Synergy Pharmaceuticals (SGYP) 10-Q 8 Aug 16 2016 Q2 Quarterly report Financial data

Document and Entity Information

Document and Entity Information - shares	6 Months Ended
	Jun. 30, 2016	Aug. 05, 2016
Document and Entity Information
Entity Registrant Name	SYNERGY PHARMACEUTICALS, INC.
Entity Central Index Key	1,347,613
Current Fiscal Year End Date	--12-31
Entity Current Reporting Status	Yes
Entity Filer Category	Accelerated Filer
Document Type	10-Q
Document Period End Date	Jun. 30, 2016
Document Fiscal Year Focus	2,016
Document Fiscal Period Focus	Q2
Amendment Flag	false
Entity Common Stock, Shares Outstanding		179,446,971

CONDENSED CONSOLIDATED BALANCE

CONDENSED CONSOLIDATED BALANCE SHEETS - USD ($) $ in Thousands	Jun. 30, 2016	Dec. 31, 2015
Current Assets:
Cash and cash equivalents	$ 141,219	$ 61,653
Available-for-sale securities	0	50,097
Prepaid expenses and other current assets	4,266	3,305
Total Current Assets	145,485	115,055
Property and equipment, net	724	531
Security deposits	343	343
Total Assets	146,552	115,929
Current Liabilities:
Accounts payable	19,028	13,263
Accrued expenses	3,109	4,328
Interest payable on Senior Convertible Debentures	990	1,988
Total Current Liabilities	23,127	19,579
Senior Convertible Notes, net	75,818	151,241
Derivative financial instruments, at estimated fair value-warrants	85	322
Total Liabilities	99,030	171,142
Commitments and contingencies
Stockholders’ Equity/(Deficit):
Preferred stock, Authorized 20,000,000 shares and none outstanding, at June 30, 2016 and December 31, 2015	0	0
Common stock, par value of $.0001, 350,000,000 shares authorized at June 30, 2016 and December 31, 2015. Issued and outstanding 179,776,089 shares and 113,694,606 shares at June 30, 2016 and December 31, 2015, respectively.	18	11
Additional paid-in capital	530,386	329,161
Accumulated Deficit	(482,882)	(384,385)
Total Stockholders’ Equity/(Deficit)	47,522	(55,213)
Total Liabilities and Stockholders’ Equity/(Deficit)	$ 146,552	$ 115,929

CONDENSED CONSOLIDATED BALANCE3

CONDENSED CONSOLIDATED BALANCE SHEETS (Parenthetical) - $ / shares	Jun. 30, 2016	Dec. 31, 2015
Statement of Financial Position [Abstract]
Preferred stock, authorized shares (in shares)	20,000,000	20,000,000
Preferred stock, outstanding shares (in shares)	0	0
Common stock, par value (in dollars per share)	$ 0.0001	$ 0.0001
Common stock, shares authorized (in shares)	350,000,000	350,000,000
Common stock, issued shares (in shares)	179,776,089	113,694,606
Common stock, outstanding shares (in shares)	179,776,089	113,694,606

CONDENSED CONSOLIDATED STATEMEN

CONDENSED CONSOLIDATED STATEMENTS OF OPERATIONS (Unaudited) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2016	Jun. 30, 2015
Income Statement [Abstract]
Revenues	$ 0	$ 0	$ 0	$ 0
Costs and Expenses:
Research and development	26,611	19,525	47,786	37,723
Selling, general and administrative	10,249	7,394	16,624	12,000
Loss from Operations	(36,860)	(26,919)	(64,410)	(49,723)
Other Loss
Interest and investment expense, net	(1,673)	(5,207)	(8,709)	(9,524)
Debt conversion expense	0	0	(25,615)	0
Change in fair value of derivative instruments-warrants	(23)	(1,542)	237	(1,810)
Total Other Loss	(1,696)	(6,749)	(34,087)	(11,334)
Net Loss	$ (38,556)	$ (33,668)	$ (98,497)	$ (61,057)
Weighted Average Common Shares Outstanding
Basic and Diluted (in shares)	168,127,144	100,343,637	143,017,970	98,523,696
Net Loss per Common Share, Basic and Diluted
Net Loss per Common Share, Basic and Diluted (in dollars per share)	$ (0.23)	$ (0.34)	$ (0.69)	$ (0.62)

CONDENSED CONSOLIDATED STATEME5

CONDENSED CONSOLIDATED STATEMENT OF CHANGES IN STOCKHOLDERS' DEFICIT (Unaudited) - 6 months ended Jun. 30, 2016 - USD ($) $ in Thousands	Total	Common Shares	Additional Paid in Capital	Deficit Accumulated
December 31, 2015 at Dec. 31, 2015	$ (55,213)	$ 11	$ 329,161	$ (384,385)
Balance, January 1, 2016 (in shares) at Dec. 31, 2015	113,694,606	113,694,606
Increase (Decrease) in Stockholders' Equity
Notes conversions including shares issued for accrued interest	$ 82,274	$ 3	82,271
Notes conversions including shares issued for accrued interest (in shares)		26,532,731
Debt conversion expense	25,615	$ 1	25,614
Debt conversion expense (in shares)		9,600,000
Transaction fees on Note conversions	(434)		(434)
Common stock issued in connection with exercise of stock options	23		23
Common stock issued in connection with exercise of stock options (in shares)		6,667
Common stock issued in registered direct offering	89,845	$ 3	89,842
Common stock issued to select investment funds (in shares)		29,948,334
Stock based compensation expense	3,909		3,909
Net loss for the period	(98,497)			(98,497)
Balance, June 30, 2016 at Jun. 30, 2016	$ 47,522	$ 18	$ 530,386	$ (482,882)
Balance, March 31, 2016 (in shares) at Jun. 30, 2016	179,776,089	179,776,089

CONDENSED CONSOLIDATED STATEME6

CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS (Unaudited) - USD ($) $ in Thousands	6 Months Ended
	Jun. 30, 2016	Jun. 30, 2015
Cash Flows From Operating Activities:
Net loss	$ (98,497)	$ (61,057)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization	79	67
Amortization of deferred transaction costs	4,406	2,516
Stock-based compensation expense	3,909	7,794
Accretion of discount/premium on available for sale securities	0	(87)
Change in fair value of derivative instruments—warrants	(237)	1,810
Common stock issued for interest on Notes	2,445	0
Debt conversion expense	25,615	0
Transaction fees on Note conversions	(434)	0
Changes in operating assets and liabilities:
Security deposit	0	(56)
Accounts payable and accrued expenses	4,546	(1,294)
Prepaid expenses and other current assets	(961)	1,549
Accrued interest expense on Senior Convertible Debentures	(998)	(277)
Total Adjustments	38,370	12,022
Net Cash used in Operating Activities	(60,127)	(49,035)
Cash Flows From Investing Activities:
Net sales (purchases) of available-for-sale securities	50,097	(50,000)
Additions to property and equipment	(272)	(8)
Net Cash provided by (used in) Investing Activities	49,825	(50,008)
Cash Flows From Financing Activities:
Proceeds of sale of common stock	89,845	14,672
Fees and expenses — sale of common stock	0	(404)
Proceeds from exercise of stock options	23	0
Net Cash provided by Financing Activities	89,868	14,268
Net increase (decrease) in cash and cash equivalents	79,566	(84,775)
Cash and cash equivalents at beginning of period	61,653	146,470
Cash and cash equivalents at end of period	141,219	61,695
Supplementary disclosure of cash flow information:
Cash paid for taxes	45	224
Supplementary disclosure of non-cash investing and financing activities:
Conversion of Senior Convertible Debentures to Synergy Common Stock	$ 82,274	$ 22,213

Business Overview

Business Overview	6 Months Ended
	Jun. 30, 2016
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Business Overview	Business Overview Synergy Pharmaceuticals Inc. ("the Company" or "Synergy") is a biopharmaceutical company focused on the development and commercialization of novel gastrointestinal (GI) therapies. The Company has pioneered discovery, research and development efforts around analogs of uroguanylin, a naturally occurring human GI peptide, for the treatment of functional GI disorders and inflammatory bowel disease. Synergy discovered, is developing and retains 100% worldwide rights to its proprietary uroguanylin analog technology platform that includes two lead product candidates - plecanatide and dolcanatide. Plecanatide is Synergy's first uroguanylin analog currently being evaluated for use as a once-daily tablet for chronic idiopathic constipation (CIC) and irritable bowel syndrome with constipation (IBS-C). Dolcanatide is Synergy's second uroguanylin analog currently being explored for ulcerative colitis. Net cash used in operating activities was approximately $60.1 million for the six months ended June 30, 2016 . As of June 30, 2016 , Synergy had approximately $141.2 million of cash and cash equivalents. During the six months ended June 30, 2016 , Synergy incurred losses from operations of $64.4 million . As of June 30, 2016 , Synergy had working capital of approximately $122.4 million . On May 5, 2016 , Synergy announced that it had entered into definitive agreements with certain institutional investors to sell 29,948,334 shares of common stock at a price of $3.00 per share. The shares were offered and sold directly to institutional investors by the company in a registered direct offering conducted without an underwriter or placement agent. The gross proceeds from the offering were approximately $89.8 million . The offering closed on May 6, 2016.

Basis of Presentation

Basis of Presentation	6 Months Ended
	Jun. 30, 2016
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Basis of Presentation	Basis of Presentation These unaudited condensed consolidated financial statements include Synergy and its wholly-owned subsidiaries: (1) Synergy Advanced Pharmaceuticals, Inc., (2) IgX, Ltd (Ireland—inactive). These unaudited condensed consolidated financial statements have been prepared following the requirements of the Securities and Exchange Commission (“SEC”) and United States generally accepted accounting principles (“GAAP”) for interim reporting. In the opinion of management, the accompanying unaudited condensed consolidated financial statements include all adjustments, which include only normal recurring adjustments, necessary to present fairly Synergy’s interim financial information. The accompanying unaudited condensed consolidated financial statements should be read in conjunction with the audited financial statements as of and for the year ended December 31, 2015 contained in the Company’s Annual Report on Form 10-K filed with the SEC on February 25, 2016 . All intercompany balances and transactions have been eliminated. Notwithstanding the Company's recent equity financing, Synergy will be required to raise additional capital within the next year to continue the development and commercialization of current product candidates and to continue to fund operations at the current cash expenditure levels. Synergy cannot be certain that additional funding will be available on acceptable terms, or at all. To the extent that Synergy raises additional funds by issuing equity securities, Synergy’s stockholders may experience significant dilution. Any debt financing, if available, may involve restrictive covenants that impact Synergy’s ability to conduct business. If Synergy is unable to raise additional capital when required or on acceptable terms, Synergy may have to (i) significantly delay, scale back or discontinue the development and/or commercialization of one or more product candidates; (ii) seek collaborators for product candidates at an earlier stage than otherwise would be desirable and on terms that are less favorable than might otherwise be available; or (iii) relinquish or otherwise dispose of rights to technologies, product candidates or products that Synergy would otherwise seek to develop or commercialize ourselves on unfavorable terms. Synergy's consolidated financial statements as of December 31, 2015 and its unaudited condensed consolidated financial statements as of June 30, 2016 have been prepared under the assumption that the Company will continue as a going concern for the next twelve months. Synergy's independent registered public accounting firm has issued a report as of December 31, 2015 that includes an explanatory paragraph referring to the Company's recurring and continuing losses from operations and expressing substantial doubt in the Company's ability to continue as a going concern without additional capital becoming available. Synergy's ability to continue as a going concern is dependent upon its ability to obtain additional equity or debt financing, attain further operating efficiencies, reduce expenditures, and, ultimately, to generate revenue. Synergy's consolidated financial statements as of December 31, 2015 and its unaudited condensed consolidated financial statements as of June 30, 2016 do not include any adjustments that might result from the outcome of this uncertainty.

Recent Accounting Pronouncement

Recent Accounting Pronouncements	6 Months Ended
	Jun. 30, 2016
New Accounting Pronouncements and Changes in Accounting Principles [Abstract]
Recent Accounting Pronouncements	Recent Accounting Pronouncements In March 2016, the Financial Accounting Standards Board ("FASB") issued Accounting Standards Update ("ASU") No. 2016-09, “Compensation - Stock Compensation (Topic 718): Improvements to Employee Share-Based Payment Accounting” (“ASU 2016-09”). The standard is intended to simplify several areas of accounting for share-based compensation arrangements, including the income tax impact, classification on the statement of cash flows and forfeitures. ASU 2016-09 is effective for fiscal years, and interim periods within those years, beginning after December 15, 2016, and early adoption is permitted. The Company is currently evaluating the impact that the standard will have on its consolidated financial statements and disclosures. In February 2016, the FASB issued ASU 2016-02 “Leases (Topic 842)” (“ASU 2016-02”). The FASB issued ASU 2016-02 to increase transparency and comparability among organizations by recognizing lease assets and lease liabilities on the balance sheet and disclosing key information about leasing arrangements. Under ASU 2016-02, a lessee will recognize in the statement of financial position a liability to make lease payments (the lease liability) and a right-to-use asset representing its right to use the underlying asset for the lease term. The amendments of this ASU are effective for reporting periods beginning after December 15, 2018, with early adoption permitted. An entity will be required to recognize and measure leases at the beginning of the earliest period presented using a modified retrospective approach. Management is currently assessing the impact the adoption of ASU 2016-02 will have on its consolidated financial statements and disclosures. In January 2016, the FASB issued ASU 2016-01, "Financial Instruments—Overall (Topic 825-10): "Recognition and Measurement of Financial Assets and Financial Liabilities." ASU 2016-01 amends the guidance on the classification and measurement of financial instruments. Some of the amendments in ASU 2016-01 include the following: 1) requires equity investments (except those accounted for under the equity method of accounting or those that result in consolidation of the investee) to be measured at fair value with changes in fair value recognized in net income; 2) simplifies the impairment assessment of equity investments without readily determinable fair values by requiring a qualitative assessment to identify impairment; 3) requires public business entities to use the exit price notion when measuring the fair value of financial instruments for disclosure purposes; and 4) requires an entity to present separately in other comprehensive income the portion of the total change in the fair value of a liability resulting from a change in the instrument-specific credit risk when the entity has elected to measure the liability at fair value; among others. For public business entities, the amendments of ASU 2016-01 are effective for fiscal years beginning after December 15, 2017, including interim periods within those fiscal years. The Company is currently evaluating the effects of ASU 2016-01 on its consolidated financial statements and disclosures. In April 2015, the FASB issued ASU 2015-05, "Intangibles - Goodwill and Other - Internal-Use Software (Subtopic 350-40): Customer's Accounting for Fees Paid in a Cloud Computing Arrangement". ASU 2015-05 provides guidance regarding whether a cloud computing arrangement includes a software license. If a cloud computing arrangement includes a software license, then the entity should account for the software license element of the arrangement consistent with the acquisition of other software licenses. If a cloud computing arrangement does not include a software license, the entity should account for the arrangement as a service contract. ASU 2015-05 does not change the accounting for service contracts. ASU 2015-05 is effective for fiscal years, including interim periods within those fiscal years, beginning after December 15, 2015 with early adoption permitted. The Company is considering entering into a cloud computing arrangement but has not done so as of June 30, 2016 , and is currently evaluating the effects of ASU 2015-05 on its consolidated financial statements and disclosures.

Cash, Cash Equivalents and Avai

Cash, Cash Equivalents and Available-for-sale Securities	6 Months Ended
	Jun. 30, 2016
Cash, Cash Equivalents, and Short-term Investments [Abstract]
Cash, Cash Equivalents and Available-for-sale Securities	Cash, Cash Equivalents and Available-for-sale Securities All highly liquid investments with maturities of three months or less at the date of purchase are classified as cash equivalents. As of June 30, 2016 and December 31, 2015 , the amount of cash and cash equivalents was $141.2 million and $61.7 million , respectively and consists of checking accounts and short-term U.S. Treasury money market mutual funds. Checking accounts are held at U.S. commercial banks, and balances were in excess of the FDIC insurance limit. The Company had no available-for-sale securities as of June 30, 2016 and $50.1 million of available-for-sale securities as of December 31, 2015 . Management determines the appropriate classification of its investments at the time of purchase and reevaluates the available-for-sale designations as of each balance sheet date.

Senior Convertible Notes

Senior Convertible Notes	6 Months Ended
	Jun. 30, 2016
Debt Disclosure [Abstract]
Senior Convertible Notes	Senior Convertible Notes On November 3, 2014, Synergy closed a private offering of $200 million aggregate principal amount of 7.50% Convertible Senior Notes due 2019, (the "Notes"), including the full exercise of the over-allotment option granted to the initial purchasers to purchase an additional $25 million aggregate principal amount of the Notes, interest payable semiannually in arrears on May 1 and November 1 of each year, beginning on May 1, 2015. The net proceeds from the offering were $187.3 million after deducting the initial purchasers’ discounts and offering expenses. The Notes are unsecured. Interest expense not including amortization of deferred transaction costs for three and six months ended June 30, 2016 was $1.5 million and $4.4 million , respectively. Interest expense not including amortization of deferred transaction costs for the three and six months ended June 30, 2015 was $3.4 million and $7.1 million , respectively. Accrued interest payable was $1.0 million and $2.0 million as of June 30, 2016 and December 31, 2015 respectively. A summary of quarterly interest activity is listed below (dollars in thousands): Interest payable on Senior Convertible Debenture at 1/1/2015 $ 2,500 Accrued interest expense during the 3 months ended March 31, 2015 3,750 Interest Payable on Senior Convertible Debenture at March 31, 2015 6,250 Accrued interest expense during the 3 months ended June 30, 2015 3,388 Interest Payment on Senior Convertible Debenture at May 1, 2015 (7,416 ) Interest payable on Senior Convertible Debenture as of June 30, 2015 2,222 Accrued interest expense during the 3 months ended September 30, 2015 2,747 Interest payable on Senior Convertible Debenture as of September 30, 2015 4,969 Interest payment at November 1, 2015 (5,963 ) Accrued interest expense during the 3 months ended December 31, 2015 2,982 Interest payable as of December 31, 2015 1,988 Accrued interest expense during the 3 months ended March 31, 2016 486 Interest payable as of March 31, 2016 2,474 Accrued interest expense during the 3 months ended June 30, 2016 1,485 Interest Payment on Senior Convertible Debenture at May 1, 2016 (2,969 ) Interest payable as of June 30, 2016 $ 990 The Notes will mature on November 1, 2019, unless earlier purchased or converted. The Notes are convertible, at any time, into shares of Synergy’s common stock at an initial conversion rate of 321.5434 shares per $1,000 principal amount of notes, which is equivalent to the original conversion price of $3.11 per share. Subsequent to the exchange described below, the principal balance of the Notes at June 30, 2016 was $79.2 million as compared to $159.0 million at December 31, 2015 . Transaction costs associated with the sale of the Notes of $12.7 million have been deferred and are being recognized as expense over the expected term of the Notes, calculated using the effective interest rate method. Amortization expense, including amortization associated with reduction of the principal due to the conversion and exchanges of the debentures on a prorated basis for three and six months ended June 30, 2016 was $0.3 million and $4.4 million , respectively, and for the three and six months ended June 30, 2015 was $1.9 million and $2.5 million , respectively. The remaining deferred transaction costs have been presented as a reduction of the Notes in accordance with the newly adopted Accounting Standards Update (“ASU”) No. 2015-3 “ Simplifying the Presentation of Debt Issuance Costs” . On March 18, 2016 Synergy entered into an agreement (the "Exchange") for the exchange of $79.8 million in aggregate principal amount of the Notes, representing approximately 50% of the outstanding aggregate principal amount of Notes, for 35.3 million shares of Synergy's common stock, with a total of 25.6 million shares representing the conversion price of $3.11 pursuant to the existing terms of the Notes. Synergy also issued approximately 872,000 shares at the five day average share price of $2.81 in payment of accrued and unpaid interest of $2.4 million on Notes accepted in the Exchanges, from the applicable last interest payment date to, but not including, March 28, 2016. The amortization of deferred transaction costs was accelerated consistent with the 50% reduction of aggregate principal amount this transaction represented, and resulted in additional interest expense of approximately $3.6 million . GAAP requires that such conversions be treated as induced conversions with an expense recognized equal to the fair value of the 9.6 million shares transferred in the transaction in excess of the fair value of the securities issuable pursuant to the original conversion terms, with such fair value being measured as of the date the inducement offer is accepted by the convertible debt holder. Accordingly, the Company recognized a debt conversion expense of $25.6 million for the six months ended June 30, 2016 . A summary of quarterly activity and balances associated with the Notes and related deferred transaction costs is presented below ($ in thousands): Notes Balance Deferred Transactions Notes, net of Balance at issuance November 1, 2014 $ 200,000 $ 12,747 $ 187,253 Less: amortization two months ended December 31, 2014 — (411 ) 411 Balance December 31, 2014 200,000 12,336 187,664 Less: amortization three months ended March 31, 2015 — (617 ) 617 Balance March 31, 2015 200,000 11,719 188,281 Less: amortization three months ended June 30, 2015 (1) — (1,899 ) 1,899 Conversions (22,213 ) — (22,213 ) Balance June 30, 2015 177,787 9,820 167,967 Less: amortization three months ended September 30, 2015 (1) — (1,544 ) 1,544 Conversions (18,776 ) — (18,776 ) Balance, September 30, 2015 159,011 8,276 150,735 Less: amortization three months ended December 31, 2015 — (506 ) 506 Balance December 31, 2015 159,011 7,770 151,241 Less: amortization three months ended March 31, 2016 (1) — (4,153 ) 4,153 Conversions (79,829 ) — (79,829 ) Balance, March 31, 2016 79,182 3,617 75,565 Less: amortization three months ended June 30, 2016 — (253 ) 253 Balance, June 30, 2016 $ 79,182 $ 3,364 $ 75,818 _____________________ (1) Includes accelerated amortization of deferred transaction costs attributable to conversions and exchanges

Accounting for Shared-Based Pay

Accounting for Shared-Based Payments	6 Months Ended
	Jun. 30, 2016
Disclosure of Compensation Related Costs, Share-based Payments [Abstract]
Accounting for Shared-Based Payments	Accounting for Shared-Based Payments Stock Options ASC Topic 718 “Compensation—Stock Compensation” requires companies to measure the cost of employee services received in exchange for the award of equity instruments based on the estimated fair value of the award at the date of grant. The expense is to be recognized over the period during which an employee is required to provide services in exchange for the award. Synergy accounts for shares of common stock, stock options and warrants issued to employees based on the fair value of the stock, stock option or warrant, if that value is more reliably measurable than the fair value of the consideration or services received. The Company accounts for stock options issued and vesting to non-employees in accordance with ASC Topic 505-50 “ Equity -Based Payment to Non-Employees” and accordingly the value of the stock compensation to non-employees is based upon the measurement date as determined at either a) the date at which a performance commitment is reached, or b) at the date at which the necessary performance to earn the equity instruments is complete. Accordingly the fair value of these options is being “marked to market” quarterly until the measurement date is determined. Synergy adopted the 2008 Equity Compensation Incentive Plan (the “Plan”) during the quarter ended September 30, 2008. Stock options granted under the Plan typically vest after three years of continuous service from the grant date and have a contractual term of ten years . On June 8, 2015, Synergy amended its 2008 Equity Compensation Incentive Plan and increased the number of shares of its common stock reserved for issuance under the Plan from 15,000,000 to 30,000,000 . Stock-based compensation has been recognized in operating results as follows: Three Months Ended Six Months Ended ($ in thousands) 2016 2015 2016 2015 Included in research and development 784 580 1,594 1,110 Included in general and administrative 1,923 4,809 2,315 6,684 Total stock-based compensation expense $ 2,707 $ 5,389 $ 3,909 $ 7,794 The unrecognized compensation cost related to non-vested stock options outstanding at June 30, 2016 , net of expected forfeitures, was approximately $22 million to be recognized over a weighted-average remaining vesting period of approximately 2.66 years . This unrecognized compensation cost does not include amounts related to 4,319,000 shares of stock options which vest and will be measured upon a change of control. The estimated fair value of stock option awards was determined on the date of grant using the Black-Scholes option valuation model with the following weighted-average assumptions during the periods indicated. Six Months Ended Six Months Ended Risk-free interest rate 1.22%-1.49% 1.46%-2.35% Dividend yield — — Expected volatility 50 % 60 % Expected term (in years) 6 years 6 years A summary of stock option activity and of changes in stock options outstanding under the Plan is presented below: Number of Options Exercise Price Per Share Weighted Average Exercise Price Per Share Intrinsic Value (in thousands) Weighted Average Remaining Contractual Term Balance outstanding, December 31, 2015 (1) 20,953,375 $0.44-9.12 $ 3.86 $ 42,438 7.15 years Granted 5,943,000 $2.93-4.14 3.70 — Exercised (6,667 ) 3.33 3.33 — Forfeited (533,760 ) $2.98-9.12 6.04 — Balance outstanding, June 30, 2016 (1) 26,355,948 $0.44-9.12 $ 3.77 $ — 7.39 years Exercisable, at June 30, 2016 10,715,881 $0.44-9.12 $ 3.39 $ 8,607 5.74 years __________________________ (1) Number of options represented above includes 2,159,500 options vesting upon a change of control, granted between November 20, 2009 and June 22, 2010. The fair value at the date of grant was approximately $28.6 million . Because the probability of a change of control transaction is not predictable no stock based compensation expense associated with these options has been recognized since the grant date.

Stockholders' Equity_(Deficit)

Stockholders' Equity/(Deficit)	6 Months Ended
	Jun. 30, 2016
Stockholders' Equity Note [Abstract]
Stockholders' Equity/(Deficit)	Stockholders’ Equity/(Deficit) On March 18, 2016, Synergy entered into an exchange agreement for the exchange of $79.8 million in aggregate principal amount of the Notes, representing approximately 50% of the outstanding aggregate principal amount of Notes, for 35.3 million shares of Synergy's common stock, with a total of 25.6 million shares representing the conversion price of $3.11 pursuant to the existing terms of the Notes. Synergy also issued approximately 872,000 shares at the five day average share price of $2.81 in payment of accrued and unpaid interest of $2.4 million on Notes accepted in the Exchanges. In addition, Synergy issued 9.6 million shares of common stock as an inducement for Note holders to convert. On May 5, 2016 , Synergy announced that it had entered into definitive agreements with certain institutional investors to sell 29,948,334 shares of common stock at a price of $3.00 per share. The shares were offered and sold directly to institutional investors by the company in a registered direct offering conducted without an underwriter or placement agent. The gross proceeds from the offering were approximately $89.8 million . The offering closed on May 6, 2016.

Research and Development Expens

Research and Development Expense	6 Months Ended
	Jun. 30, 2016
Research and Development [Abstract]
Research and Development Expense	Research and Development Expense Research and development costs include expenditures in connection with an in-house research and development laboratory, salaries and staff costs, application and filing for regulatory approval of proposed products, regulatory and scientific consulting fees, as well as contract research, patient costs, drug formulation and tableting, data collection, monitoring, and clinical insurance. In accordance with FASB ASC Topic 730-10-55, Research and Development , Synergy recorded prepaid research and development costs of approximately $3.9 million as of June 30, 2016 and $3.1 million as of December 31, 2015 , for nonrefundable advances for production of drug substance and analytical testing services for its drug candidates. In accordance with this guidance, Synergy expenses these costs when drug compound is delivered and services are performed.

Derivative Financial Instrument

Derivative Financial Instruments	6 Months Ended
	Jun. 30, 2016
Derivative Instruments and Hedging Activities Disclosure [Abstract]
Derivative Financial Instruments	Derivative Financial Instruments Synergy Derivative Financial Instruments Effective January 1, 2009, the Company adopted provisions of ASC Topic 815-40, “Derivatives and Hedging: Contracts in Entity’s Own Equity” (“ASC Topic 815-40”). ASC Topic 815-40 clarifies the determination of whether an instrument issued by an entity (or an embedded feature in the instrument) is indexed to an entity’s own stock, which would qualify as a scope exception under ASC Topic 815-10. Based upon the Company’s analysis of the criteria contained in ASC Topic 815-40, Synergy has determined that certain warrants issued in connection with sale of its common stock must be classified as derivative instruments. In accordance with ASC Topic 815-40, these warrants are also being re-measured at each balance sheet date based on estimated fair value, and any resultant changes in fair value are being recorded in the Company’s statement of operations. The Company estimates the fair value of certain warrants using the Black-Scholes option pricing model in order to determine the associated derivative instrument liability and change in fair value described above. The range of assumptions used to determine the fair value of the warrants at each period end was: Six Months Ended Six Months Ended Fair value of Synergy common stock $ 3.80 $ 8.30 Expected warrant term 1.7 0.25—2.9 years Risk-free interest rate 0.52 % 0.185%—1.32% Expected volatility 50 % 57%—80% Dividend yield — — Fair value of stock is the closing market price of the Company’s common stock at the end of each reporting period when the derivative instruments are marked to market. Expected volatility is a management estimate of future volatility, over the expected warrant term, based on historical volatility of Synergy’s common stock. The warrants have a transferability provision and based on guidance provided in SAB 107 for instruments issued with such a provision, Synergy used the full contractual term as the expected term of the warrants. The risk free rate is based on the U.S. Treasury security rates for maturities consistent with the expected remaining term of the warrants at the date quarterly revaluation. The following table sets forth the components of changes in the Synergy’s outstanding warrants which were deemed derivative financial instruments and the associated liability balance for the periods indicated: Date Description Warrants Derivative Instrument Liability (in thousands) 12/31/2015 Balance of derivative financial instruments liability 210,000 $ 322 3/31/2016 Change in fair value of warrants during the 3 months ended March 31, 2016 — (260 ) 6/30/2016 Change in fair value of warrants during the 3 months ended June 30, 2016 — $ 23 6/30/2016 Balance of derivative financial instruments liability 210,000 $ 85

Fair Value Measurements

Fair Value Measurements	6 Months Ended
	Jun. 30, 2016
Fair Value Disclosures [Abstract]
Fair Value Measurements	Fair Value Measurements Financial instruments consist of cash and cash equivalents, available-for-sale securities, accounts payable and derivative instruments. These financial instruments are stated at their respective historical carrying amounts, which approximate fair value due to their short term nature, except for available-for-sale securities and derivative instruments which are marked to market at the end of each reporting period. The value of Senior Convertible Notes is stated at its carrying value at June 30, 2016 . The Company believes it could obtain borrowings at June 30, 2016 at comparable interest rates as the November 2014 Notes, therefore, the carrying value approximates fair value. The following table presents the Company’s liabilities that are measured and recognized at fair value on a recurring basis classified under the appropriate level of the fair value hierarchy as of December 31, 2015 and June 30, 2016 : ($ in thousands) Description Quoted Prices in Active Markets for Identical Assets and Liabilities (Level 1) Significant Other Observable Inputs (Level 2) Significant Unobservable Inputs (Level 3) Balance as of Quoted Prices in Active Markets for Identical Assets and Liabilities (Level 1) Significant Other Observable Inputs (Level 2) Significant Unobservable Inputs (Level 3) Balance as of Derivative liabilities related to Warrants $ — $ — $ 322 $ 322 $ — $ — $ 85 $ 85 The following table sets forth a summary of changes in the fair value of the Company’s Level 3 liabilities for the six months ended June 30, 2016 : ($ in thousands) Description Balance as of (Gain) or loss recognized in earning from Change in Fair Value Expiration of warrants Balance as of Derivative liabilities related to Warrants $ 322 $ (237 ) $ — $ 85 The unrealized gains or losses on the derivative liabilities are recorded as a change in fair value of derivative liabilities in the Company’s statement of operations. A financial instrument’s level within the fair value hierarchy is based on the lowest level of any input that is significant to the fair value measurement. At each reporting period, Synergy reviews the assets and liabilities that are subject to ASC Topic 815-40. At each reporting period, all assets and liabilities for which the fair value measurement is based on significant unobservable inputs or instruments which trade infrequently and therefore have little or no price transparency are classified as Level 3.

Loss per Share

Loss per Share	6 Months Ended
	Jun. 30, 2016
Earnings Per Share [Abstract]
Loss per Share	Loss per Share Basic and diluted net loss per share is presented in conformity with ASC Topic 260, Earnings per Share, (“ASC Topic 260”) for periods presented. In accordance with ASC Topic 260, basic and diluted net loss per common share was determined by dividing net loss applicable to common stockholders by the weighted-average common shares outstanding during the period. Diluted weighted-average shares are the same as basic weighted-average shares because shares issuable pursuant to the exercise of stock options and warrants would be antidilutive. The following table sets forth potential common shares issuable upon the exercise of outstanding options, the exercise of warrants, and the conversion of the Senior Convertible Notes, all of which have been excluded from the computation of diluted weighted average shares outstanding as they would be anti-dilutive, including the impact on dilutive net loss per share of in-the-money warrants as per ASC 260-10-45-35 through ASC 260-10-45-37: Six Months Ended Six Months Ended Stock Options 26,355,948 17,041,722 Warrants 4,726,823 5,246,703 Senior Convertible Notes 25,460,450 57,166,238 Total shares issuable upon exercise or conversion 56,543,221 79,454,663

Basis of Presentation (Policies

Basis of Presentation (Policies)	6 Months Ended
	Jun. 30, 2016
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Basis of Presentation	These unaudited condensed consolidated financial statements include Synergy and its wholly-owned subsidiaries: (1) Synergy Advanced Pharmaceuticals, Inc., (2) IgX, Ltd (Ireland—inactive). These unaudited condensed consolidated financial statements have been prepared following the requirements of the Securities and Exchange Commission (“SEC”) and United States generally accepted accounting principles (“GAAP”) for interim reporting. In the opinion of management, the accompanying unaudited condensed consolidated financial statements include all adjustments, which include only normal recurring adjustments, necessary to present fairly Synergy’s interim financial information. The accompanying unaudited condensed consolidated financial statements should be read in conjunction with the audited financial statements as of and for the year ended December 31, 2015 contained in the Company’s Annual Report on Form 10-K filed with the SEC on February 25, 2016 . All intercompany balances and transactions have been eliminated
Recent Accounting Pronouncements	In March 2016, the Financial Accounting Standards Board ("FASB") issued Accounting Standards Update ("ASU") No. 2016-09, “Compensation - Stock Compensation (Topic 718): Improvements to Employee Share-Based Payment Accounting” (“ASU 2016-09”). The standard is intended to simplify several areas of accounting for share-based compensation arrangements, including the income tax impact, classification on the statement of cash flows and forfeitures. ASU 2016-09 is effective for fiscal years, and interim periods within those years, beginning after December 15, 2016, and early adoption is permitted. The Company is currently evaluating the impact that the standard will have on its consolidated financial statements and disclosures. In February 2016, the FASB issued ASU 2016-02 “Leases (Topic 842)” (“ASU 2016-02”). The FASB issued ASU 2016-02 to increase transparency and comparability among organizations by recognizing lease assets and lease liabilities on the balance sheet and disclosing key information about leasing arrangements. Under ASU 2016-02, a lessee will recognize in the statement of financial position a liability to make lease payments (the lease liability) and a right-to-use asset representing its right to use the underlying asset for the lease term. The amendments of this ASU are effective for reporting periods beginning after December 15, 2018, with early adoption permitted. An entity will be required to recognize and measure leases at the beginning of the earliest period presented using a modified retrospective approach. Management is currently assessing the impact the adoption of ASU 2016-02 will have on its consolidated financial statements and disclosures. In January 2016, the FASB issued ASU 2016-01, "Financial Instruments—Overall (Topic 825-10): "Recognition and Measurement of Financial Assets and Financial Liabilities." ASU 2016-01 amends the guidance on the classification and measurement of financial instruments. Some of the amendments in ASU 2016-01 include the following: 1) requires equity investments (except those accounted for under the equity method of accounting or those that result in consolidation of the investee) to be measured at fair value with changes in fair value recognized in net income; 2) simplifies the impairment assessment of equity investments without readily determinable fair values by requiring a qualitative assessment to identify impairment; 3) requires public business entities to use the exit price notion when measuring the fair value of financial instruments for disclosure purposes; and 4) requires an entity to present separately in other comprehensive income the portion of the total change in the fair value of a liability resulting from a change in the instrument-specific credit risk when the entity has elected to measure the liability at fair value; among others. For public business entities, the amendments of ASU 2016-01 are effective for fiscal years beginning after December 15, 2017, including interim periods within those fiscal years. The Company is currently evaluating the effects of ASU 2016-01 on its consolidated financial statements and disclosures. In April 2015, the FASB issued ASU 2015-05, "Intangibles - Goodwill and Other - Internal-Use Software (Subtopic 350-40): Customer's Accounting for Fees Paid in a Cloud Computing Arrangement". ASU 2015-05 provides guidance regarding whether a cloud computing arrangement includes a software license. If a cloud computing arrangement includes a software license, then the entity should account for the software license element of the arrangement consistent with the acquisition of other software licenses. If a cloud computing arrangement does not include a software license, the entity should account for the arrangement as a service contract. ASU 2015-05 does not change the accounting for service contracts. ASU 2015-05 is effective for fiscal years, including interim periods within those fiscal years, beginning after December 15, 2015 with early adoption permitted. The Company is considering entering into a cloud computing arrangement but has not done so as of June 30, 2016 , and is currently evaluating the effects of ASU 2015-05 on its consolidated financial statements and disclosures.

Senior Convertible Notes (Table

Senior Convertible Notes (Tables)	6 Months Ended
	Jun. 30, 2016
Debt Disclosure [Abstract]
Schedule of interest activity	A summary of quarterly interest activity is listed below (dollars in thousands): Interest payable on Senior Convertible Debenture at 1/1/2015 $ 2,500 Accrued interest expense during the 3 months ended March 31, 2015 3,750 Interest Payable on Senior Convertible Debenture at March 31, 2015 6,250 Accrued interest expense during the 3 months ended June 30, 2015 3,388 Interest Payment on Senior Convertible Debenture at May 1, 2015 (7,416 ) Interest payable on Senior Convertible Debenture as of June 30, 2015 2,222 Accrued interest expense during the 3 months ended September 30, 2015 2,747 Interest payable on Senior Convertible Debenture as of September 30, 2015 4,969 Interest payment at November 1, 2015 (5,963 ) Accrued interest expense during the 3 months ended December 31, 2015 2,982 Interest payable as of December 31, 2015 1,988 Accrued interest expense during the 3 months ended March 31, 2016 486 Interest payable as of March 31, 2016 2,474 Accrued interest expense during the 3 months ended June 30, 2016 1,485 Interest Payment on Senior Convertible Debenture at May 1, 2016 (2,969 ) Interest payable as of June 30, 2016 $ 990
Schedule of activity and balances associated with the Notes and related deferred transaction costs	A summary of quarterly activity and balances associated with the Notes and related deferred transaction costs is presented below ($ in thousands): Notes Balance Deferred Transactions Notes, net of Balance at issuance November 1, 2014 $ 200,000 $ 12,747 $ 187,253 Less: amortization two months ended December 31, 2014 — (411 ) 411 Balance December 31, 2014 200,000 12,336 187,664 Less: amortization three months ended March 31, 2015 — (617 ) 617 Balance March 31, 2015 200,000 11,719 188,281 Less: amortization three months ended June 30, 2015 (1) — (1,899 ) 1,899 Conversions (22,213 ) — (22,213 ) Balance June 30, 2015 177,787 9,820 167,967 Less: amortization three months ended September 30, 2015 (1) — (1,544 ) 1,544 Conversions (18,776 ) — (18,776 ) Balance, September 30, 2015 159,011 8,276 150,735 Less: amortization three months ended December 31, 2015 — (506 ) 506 Balance December 31, 2015 159,011 7,770 151,241 Less: amortization three months ended March 31, 2016 (1) — (4,153 ) 4,153 Conversions (79,829 ) — (79,829 ) Balance, March 31, 2016 79,182 3,617 75,565 Less: amortization three months ended June 30, 2016 — (253 ) 253 Balance, June 30, 2016 $ 79,182 $ 3,364 $ 75,818 _____________________ (1) Includes accelerated amortization of deferred transaction costs attributable to conversions and exchanges

Accounting for Shared-Based P20

Accounting for Shared-Based Payments (Tables)	6 Months Ended
	Jun. 30, 2016
Disclosure of Compensation Related Costs, Share-based Payments [Abstract]
Schedule of stock-based compensation expense	Stock-based compensation has been recognized in operating results as follows: Three Months Ended Six Months Ended ($ in thousands) 2016 2015 2016 2015 Included in research and development 784 580 1,594 1,110 Included in general and administrative 1,923 4,809 2,315 6,684 Total stock-based compensation expense $ 2,707 $ 5,389 $ 3,909 $ 7,794
Schedule of weighted-average assumptions used to estimate fair value of stock option awards using the Black-Scholes option valuation model	The estimated fair value of stock option awards was determined on the date of grant using the Black-Scholes option valuation model with the following weighted-average assumptions during the periods indicated. Six Months Ended Six Months Ended Risk-free interest rate 1.22%-1.49% 1.46%-2.35% Dividend yield — — Expected volatility 50 % 60 % Expected term (in years) 6 years 6 years
Summary of stock option activity and of changes in stock options outstanding under the Plan	A summary of stock option activity and of changes in stock options outstanding under the Plan is presented below: Number of Options Exercise Price Per Share Weighted Average Exercise Price Per Share Intrinsic Value (in thousands) Weighted Average Remaining Contractual Term Balance outstanding, December 31, 2015 (1) 20,953,375 $0.44-9.12 $ 3.86 $ 42,438 7.15 years Granted 5,943,000 $2.93-4.14 3.70 — Exercised (6,667 ) 3.33 3.33 — Forfeited (533,760 ) $2.98-9.12 6.04 — Balance outstanding, June 30, 2016 (1) 26,355,948 $0.44-9.12 $ 3.77 $ — 7.39 years Exercisable, at June 30, 2016 10,715,881 $0.44-9.12 $ 3.39 $ 8,607 5.74 years __________________________ (1) Number of options represented above includes 2,159,500 options vesting upon a change of control, granted between November 20, 2009 and June 22, 2010. The fair value at the date of grant was approximately $28.6 million . Because the probability of a change of control transaction is not predictable no stock based compensation expense associated with these options has been recognized since the grant date.

Derivative Financial Instrume21

Derivative Financial Instruments (Tables)	6 Months Ended
	Jun. 30, 2016
Derivative Instruments and Hedging Activities Disclosure [Abstract]
Schedule of range of assumptions used to determine the fair value of the warrants	The range of assumptions used to determine the fair value of the warrants at each period end was: Six Months Ended Six Months Ended Fair value of Synergy common stock $ 3.80 $ 8.30 Expected warrant term 1.7 0.25—2.9 years Risk-free interest rate 0.52 % 0.185%—1.32% Expected volatility 50 % 57%—80% Dividend yield — —
Schedule of changes in derivative financial instruments and associated liability balance	The following table sets forth the components of changes in the Synergy’s outstanding warrants which were deemed derivative financial instruments and the associated liability balance for the periods indicated: Date Description Warrants Derivative Instrument Liability (in thousands) 12/31/2015 Balance of derivative financial instruments liability 210,000 $ 322 3/31/2016 Change in fair value of warrants during the 3 months ended March 31, 2016 — (260 ) 6/30/2016 Change in fair value of warrants during the 3 months ended June 30, 2016 — $ 23 6/30/2016 Balance of derivative financial instruments liability 210,000 $ 85

Fair Value Measurements (Tables

Fair Value Measurements (Tables)	6 Months Ended
	Jun. 30, 2016
Fair Value Disclosures [Abstract]
Schedule of liabilities that are measured and recognized at fair value on a recurring basis	The following table presents the Company’s liabilities that are measured and recognized at fair value on a recurring basis classified under the appropriate level of the fair value hierarchy as of December 31, 2015 and June 30, 2016 : ($ in thousands) Description Quoted Prices in Active Markets for Identical Assets and Liabilities (Level 1) Significant Other Observable Inputs (Level 2) Significant Unobservable Inputs (Level 3) Balance as of Quoted Prices in Active Markets for Identical Assets and Liabilities (Level 1) Significant Other Observable Inputs (Level 2) Significant Unobservable Inputs (Level 3) Balance as of Derivative liabilities related to Warrants $ — $ — $ 322 $ 322 $ — $ — $ 85 $ 85
Summary of changes in the fair value of Level 3 liabilities	The following table sets forth a summary of changes in the fair value of the Company’s Level 3 liabilities for the six months ended June 30, 2016 : ($ in thousands) Description Balance as of (Gain) or loss recognized in earning from Change in Fair Value Expiration of warrants Balance as of Derivative liabilities related to Warrants $ 322 $ (237 ) $ — $ 85

Loss per Share (Tables)

Loss per Share (Tables)	6 Months Ended
	Jun. 30, 2016
Earnings Per Share [Abstract]
Schedule of potential common shares excluded from the computation of diluted weighted average shares outstanding	The following table sets forth potential common shares issuable upon the exercise of outstanding options, the exercise of warrants, and the conversion of the Senior Convertible Notes, all of which have been excluded from the computation of diluted weighted average shares outstanding as they would be anti-dilutive, including the impact on dilutive net loss per share of in-the-money warrants as per ASC 260-10-45-35 through ASC 260-10-45-37: Six Months Ended Six Months Ended Stock Options 26,355,948 17,041,722 Warrants 4,726,823 5,246,703 Senior Convertible Notes 25,460,450 57,166,238 Total shares issuable upon exercise or conversion 56,543,221 79,454,663

Business Overview (Details)

Business Overview (Details) - USD ($) $ / shares in Units, $ in Thousands	May 06, 2016	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2016	Jun. 30, 2015	Dec. 31, 2015	Dec. 31, 2014
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Net cash (used in) operating activities				$ (60,127)	$ (49,035)
Cash and cash equivalents		$ 141,219	$ 61,695	141,219	61,695	$ 61,653	$ 146,470
Income (Loss) from operations		(36,860)	$ (26,919)	(64,410)	(49,723)
Working Capital		$ 122,400		122,400
Subsidiary, Sale of Stock [Line Items]
Net proceeds from private placement				$ 89,845	$ 14,672
Private Placement
Subsidiary, Sale of Stock [Line Items]
Shares sold in private placement (in shares)	29,948,334
Shares issued (in dollars per share)	$ 3
Net proceeds from private placement	$ 89,800

Cash, Cash Equivalents and Av25

Cash, Cash Equivalents and Available-for-sale Securities (Details) - USD ($) $ in Thousands	Jun. 30, 2016	Dec. 31, 2015	Jun. 30, 2015	Dec. 31, 2014
Cash, Cash Equivalents, and Short-term Investments [Abstract]
Cash and cash equivalents	$ 141,219	$ 61,653	$ 61,695	$ 146,470
Available-for-sale securities	$ 0	$ 50,097

Senior Convertible Notes - Narr

Senior Convertible Notes - Narrative (Details) $ / shares in Units, shares in Thousands	Mar. 18, 2016USD ($)$ / sharesshares	Nov. 03, 2014USD ($)	Dec. 31, 2014USD ($)	Jun. 30, 2016USD ($)	Mar. 31, 2016USD ($)	Dec. 31, 2015USD ($)	Sep. 30, 2015USD ($)	Jun. 30, 2015USD ($)	Mar. 31, 2015USD ($)	Jun. 30, 2016USD ($)shares	Jun. 30, 2015USD ($)	Nov. 01, 2014USD ($)
Debt Instrument [Line Items]
Accrued interest payable				$ 990,000		$ 1,988,000				$ 990,000
Amortization of deferred transaction costs										4,406,000	$ 2,516,000
Debt conversion amount										82,274,000	22,213,000
Common stock issued for interest on Notes										2,445,000	0
Debt conversion expense				0				$ 0		25,615,000	0
Convertible Senior Notes Due 2019
Debt Instrument [Line Items]
Aggregate principal amount (in dollars)		$ 200,000,000
Interest rate (as a percent)		7.50%
Additional aggregate principal amount pertaining to the over-allotment option granted (in dollars)		$ 25,000,000
Net proceeds from offering (in dollars)		$ 187,300,000
Accrued interest expense				1,485,000	$ 486,000	2,982,000	$ 2,747,000	3,388,000	$ 3,750,000	4,400,000	7,100,000
Accrued interest payable			$ 2,500,000	990,000	2,474,000	2,000,000	4,969,000	2,222,000	6,250,000	990,000	2,222,000
Conversion rate (as a percent)		0.3215434
Conversion price (in dollars per share) | $ / shares	$ 3.11
Notes balance			200,000,000	79,182,000	79,182,000	159,011,000	159,011,000	177,787,000	200,000,000	79,182,000	177,787,000	$ 200,000,000
Transactions costs												$ 12,700,000
Amortization of deferred transaction costs	$ 3,600,000		$ 411,000	$ 253,000	4,153,000	$ 506,000	1,544,000	1,899,000	$ 617,000	$ 4,400,000	$ 2,500,000
Debt conversion amount	$ 79,800,000				$ 79,829,000		$ 18,776,000	$ 22,213,000
Percent of principal converted	50.00%
Number of shares issued on conversion of debt (in shares) | shares	35,300
Number of shares issued on conversion price excluding share issued for accrued interest (in shares) | shares	25,600
Number of shares issued for accrued interest (in shares) | shares	872
Five day average conversion price for accrued interest (in dollars per share) | $ / shares	$ 2.81
Common stock issued for interest on Notes	$ 2,400,000
Common Shares
Debt Instrument [Line Items]
Debt conversion expense (in shares) | shares										9,600

Senior Convertible Notes - Sche

Senior Convertible Notes - Schedule of Interest Activity (Details) - USD ($) $ in Thousands	3 Months Ended						6 Months Ended		12 Months Ended
	Jun. 30, 2016	Mar. 31, 2016	Dec. 31, 2015	Sep. 30, 2015	Jun. 30, 2015	Mar. 31, 2015	Jun. 30, 2016	Jun. 30, 2015	Dec. 31, 2015
Interest Expense Debt [Roll Forward]
Interest payable on Senior Convertible Debenture, beginning of period		$ 1,988					$ 1,988
Interest paid on Senior Convertible Debentures							(2,969)		$ (7,416)
Interest payable on Senior Convertible Debenture, end of period	$ 990		$ 1,988				990		1,988
Convertible Senior Notes Due 2019
Interest Expense Debt [Roll Forward]
Interest payable on Senior Convertible Debenture, beginning of period	2,474	2,000	4,969	$ 2,222	$ 6,250	$ 2,500	2,000	$ 2,500	2,500
Accrued interest expense	1,485	486	2,982	2,747	3,388	3,750	4,400	7,100
Interest paid on Senior Convertible Debentures	(2,969)		(5,963)		(7,416)
Interest payable on Senior Convertible Debenture, end of period	$ 990	$ 2,474	$ 2,000	$ 4,969	$ 2,222	$ 6,250	$ 990	$ 2,222	$ 2,000

Senior Convertible Notes - Sc28

Senior Convertible Notes - Schedule of Activity and Balances Associated with the Notes and Related Deferred Transaction Costs (Details) - USD ($) $ in Thousands	Mar. 18, 2016	Dec. 31, 2014	Jun. 30, 2016	Mar. 31, 2016	Dec. 31, 2015	Sep. 30, 2015	Jun. 30, 2015	Mar. 31, 2015	Jun. 30, 2016	Jun. 30, 2015
Convertible Notes And Deferred Transaction Costs[Roll forward]
Less: amortization									$ (4,406)	$ (2,516)
Conversions									(82,274)	(22,213)
Convertible Senior Notes Due 2019
Convertible Notes And Deferred Transaction Costs[Roll forward]
Notes Balance, beginning of period		$ 200,000	$ 79,182	$ 159,011	$ 159,011	$ 177,787	$ 200,000	$ 200,000	159,011	200,000
Transactions Costs, beginning of period		12,747	3,617	7,770	8,276	9,820	11,719	12,336	7,770	12,336
Notes, net of Transaction Costs, beginning of period		187,253	75,565	151,241	150,735	167,967	188,281	187,664	151,241	187,664
Less: amortization	$ (3,600)	(411)	(253)	(4,153)	(506)	(1,544)	(1,899)	(617)	(4,400)	(2,500)
Conversions	$ (79,800)			(79,829)		(18,776)	(22,213)
Notes Balance, end of period		200,000	79,182	79,182	159,011	159,011	177,787	200,000	79,182	177,787
Notes, net of Transaction Costs, end of period		187,664	75,818	75,565	151,241	150,735	167,967	188,281	75,818	167,967
Transactions Costs, end of period		$ 12,336	$ 3,364	$ 3,617	$ 7,770	$ 8,276	$ 9,820	$ 11,719	$ 3,364	$ 9,820

Accounting for Shared-Based P29

Accounting for Shared-Based Payments - Stock Options (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2016	Jun. 30, 2015	Jun. 08, 2015	Jun. 07, 2015
Shared-based payments
Total stock-based compensation expense (income)	$ 2,707	$ 5,389	$ 3,909	$ 7,794
Research and development | Employee
Shared-based payments
Total stock-based compensation expense (income)	784	580	1,594	1,110
General and administrative | Employee
Shared-based payments
Total stock-based compensation expense (income)	1,923	$ 4,809	$ 2,315	$ 6,684
2008 Equity Compensation Incentive Plan
Shared-based payments
Number of shares reserved under the plan (in shares)					30,000,000	15,000,000
Stock Options
Shared-based payments
Vesting period			3 years
Contractual term			10 years
Unrecognized compensation cost related to non-vested employee stock options, net of expected forfeitures	$ 22,000		$ 22,000
Weighted-average remaining vesting period over which unrecognized compensation cost is to be recognized			2 years 7 months 28 days
Number of stock options which vest upon a change of control (in shares)	4,319,000		4,319,000
Weighted-average assumptions used to estimate fair value of stock option awards using the Black-Scholes option valuation model
Risk-free interest rate, minimum (as a percent)			1.22%	1.46%
Risk-free interest rate, maximum (as a percent)			1.49%	2.35%
Dividend yield (as percent)			0.00%	0.00%
Expected volatility (as a percent)			50.00%	60.00%
Expected term			6 years	6 years
Minimum | Stock Options
Weighted-average assumptions used to estimate fair value of stock option awards using the Black-Scholes option valuation model
Expected term				6 years
Maximum | Stock Options
Weighted-average assumptions used to estimate fair value of stock option awards using the Black-Scholes option valuation model
Expected term				9 years 3 months 18 days

Accounting for Shared-Based P30

Accounting for Shared-Based Payments - Schedule of Stock Option Activity (Details) - USD ($)	3 Months Ended		6 Months Ended		7 Months Ended	12 Months Ended	87 Months Ended
	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2016	Jun. 30, 2015	Jun. 22, 2010	Dec. 31, 2015	Mar. 31, 2016
Exercise Price Per Share
Common stock issued in connection with exercise of stock options			$ 23,000
Weighted Average Remaining Contractual Term
Stock based compensation expense	$ 2,707,000	$ 5,389,000	$ 3,909,000	$ 7,794,000
Stock Options | Contingent vesting
Weighted Average Remaining Contractual Term
Stock based compensation expense							$ 0
Stock Options | $0.44-9.12
Number of Options
Balance outstanding, beginning of period (in shares)			20,953,375
Balance outstanding, end of period (in shares)	26,355,948		26,355,948			20,953,375
Exercisable at the end of the period (in shares)	10,715,881		10,715,881
Exercise Price Per Share
Exercise price, low end of the range (in dollars per share)			$ 0.44			$ 0.44
Exercise price, high end of the range (in dollars per share)			9.12			9.12
Weighted Average Exercise Price Per Share
Balance outstanding, beginning of period (in dollars per share)			3.86
Balance outstanding, end of period (in dollars per share)	$ 3.77		3.77			$ 3.86
Exercisable at the end of the period (in dollars per share)	$ 3.39		$ 3.39
Intrinsic Value
Intrinsic value of options outstanding	$ 0		$ 0			$ 42,438,000
Intrinsic value of options exercisable, end of period	$ 8,607,000		$ 8,607,000
Weighted Average Remaining Contractual Term
Balance			7 years 4 months 21 days			7 years 1 month 24 days
Exercisable at the end of the period			5 years 8 months 27 days
Stock Options | $0.44-9.12 | Contingent vesting
Number of Options
Balance outstanding, end of period (in shares)					2,159,500
Weighted Average Remaining Contractual Term
Grant date fair value					$ 28,600,000
Stock Options | $2.93-4.14
Number of Options
Granted (in shares)			5,943,000
Exercise Price Per Share
Exercise price, low end of the range (in dollars per share)			$ 2.93
Exercise price, high end of the range (in dollars per share)			4.14
Weighted Average Exercise Price Per Share
Granted (in dollars per share)			$ 3.70
Stock Options | 3.33
Number of Options
Exercised (in shares)			(6,667)
Exercise Price Per Share
Exercise price, low end of the range (in dollars per share)			$ 3.33
Exercise price, high end of the range (in dollars per share)			3.33
Weighted Average Exercise Price Per Share
Exercised (in dollars per share)			$ 3.33
Stock Options | $2.98-9.12
Number of Options
Forfeited (in shares)			(533,760)
Exercise Price Per Share
Exercise price, low end of the range (in dollars per share)			$ 2.98
Exercise price, high end of the range (in dollars per share)			9.12
Weighted Average Exercise Price Per Share
Forfeited (in dollars per share)			$ 6.04

Stockholders' Equity_( Deficit)

Stockholders' Equity/( Deficit) (Details) - USD ($) $ / shares in Units, $ in Thousands	May 06, 2016	Mar. 18, 2016	Mar. 31, 2016	Sep. 30, 2015	Jun. 30, 2015	Jun. 30, 2016	Jun. 30, 2015
Debt Instrument [Line Items]
Debt conversion amount						$ 82,274	$ 22,213
Common stock issued for interest on Notes						2,445	0
Net proceeds from private placement						$ 89,845	$ 14,672
Convertible Senior Notes Due 2019
Debt Instrument [Line Items]
Debt conversion amount		$ 79,800	$ 79,829	$ 18,776	$ 22,213
Percent of principal converted		50.00%
Number of shares issued on conversion of debt (in shares)		35,300,000
Number of shares issued on conversion price excluding share issued for accrued interest (in shares)		25,600,000
Conversion price (in dollars per share)		$ 3.11
Number of shares issued for accrued interest (in shares)		872,000
Five day average conversion price for accrued interest (in dollars per share)		$ 2.81
Common stock issued for interest on Notes		$ 2,400
Private Placement
Debt Instrument [Line Items]
Shares sold in private placement (in shares)	29,948,334
Shares issued (in dollars per share)	$ 3
Net proceeds from private placement	$ 89,800
Common Shares
Debt Instrument [Line Items]
Debt conversion expense (in shares)						9,600,000
Shares sold in private placement (in shares)						29,948,334

Research and Development Expe32

Research and Development Expense (Details) - USD ($) $ in Millions	Jun. 30, 2016	Dec. 31, 2015
Research and Development [Abstract]
Prepaid research and development costs	$ 3.9	$ 3.1

Derivative Financial Instrume33

Derivative Financial Instruments - Range of Assumptions (Details) - Derivative instrument liability - Warrants - Black-Scholes option pricing model - $ / shares	6 Months Ended
	Jun. 30, 2016	Jun. 30, 2015
Range of assumptions used to determine the fair value of the warrants
Fair value of Synergy common stock (in dollars per share)	$ 3.80	$ 8.30
Expected warrant term	1 year 8 months 12 days
Risk-free interest rate (as a percent)	0.50%
Expected volatility (as a percent)	50.00%
Dividend yield (as a percent)	0.00%	0.00%
Minimum
Range of assumptions used to determine the fair value of the warrants
Expected warrant term		3 months
Risk-free interest rate (as a percent)		0.185%
Expected volatility (as a percent)		57.00%
Maximum
Range of assumptions used to determine the fair value of the warrants
Expected warrant term		2 years 10 months 24 days
Risk-free interest rate (as a percent)		1.32%
Expected volatility (as a percent)		80.00%

Derivative Financial Instrume34

Derivative Financial Instruments - Changes in Outstanding Warrants (Details) - USD ($) $ in Thousands	3 Months Ended			6 Months Ended
	Jun. 30, 2016	Mar. 31, 2016	Jun. 30, 2015	Jun. 30, 2016	Jun. 30, 2015	Dec. 31, 2015
Changes in derivative instrument liability
Balance at the beginning of the period		$ 322		$ 322
Change in fair value of warrants during the quarter	$ 23		$ 1,542	(237)	$ 1,810
Balance at the end of the period	$ 85			$ 85
Derivative instrument liability
Derivative Financial Instruments
Balance of warrants outstanding	210,000			210,000		210,000
Changes in derivative instrument liability
Balance at the beginning of the period		322		$ 322
Change in fair value of warrants during the quarter	$ 23	$ (260)
Balance at the end of the period	$ 85			$ 85

Fair Value Measurements - Fair

Fair Value Measurements - Fair Value of Liabilities Measured on Recurring Basis (Details) - USD ($) $ in Thousands	Jun. 30, 2016	Dec. 31, 2015
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Derivative financial instruments, at estimated fair value-warrants	$ 85	$ 322
Derivative instrument liability
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Derivative financial instruments, at estimated fair value-warrants	85	322
Fair value on a recurring basis | Warrants | Derivative instrument liability
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Derivative financial instruments, at estimated fair value-warrants	85	322
Fair value on a recurring basis | Warrants | Derivative instrument liability | Level 3
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Derivative financial instruments, at estimated fair value-warrants	$ 85	$ 322

Fair Value Measurements - Level

Fair Value Measurements - Level 3 Roll Forward (Details) - Warrants - Derivative instrument liability $ in Thousands	6 Months Ended
	Jun. 30, 2016USD ($)
Changes in the fair value of Level 3 liabilities
Balance at the beginning of the period	$ 322
(Gain) or loss recognized in earning from Change in Fair Value	(237)
Expiration of Warrants	0
Balance at the end of the period	$ 85

Loss per Share (Details)

Loss per Share (Details) - shares	6 Months Ended
	Jun. 30, 2016	Jun. 30, 2015
Loss per Share
Total shares issuable upon exercise or conversion (in shares)	56,543,221	79,454,663
Stock Options
Loss per Share
Total shares issuable upon exercise or conversion (in shares)	26,355,948	17,041,722
Warrants
Loss per Share
Total shares issuable upon exercise or conversion (in shares)	4,726,823	5,246,703
Senior Convertible Notes
Loss per Share
Total shares issuable upon exercise or conversion (in shares)	25,460,450	57,166,238