,946

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Company Overview

6 Months Ended

Jun. 30, 2012

Company Overview [Abstract]

Company Overview

1. Company Overview

Description of Business

Sunesis Pharmaceuticals, Inc. (the “Company” or “Sunesis”) was incorporated in the state of Delaware on February 10, 1998, and its facilities are located in South San Francisco, California. Sunesis is a biopharmaceutical company focused on the development and commercialization of new oncology therapeutics for the treatment of solid and hematologic cancers. The Company’s primary activities since incorporation have been conducting research and development internally and through corporate collaborators, in-licensing and out-licensing pharmaceutical compounds and technology, conducting clinical trials and raising capital.

In December 2010, the Company commenced enrollment of a Phase 3, multi-national, randomized, double-blind, placebo-controlled, pivotal clinical trial of vosaroxin in combination with cytarabine in patients with relapsed or refractory acute myeloid leukemia (the “VALOR trial”).

Significant Risks and Uncertainties

The Company has incurred significant losses and negative cash flows from operations since its inception, and as of June 30, 2012, had cash, cash equivalents and marketable securities totaling $29.3 million and an accumulated deficit of $423.6 million.

While the Company believes that it currently has access to resources to fund its operations until the unblinding of the VALOR trial, including if a sample size adjustment occurs, the Company may need to raise additional capital if the costs of the trial exceed the Company’s current estimates or unblinding does not occur within the currently anticipated timeframe. The Company will need to raise substantial additional capital to complete development and the potential commercialization of vosaroxin.

The Company expects to finance its future cash needs primarily through equity issuances, the potential sale of revenue participation rights, debt arrangements, a possible license, collaboration or other similar arrangement with respect to development and/or commercialization rights to vosaroxin, or a combination of the above.

Concentrations of Credit Risk

In accordance with its investment policy, the Company invests cash that is not currently being used for operational purposes. The policy allows for the purchase of low risk debt securities issued by: (a) the United States and certain European governments and government agencies, and (b) highly rated banks and corporations, denominated in U.S. dollars, Euros or British pounds, subject to certain concentration limits. The policy limits maturities of securities purchased to no longer than 18 months and the weighted average maturity of the portfolio to nine months. Management believes these guidelines ensure both the safety and liquidity of any investment portfolio the Company may hold.

Financial instruments that potentially subject the Company to concentrations of credit risk generally consist of cash, cash equivalents and marketable securities. The Company is exposed to credit risk in the event of default by the institutions holding its cash, cash equivalents and any marketable securities to the extent of the amounts recorded in the balance sheets.

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Financial Instruments

6 Months Ended

Jun. 30, 2012

Financial Instruments [Abstract]

Financial Instruments

6. Financial Instruments

Financial Assets

The following tables summarize the estimated fair value of the Company’s financial assets measured on a recurring basis as of the dates indicated, which were comprised solely of available-for-sale securities with remaining contractual maturities of one year or less (in thousands):

June 30, 2012	Input Level		Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Estimated Fair Value
Money market funds		Level 1	$	8,848	$	—	$	—		$	8,848
U.S. corporate debt obligations		Level 2		7,587		—		—			7,587
U.S. commercial paper		Level 2		8,745		3		—			8,748
Foreign corporate debt obligations		Level 2		3,954		—		(8	)		3,946
Total available-for-sale securities				29,134		3		(8	)		29,129
Less: amounts classified as cash equivalents				11,597		1		—			11,598
Amounts classified as marketable securities			$	17,537	$	2	$	(8	)	$	17,531

December 31, 2011	Input Level		Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Estimated Fair Value
Money market funds		Level 1	$	7,156	$	—	$	—		$	7,156
U.S. corporate debt obligations		Level 2		16,619		5		(1	)		16,623
U.S. commercial paper		Level 2		14,556		18		—			14,574
Foreign government obligations		Level 2		3,607		1		—			3,608
Foreign corporate debt obligations		Level 2		1,476		—		(3	)		1,473
Total available-for-sale securities				43,414		24		(4	)		43,434
Less: amounts classified as cash equivalents				8,632		—		(2	)		8,630
Amounts classified as marketable securities			$	34,782	$	24	$	(2	)	$	34,804

The following table summarizes the available-for-sale securities that were in an unrealized loss position as of June 30, 2012, each having been in such a position for less than 12 months, and none deemed to be other-than-temporarily impaired (in thousands):

June 30, 2012	Gross Unrealized Losses		Estimated Fair Value
Corporate debt obligations	$	8	$	3,946

No significant facts or circumstances have arisen to indicate that there has been any deterioration in the creditworthiness of the issuers of these securities. The gross unrealized losses are not considered to be significant and have been for relatively short durations. The Company does not intend to sell these securities and it is not more likely than not that they will need to be sold prior to the recovery of their amortized cost basis. There were no sales of available-for-sale securities in the six months ended June 30, 2012 and 2011.

Financial Liabilities

The following table summarizes the inputs and assumptions and estimated fair value of the Company’s financial liabilities measured on a recurring basis as of the dates indicated, which were comprised solely of a liability for warrants issued in connection with an underwritten offering completed in October 2010:

	June 30, 2012			December 31, 2011
Inputs and assumptions:
Fair market value of Company’s common stock	$	2.87		$	1.17
Exercise price	$	2.52		$	2.52
Expected term (years)		3.3			3.8
Expected volatility		88.7	%		98.9	%
Risk-free interest rate		0.5	%		0.5	%
Expected dividend yield		0.0	%		0.0	%
Fair value:
Estimated fair value per warrant share	$	1.74		$	0.62
Shares underlying outstanding warrants classified as liabilities (in thousands)		3,671			3,679
Total estimated fair value of outstanding warrants (in thousands)	$	6,402		$	2,276

The warrants have been classified as a derivative liability on the Company’s balance sheet due to the potential for the warrants to be settled in cash upon the occurrence of certain transactions specified in the warrant agreements. The warrants were initially recorded at their fair value of $4.5 million, which was estimated using the Black-Scholes model. At each subsequent balance sheet date, the estimated fair value of the outstanding warrants is determined using the Black-Scholes model and recorded to the balance sheet, with the change in fair value recorded to other income (expense) in the statements operations and of comprehensive income (loss).

The Black-Scholes model requires Level 3 inputs such as the expected term of the warrants and share price volatility. These inputs are subjective and generally require significant analysis and judgment to develop. Any changes in these inputs could result in a significantly higher or lower fair value measurement. The following table summarizes the changes in the fair value of the Company’s Level 3 financial liabilities for the periods indicated (in thousands):

	Warrant Liability
Balance as of December 31, 2010	$	8,154
Change in fair value of warrant liability		(5,878	)
Balance as of December 31, 2011		2,276
Change in fair value of warrant liability		4,126
Balance as of June 30, 2012	$	6,402

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Financial Instruments (Details 2) (USD $) In Thousands, except Per Share data, unless otherwise specified	6 Months Ended	12 Months Ended
	Jun. 30, 2012	Dec. 31, 2011		Dec. 31, 2010
Inputs and assumptions:
Fair market value of Company's common stock	$ 2.87	$ 1.17
Exercise price	$ 2.52	$ 2.52
Expected term (years)	3 years 3 months 18 days	3 years 9 months 18 days
Expected volatility	88.70%	98.90%
Risk-free interest rate	0.50%	0.50%
Expected dividend yield	0.00%	0.00%
Fair value:
Estimated fair value per warrant share	$ 1.74	$ 0.62
Shares underlying outstanding warrants classified as liabilities (in thousands)	3,671	3,679
Total estimated fair value of outstanding warrants (in thousands)	$ 6,402	$ 2,276	[1]	$ 8,154

[1] The condensed consolidated balance sheet as of December 31, 2011 has been derived from the audited financial statements as of that date included in the Company's Annual Report on Form 10-K for the year ended December 31, 2011

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Loss per Common Share (Details) (USD $) In Thousands, except Per Share data, unless otherwise specified	3 Months Ended		6 Months Ended
	Jun. 30, 2012	Jun. 30, 2011	Jun. 30, 2012	Jun. 30, 2011
Numerator:
Net loss - basic	$ (8,579)	$ (8,227)	$ (22,503)	$ (6,387)
Adjustment for change in fair value of warrant liability	(753)
Net loss - diluted	$ (9,332)	$ (8,227)	$ (22,503)	$ (6,387)
Denominator:
Weighted-average common shares outstanding - basic	46,953	46,295	46,873	46,095
Dilutive effect of warrants	333
Weighted-average common shares outstanding - diluted	47,286	46,295	46,873	46,095
Net loss per common share:
Basic	$ (0.18)	$ (0.18)	$ (0.48)	$ (0.14)
Diluted	$ (0.20)	$ (0.18)	$ (0.48)	$ (0.14)