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Document and Entity Information - shares	9 Months Ended
Document and Entity Information - shares	Sep. 30, 2018	Oct. 31, 2018
Document and Entity Information
Entity Registrant Name	IDERA PHARMACEUTICALS, INC.
Trading Symbol	IDRA
Entity Central Index Key	0000861838
Document Type	10-Q
Document Period End Date	Sep. 30, 2018
Amendment Flag	false
Current Fiscal Year End Date	--12-31
Entity Current Reporting Status	Yes
Entity Filer Category	Accelerated Filer
Entity Small Business	true
Entity Emerging Growth Company	false
Entity Common Stock, Shares Outstanding		27,181,436
Document Fiscal Year Focus	2018
Document Fiscal Period Focus	Q3

CONDENSED BALANCE SHEETS - USD ($) $ in Thousands	Sep. 30, 2018	Dec. 31, 2017
Current assets:
Cash and cash equivalents	$ 82,462	$ 112,629
Prepaid expenses and other current assets	2,518	3,992
Total current assets	84,980	116,621
Property and equipment, net	241	1,472
Other assets	9	324
Total assets	85,230	118,417
Current liabilities:
Accounts payable	1,036	1,334
Accrued expenses	9,171	8,000
Note payable		209
Deferred revenue	94	566
Total current liabilities	10,301	10,109
Other liabilities	63	613
Total liabilities	10,364	10,722
Commitments and contingencies
Stockholders' equity:
Common stock, $0.001 par value, Authorized — 70,000 shares; Issued and outstanding — 27,179 and 24,453 shares at September 30, 2018 and December 31, 2017, respectively	27	24
Additional paid-in capital	727,064	712,165
Accumulated deficit	(652,225)	(604,494)
Total stockholders' equity	74,866	107,695
Total liabilities and stockholders' equity	85,230	118,417
Series A Preferred Stock
Stockholders' equity:
Preferred stock, $0.01 par value, Authorized — 5,000 shares: Series A convertible preferred stock; Designated — 1,500 shares, Issued and outstanding — 1 share

CONDENSED STATEMENTS OF OPERATIONS AND COMPREHENSIVE LOSS - USD ($) shares in Thousands, $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2018	Sep. 30, 2017	Sep. 30, 2018	Sep. 30, 2017
STATEMENTS OF OPERATIONS AND COMPREHENSIVE LOSS
Alliance revenue	$ 145	$ 164	$ 563	$ 729
Operating expenses:
Research and development	8,860	10,912	32,912	40,288
General and administrative	3,984	3,919	11,849	11,888
Merger-related costs, net	(3,836)		1,245
Restructuring costs	3,017		3,017
Total operating expenses	12,025	14,831	49,023	52,176
Loss from operations	(11,880)	(14,667)	(48,460)	(51,447)
Other income (expense):
Interest income	277	159	759	456
Interest expense		(11)	(11)	(40)
Foreign currency exchange loss	(2)	(11)	(19)	(27)
Net loss	$ (11,605)	$ (14,530)	$ (47,731)	$ (51,058)
Net loss per share applicable to common stockholders - basic and diluted (Note 12)	$ (0.43)	$ (0.78)	$ (1.81)	$ (2.73)
Weighted-average number of common shares used in computing net loss per share applicable to common stockholders - basic and diluted	27,175	18,704	26,404	18,673
Comprehensive loss:
Net loss	$ (11,605)	$ (14,530)	$ (47,731)	$ (51,058)
Unrealized (loss) gain on available-for-sale securities		(1)		17
Total other comprehensive (loss) income		(1)		17
Comprehensive loss	$ (11,605)	$ (14,531)	$ (47,731)	$ (51,041)

CONDENSED STATEMENTS OF CASH FLOWS - USD ($) $ in Thousands	9 Months Ended
CONDENSED STATEMENTS OF CASH FLOWS - USD ($) $ in Thousands	Sep. 30, 2018	Sep. 30, 2017
Cash Flows from Operating Activities:
Net loss	$ (47,731)	$ (51,058)
Adjustments to reconcile net loss to net cash used in operating activities:
Stock-based compensation	4,454	9,165
Issuance of common stock for services rendered	77	119
Accretion of discounts and premiums on investments		94
Depreciation and amortization expense	395	559
Loss on disposal or impairment of property and equipment	497
Changes in operating assets and liabilities:
Prepaid expenses and other current assets	1,881	(1,639)
Accounts payable, accrued expenses, and other liabilities	455	(393)
Deferred revenue	(472)	(606)
Net cash used in operating activities	(40,444)	(43,759)
Cash Flows from Investing Activities:
Proceeds from maturity of available-for-sale securities		26,870
Proceeds from the sale of property and equipment	193
Purchases of property and equipment	(71)	(100)
Net cash provided by investing activities	122	26,770
Cash Flows from Financing Activities:
Proceeds from employee stock purchases	205	184
Proceeds from exercise of common stock options and warrants	10,166	304
Payments on note payable	(209)	(216)
Payments on capital leases	(7)	(9)
Net cash provided by financing activities	10,155	263
Net decrease in cash, cash equivalents and restricted cash	(30,167)	(16,726)
Cash, cash equivalents and restricted cash, beginning of period	112,940	80,978
Cash, cash equivalents and restricted cash, end of period	$ 82,773	$ 64,252

CONDENSED STATEMENT OF STOCKHOLDERS' EQUITY - 9 months ended Sep. 30, 2018 - USD ($) shares in Thousands, $ in Thousands	Common Stock	Additional Paid-in Capital	Accumulated Deficit	Total
Beginning balance at Dec. 31, 2017	$ 24	$ 712,165	$ (604,494)	$ 107,695
Beginning balance, shares at Dec. 31, 2017	24,453			24,453
Issuance of common stock under employee stock purchase plan		205		$ 205
Issuance of common stock under employee stock purchase plan, shares	18
Issuance of common stock upon exercise of common stock options and warrants	$ 3	10,163		10,166
Issuance of common stock upon exercise of common stock options and warrants, shares	2,702
Issuance of common stock for services rendered		77		77
Issuance of common stock for services rendered, shares	6
Stock-based compensation		4,454		4,454
Net loss			(47,731)	(47,731)
Ending balance at Sep. 30, 2018	$ 27	$ 727,064	$ (652,225)	$ 74,866
Ending balance, shares at Sep. 30, 2018	27,179			27,179

Summary of Significant Accounting Policies

9 Months Ended

Sep. 30, 2018

Summary of Significant Accounting Policies

Summary of Significant Accounting Policies

Note 2. Summary of Significant Accounting Policies

Basis of Presentation

The accompanying unaudited financial statements included herein have been prepared by the Company in accordance with U.S. generally accepted accounting principles (“GAAP”) for interim financial information and pursuant to the rules and regulations of the Securities and Exchange Commission (the “SEC”). Accordingly, certain information and footnote disclosures normally included in financial statements prepared in accordance with GAAP have been condensed or omitted pursuant to such rules and regulations. In the opinion of management, all adjustments, consisting of normal recurring adjustments, and disclosures considered necessary for a fair presentation of interim period results have been included. Interim results for the three and nine months ended September 30, 2018 are not necessarily indicative of results that may be expected for the year ending December 31, 2018. For further information, refer to the financial statements and footnotes thereto included in the Company’s Annual Report on Form 10-K for the fiscal year ended December 31, 2017 (“2017 Form 10-K”), which was filed with the SEC on March 7, 2018.

Cash and Cash Equivalents

The Company considers all highly liquid investments with maturities of 90 days or less when purchased to be “cash equivalents.” Cash and cash equivalents at September 30, 2018 and December 31, 2017 consisted of cash and money market funds.

Restricted Cash

As part of the Company’s lease arrangement for its office and laboratory facility in Cambridge, Massachusetts, the Company is required to restrict cash held in a certificate of deposit securing a line of credit for the lessor. As of September 30, 2018 and December 31, 2017, the restricted cash amounted to $0.3 million and is recorded in “Prepaid expenses and other assets” as of September 30, 2018 and “Other assets” as of December 31, 2017 in the accompanying condensed balance sheets. In July 2018, the Company terminated the lease agreement, effective September 30, 2018, and will no longer be required to restrict cash for this purpose upon payment of the related $0.2 million lease termination fee which is included in “Restructuring costs” in the accompanying condensed statements of operations. The lease was terminated in connection with restructuring activities which are more fully described in Note 9.

The following table provides a reconciliation of cash, cash equivalents, and restricted cash reported within the balance sheets that sum to the total of the same such amounts shown in the statements of cash flows:


	September 30,		December 31,
(In thousands)	2018		2017
Cash and cash equivalents	$	82,462	$	112,629
Restricted cash		311		311
Cash, cash equivalents and restricted cash	$	82,773	$	112,940

Note 2. Summary of Significant Accounting Policies (Continued)

Financial Instruments

The fair value of the Company’s financial instruments is determined and disclosed in accordance with the three-tier fair value hierarchy specified in Note 3. The Company is required to disclose the estimated fair values of its financial instruments. As of September 30, 2018, the Company’s financial instruments consisted of cash, cash equivalents, and accounts receivable. As of December 31, 2017, the Company’s financial instruments consisted of cash, cash equivalents, accounts receivable and a note payable. The estimated fair values of these financial instruments approximate their carrying values as of September 30, 2018 and December 31, 2017. As of September 30, 2018, the Company did not have any derivatives, hedging instruments or other similar financial instruments.

Revenue Recognition

Effective January 1, 2018, the Company adopted Accounting Standards Codification (“ASC”) Topic 606, Revenue from Contracts with Customers, using the modified retrospective transition method. Under this method, the Company recognizes the cumulative effect of initially adopting ASC Topic 606, if any, as an adjustment to the opening balance of retained earnings. Additionally, under this method of adoption, the Company applies the guidance to all incomplete contracts in scope as of the date of initial application. This standard applies to all contracts with customers, except for contracts that are within the scope of other standards, such as leases, insurance, collaboration arrangements and financial instruments.

In accordance with ASC Topic 606, the Company recognizes revenue when its customer obtains control of promised goods or services, in an amount that reflects the consideration which the entity expects to receive in exchange for those goods or services. To determine revenue recognition for arrangements that the Company determines are within the scope of ASC Topic 606, it performs the following five steps:

(i)

identify the contract(s) with a customer;

(ii)

identify the performance obligations in the contract;

(iii)

determine the transaction price;

(iv)

allocate the transaction price to the performance obligations in the contract; and

(v)

recognize revenue when (or as) the entity satisfies a performance obligation.

The Company only applies the five-step model to contracts when it determines that it is probable it will collect the consideration it is entitled to in exchange for the goods or services it transfers to the customer. At contract inception, once the contract is determined to be within the scope of ASC Topic 606, the Company assesses the goods or services promised within each contract and determines those that are performance obligations, and assesses whether each promised good or service is distinct. The Company then recognizes as revenue the amount of the transaction price that is allocated to the respective performance obligation when (or as) the performance obligation is satisfied.

Amounts received prior to satisfying the revenue recognition criteria are recognized as deferred revenue in the Company’s balance sheet. Amounts expected to be recognized as revenue within the 12 months following the balance sheet date are classified as current portion of deferred revenue. Amounts not expected to be recognized as revenue within the 12 months following the balance sheet date are classified as deferred revenue, net of current portion.

Note 2. Summary of Significant Accounting Policies (Continued)

Alliance Revenues

The Company’s revenues have primarily been generated through collaborative research, development and/or commercialization agreements. The terms of these agreements may include payment to the Company of one or more of the following: nonrefundable, up-front license fees; research, development and commercial milestone payments; and other contingent payments due based on the activities of the counterparty or the reimbursement by licensees of costs associated with patent maintenance. Each of these types of revenue are recorded as Alliance revenues in the Company’s statements of operations.

In determining the appropriate amount of revenue to be recognized as it fulfills its obligations under each of its agreements, the Company performs the following steps:

(i)

identification of the promised goods or services in the contract;

(ii)

determination of whether the promised goods or services are performance obligations including whether they are distinct in the context of the contract;

(iii)

measurement of the transaction price, including the constraint on variable consideration;

(iv)

allocation of the transaction price to the performance obligations; and

(v)

recognition of revenue when (or as) the Company satisfies each performance obligation.

See Note 8, “Collaboration and License Agreements” for additional details regarding the Company’s collaboration arrangements.

As part of the accounting for these arrangements, the Company allocates the transaction price to each performance obligation on a relative stand-alone selling price basis. The stand-alone selling price may be, but is not presumed to be, the contract price. In determining the allocation, the Company maximizes the use of observable inputs. When the stand-alone selling price of a good or service is not directly observable, the Company estimates the stand-alone selling price for each performance obligation using assumptions that require judgment. Acceptable estimation methods include, but are not limited to: (i) the adjusted market assessment approach, (ii) the expected cost plus margin approach, and (iii) the residual approach (when the stand-alone selling price is not directly observable and is either highly variable or uncertain). In order for the residual approach to be used, the Company must demonstrate that (a) there are observable stand-alone selling prices for one or more of the performance obligations and (b) one of the two criteria in ASC 606-10- 32-34(c)(1) and (2) is met. The residual approach cannot be used if it would result in a stand-alone selling price of zero for a performance obligation as a performance obligation, by definition, has value on a stand-alone basis.

An option in a contract to acquire additional goods or services gives rise to a performance obligation only if the option provides a material right to the customer that it would not receive without entering into that contract. Factors that the Company considers in evaluating whether an option represents a material right include, but are not limited to: (i) the overall objective of the arrangement, (ii) the benefit the collaborator might obtain from the arrangement without exercising the option, (iii) the cost to exercise the option (e.g. priced at a significant and incremental discount) and (iv) the likelihood that the option will be exercised. With respect to options determined to be performance obligations, the Company recognizes revenue when those future goods or services are transferred or when the options expire.

Note 2. Summary of Significant Accounting Policies (Continued)

The Company’s revenue arrangements may include the following:

Up-front License Fees: If a license is determined to be distinct from the other performance obligations identified in the arrangement, the Company recognizes revenues from nonrefundable, up-front fees allocated to the license when the license is transferred to the licensee and the licensee is able to use and benefit from the license. For licenses that are bundled with other promises, the Company utilizes judgment to assess the nature of the combined performance obligation to determine whether the combined performance obligation is satisfied over time or at a point in time and, if over time, the appropriate method of measuring progress for purposes of recognizing revenue from non-refundable, up-front fees. The Company evaluates the measure of progress each reporting period and, if necessary, adjusts the measure of performance and related revenue recognition.

Milestone Payments: At the inception of an agreement that includes research and development milestone payments, the Company evaluates whether each milestone is considered probable of being achieved and estimates the amount to be included in the transaction price using the most likely amount method. If it is probable that a significant revenue reversal would not occur, the associated milestone value is included in the transaction price. Milestone payments that are not within the control of the Company or the licensee, such as regulatory approvals, are not considered probable of being achieved until those approvals are received. The transaction price is then allocated to each performance obligation on a relative stand-alone selling price basis, for which the Company recognizes revenue as or when the performance obligations under the contract are satisfied. At the end of each subsequent reporting period, the Company re-evaluates the probability of achievement of such milestones and any related constraint, and if necessary, adjusts its estimate of the overall transaction price. Any such adjustments are recorded on a cumulative catch-up basis, which would affect Alliance revenues and earnings in the period of adjustment.

Research and Development Activities: If the Company is entitled to reimbursement from its collaborators for specified research and development activities or the reimbursement of costs associated with patent maintenance, the Company determines whether such funding would result in Alliance revenues or an offset to research and development expenses. Reimbursement of patent maintenance costs are recognized during the period in which the related expenses are incurred as Alliance revenues in the Company’s statements of operations.

Royalties: If the Company is entitled to receive sales-based royalties from its collaborator, including milestone payments based on the level of sales, and the license is deemed to be the predominant item to which the royalties relate, the Company recognizes revenue at the later of (i) when the related sales occur, provided the reported sales are reliably measurable, or (ii) when the performance obligation to which some or all of the royalty has been allocated has been satisfied (or partially satisfied). To date, the Company has not recognized any royalty revenue resulting from any of its collaboration and license arrangements.

Manufacturing Supply and Research Services: Arrangements that include a promise for future supply of drug substance, drug product or research services at the licensee’s discretion are generally considered as options. The Company assesses if these options provide a material right to the licensee and if so, they are accounted for as separate performance obligations. If the Company is entitled to additional payments when the licensee exercises these options, any additional payments are recorded in Alliance revenues when the licensee obtains control of the goods, which is upon delivery, or as the services are performed.

The Company receives payments from its licensees based on schedules established in each contract. Upfront payments and fees are recorded as deferred revenue upon receipt, and may require deferral of revenue recognition to a future period until the Company performs its obligations under these arrangements. Amounts are recorded as accounts receivable when the Company’s right to consideration is unconditional. The Company does not assess whether a contract has a significant financing component if the expectation at contract inception is such that the period between payment by the licensees and the transfer of the promised goods or services to the licensees will be one year or less.

Note 2. Summary of Significant Accounting Policies (Continued)

Merger-related Costs, net

Merger-related costs, net includes amounts related to the transactions contemplated under the Merger Agreement, which was terminated in July 2018, as more fully described in Note 1. The line item includes charges incurred for transaction and integration-related professional fees, employee retention costs, and other incremental costs directly related to the potential merger. These costs were offset by the $6 million termination fee, which was received by the Company in July of 2018.

Restructuring Costs

Restructuring charges are primarily comprised of severance costs related to workforce reductions, contract termination and wind-down costs and asset impairments. In accordance with ASC 420, Exit or Disposal Cost Obligations, the Company recognizes restructuring charges when the liability has been incurred, except for one-time employee termination benefits that are incurred over time. Generally, one-time employee termination benefits (i.e. severance costs) are accrued at the date management has committed to a plan of termination and employees have been notified of their termination dates and expected severance payments. Other costs will be recorded as incurred. Asset impairment charges have been, and will be, recognized when management has concluded that the assets have been impaired in accordance with ASC 360-10-35, Impairment or Disposal of Long-Lived Assets, or other applicable authoritative guidance. See Note 9 for additional details.

Income Taxes

In accordance with ASC 270, Interim Reporting, and ASC 740, Income Taxes, the Company is required at the end of each interim period to determine the best estimate of its annual effective tax rate and then apply that rate in providing for income taxes on a current year-to-date (interim period) basis. For the three and nine months ended September 30, 2018 and 2017, the Company recorded no tax expense or benefit due to the expected current year loss and its historical losses. The Company has not recorded its net deferred tax asset as of either September 30, 2018 or December 31, 2017 because it maintained a full valuation allowance against all deferred tax assets as of these dates as management has determined that it is not more likely than not that the Company will realize these future tax benefits. As of September 30, 2018 and December 31, 2017, the Company had no uncertain tax positions.

In December 2017, the Tax Cuts and Jobs Act (“TCJA”) was signed into law. Among other things, the TCJA permanently lowers the corporate federal income tax rate to 21% from the existing maximum rate of 35%, effective for tax years including or commencing January 1, 2018. As a result of the reduction of the corporate federal income tax rate to 21%, GAAP requires companies to revalue their deferred tax assets and deferred tax liabilities as of the date of enactment, with the resulting tax effects accounted for in the reporting period of enactment. This revaluation resulted in a provision of $27.6 million to income tax expense and a corresponding reduction in the valuation allowance in the fourth quarter of 2017. As a result, there was no impact to the Company’s statement of operations and comprehensive loss as a result of reduction in tax rates. The Company’s preliminary estimate of the TCJA and the remeasurement of its deferred tax assets and liabilities is subject to the finalization of management’s analysis related to certain matters, such as developing interpretations of the provisions of the TCJA, changes to certain estimates and the filing of the Company’s tax returns. U.S. Treasury regulations, administrative interpretations or court decisions interpreting the TCJA may require further adjustments and changes in the Company’s estimates. The final determination of the TCJA and the remeasurement of the Company’s deferred assets and liabilities will be completed as additional information becomes available, but no later than one year from the enactment of the TCJA.

Note 2. Summary of Significant Accounting Policies (Continued)

New Accounting Pronouncements

Recently Adopted Accounting Pronouncements

In May 2014, the Financial Accounting Standards Board (“FASB”) issued ASU No. 2014-09, Revenue from Contracts with Customers (Topic 606), which was subsequently amended by several other ASU’s related to Topic 606 to, among other things, defer the effective date and clarify various aspects of the new revenue guidance including principal versus agent considerations, identifying performance obligations, and licensing, and include other improvements and practical expedients (as amended, “ASU 2014-09”). The Company adopted ASU 2014-09 in the first quarter of 2018 using the modified retrospective transition method. See “Revenue Recognition” above. To date, the Company has derived substantially all of its revenues from a limited number of license and collaboration agreements. The consideration the Company is eligible to receive under these agreements includes upfront payments, research and development funding, contingent revenues in the form of commercial and development milestones and option payments and royalties. Each of the Company’s license and collaboration agreements has unique terms and was evaluated separately under Topic 606. With respect to its license and collaboration agreements with Vivelix Pharmaceuticals, Ltd. (“Vivelix”) and GlaxoSmithKline Intellectual Property Development Limited (“GSK”), there was no material impact to Alliance revenues for any of the years presented upon adoption of Topic 606. Additionally, there were no revisions to any balance sheet components of Alliance revenues such as accounts receivable and deferred revenues or beginning retained earnings as a result of the adoption of the modified retrospective method. The primary impact on the Company’s financial statements was that revised or additional disclosures were made with respect to revenues and cash flows arising from contracts with customers, which are included in Notes 7 and 8.

In January 2016, the FASB issued ASU No. 2016-01, Recognition and Measurement of Financial Assets and Financial Liabilities (“ASU 2016-01”). The amendments in ASU 2016-01 address certain aspects of recognition, measurement, presentation and disclosure of financial instruments. The Company adopted ASU 2016-01 in the first quarter of 2018. The adoption of this new standard did not have a material impact on the Company’s financial position or results of operations.

In November 2016, the FASB issued ASU No. 2016-18, Statement of Cash Flows (Topic 230) — Restricted Cash (“ASU 2016-18”). The amendments in ASU 2016-18 require that a statement of cash flows explain the change during the period in the total of cash, cash equivalents, and amounts generally described as restricted cash and restricted cash equivalents. Accordingly, amounts generally described as restricted cash or restricted cash equivalents should be included with cash and cash equivalents when reconciling the beginning of period and end of period total amounts shown on the statement of cash flows. The Company adopted ASU 2016-18 in the first quarter of 2018, and the guidance has been retrospectively applied to all periods presented. The total of the Company’s cash, cash equivalents and restricted cash is described earlier in this Note 2.

Recently Issued (Not Yet Adopted) Accounting Pronouncements

In February 2016, the FASB issued ASU No. 2016-02, Leases (Topic 842) (“ASU 2016-02”). ASU 2016-02 requires organizations that lease assets, with lease terms of more than 12 months, to recognize on the balance sheet the assets and liabilities for the rights and obligations created by those leases. Consistent with GAAP, the recognition, measurement, and presentation of expenses and cash flows arising from a lease by a lessee primarily will depend on its classification as a finance or operating lease. However, unlike current GAAP which requires only capital leases to be recognized on the balance sheet, ASU 2016-02 will require both types of leases to be recognized on the balance sheet. This guidance is applicable to the Company's fiscal year beginning on January 1, 2019. The Company is currently evaluating the effect that the adoption of ASU 2016-02 will have on its financial statements and related disclosures. The Company expects that the majority of its operating lease commitments will be subject to this guidance and anticipates the recognition of additional assets and corresponding liabilities related to the adoption of the standard.

Fair Value Measurements

9 Months Ended

Sep. 30, 2018

Fair Value Measurements

Fair Value Measurements

Note 3. Fair Value Measurements

Assets and Liabilities Measured at Fair Value on a Recurring Basis

The Company applies the guidance in ASC 820, Fair Value Measurement, to account for financial assets and liabilities measured on a recurring basis. Fair value is measured at the price that would be received to sell an asset or paid to transfer a liability in an orderly transaction between market participants at the measurement date. As such, fair value is a market-based measurement that is determined based on assumptions that market participants would use in pricing an asset or liability.

The Company uses a fair value hierarchy, which distinguishes between assumptions based on market data (observable inputs) and an entity's own assumptions (unobservable inputs). The guidance requires that fair value measurements be classified and disclosed in one of the following three categories:

Level 1: Unadjusted quoted prices in active markets that are accessible at the measurement date for identical, unrestricted assets or liabilities;

Level 2: Quoted prices in markets that are not active or inputs which are observable, either directly or indirectly, for substantially the full term of the asset or liability; and

Level 3: Prices or valuation techniques that require inputs that are both significant to the fair value measurement and unobservable (i.e., supported by little or no market activity).

Determining which category an asset or liability falls within the hierarchy requires significant judgment. The Company evaluates its hierarchy disclosures each reporting period. There were no transfers between Level 1, 2 and 3 during the nine months ended September 30, 2018.

The table below presents the assets and liabilities measured and recorded in the financial statements at fair value on a recurring basis at September 30, 2018 and December 31, 2017 categorized by the level of inputs used in the valuation of each asset and liability:



	September 30, 2018
(In thousands)	Total		Level 1		Level 2		Level 3
Assets
Money market funds	$	17,746	$	17,746	$	—	$	—
Total assets	$	17,746	$	17,746	$	—	$	—
Total liabilities	$	—	$	—	$	—	$	—


	December 31, 2017
(In thousands)	Total		Level 1		Level 2		Level 3
Assets
Money market funds	$	66,183	$	66,183	$	—	$	—
Total assets	$	66,183	$	66,183	$	—	$	—
Total liabilities	$	—	$	—	$	—	$	—

The Level 1 assets consist of money market funds, which are actively traded daily.

- Definition

The entire disclosure for the fair value of financial instruments (as defined), including financial assets and financial liabilities (collectively, as defined), and the measurements of those instruments as well as disclosures related to the fair value of non-financial assets and liabilities. Such disclosures about the financial instruments, assets, and liabilities would include: (1) the fair value of the required items together with their carrying amounts (as appropriate); (2) for items for which it is not practicable to estimate fair value, disclosure would include: (a) information pertinent to estimating fair value (including, carrying amount, effective interest rate, and maturity, and (b) the reasons why it is not practicable to estimate fair value; (3) significant concentrations of credit risk including: (a) information about the activity, region, or economic characteristics identifying a concentration, (b) the maximum amount of loss the entity is exposed to based on the gross fair value of the related item, (c) policy for requiring collateral or other security and information as to accessing such collateral or security, and (d) the nature and brief description of such collateral or security; (4) quantitative information about market risks and how such risks are managed; (5) for items measured on both a recurring and nonrecurring basis information regarding the inputs used to develop the fair value measurement; and (6) for items presented in the financial statement for which fair value measurement is elected: (a) information necessary to understand the reasons for the election, (b) discussion of the effect of fair value changes on earnings, (c) a description of [similar groups] items for which the election is made and the relation thereof to the balance sheet, the aggregate carrying value of items included in the balance sheet that are not eligible for the election; (7) all other required (as defined) and desired information.

+ References + Details

Stockholders' Equity

9 Months Ended

Sep. 30, 2018

Stockholders' Equity

Stockholders' Equity

Note 6. Stockholders’ Equity

On June 20, 2018, the Company's stockholders approved an amendment to the Company's Restated Certificate of Incorporation, as amended, to effect a reverse stock split of the Company's outstanding shares of common stock at a ratio within a range from 1-for-4 to 1-for-8 and set the number of authorized shares of the Company’s common stock at a number determined by calculating the product of 280,000,000 multiplied by two times (2x) the reverse stock split ratio. On July 27, 2018, the Company implemented a 1-for-8 reverse split of its issued and outstanding shares of common stock (the “Reverse Split”), and set the number of its authorized shares of common stock to 70,000,000. The Reverse Split became effective on July 27, 2018 at 5:00 p.m., Eastern Time, and the Company’s common stock began trading on the Nasdaq Capital Market on a Reverse Split-adjusted basis at the opening of trading on July 30, 2018. As of a result of the Reverse Split, every eight shares of the Company’s issued and outstanding common stock were combined into one share of its common stock, except to the extent that the Reverse Split resulted in any of the Company’s stockholders owning a fractional share, which was settled in cash. In connection with the Reverse Split, there was no change in the nominal par value per share of $0.001. The Reverse Split did not change the number of authorized shares or par value of the Company’s preferred stock.

Common Stock Warrants

In connection with various financing transactions, the Company has issued warrants to purchase shares of the Company’s common stock. The Company accounts for warrants as equity instruments, derivative liabilities, or liabilities, depending on the specific terms of the warrant. As of September 30, 2018 and December 31, 2017, all of the Company’s outstanding warrants were equity-classified.

Note 6. Stockholders’ Equity (Continued)

The following table summarizes outstanding warrants to purchase shares of the Company’s common stock as of September 30, 2018 and December 31, 2017:


	Number of Shares
	September 30,	December 31,	Weighted-Average
Description	2018	2017	Exercise Price		Expiration Date
Issued in May 2013 financing	—	2,700,791		$ 3.76	May 2018
Issued in May 2013 financing (pre-funded)	1,977,041	1,977,041		$ 0.08	May 2020
Issued in September 2013 financing (pre-funded)	521,997	521,997		$ 0.08	Sep 2020
Issued in February 2014 financing (pre-funded)	269,844	269,844		$ 0.08	Feb 2021
Total	2,768,882	5,469,673

The table below is a summary of the Company's warrant activity for the nine months ended September 30, 2018:


	Number of	Weighted-Average
	Warrants	Exercise Price
Outstanding at December 31, 2017	5,469,673	$	1.90
Issued	—		—
Exercised (1)	(2,700,791)		3.76
Expired	—		—
Outstanding at September 30, 2018	2,768,882	$	0.08

(1) During the nine months ended September 30, 2018, a related party exercised certain of these warrants as more fully described in Note 11.

Alliance Revenue

9 Months Ended

Sep. 30, 2018

Alliance Revenue

Alliance Revenue

Note 7. Alliance Revenue

Alliance revenue for the nine months ended September 30, 2018 and 2017 represents revenue from contracts with customers accounted for in accordance with ASC Topic 606, which the Company adopted in the first quarter of 2018, as more fully described in Note 2. There was no impact to Alliance revenue previously recognized by the Company as a result of the adoption of ASC Topic 606.

For the three and nine months ended September 30, 2018 and 2017, Alliance revenue in the accompanying statements of operations and comprehensive loss is comprised of the following:


	Three months ended				Nine months ended
	September 30,				September 30,
(In thousands)	2018		2017		2018		2017
GSK collaboration (1)	$	141	$	141	$	424	$	698
Vivelix collaboration (2)		—		14		56		14
Other (3)		4		9		83		17
Total Alliance revenue	$	145	$	164	$	563	$	729

(1)

For all periods presented, revenue recognized primarily relates to the amortization of the deferred up-front payment received at inception of the Company’s collaboration and license agreement with GSK Agreement, as more fully described in Note 8. Revenue recognized for the nine months ended September 30, 2017 also includes an additional $0.1 million related to additional research services provided in connection with the collaboration and license agreement with GSK.

(2)

For the nine months ended September 30, 2018, revenue recognized relates to services provided under the research program provided for under the Company’s exclusive license and collaboration agreement with Vivelix, as more fully described in Note 8.

Note 7. Alliance Revenue (Continued)

(3)

For all periods presented, revenue recognized relates to collaborations which are not material to the Company’s current operations nor expected to be material in the future, including reimbursements by licensees of costs associated with patent maintenance.

The following table presents changes in the Company’s contract assets and liabilities during the nine months ended September 30, 2018 and 2017:


	Nine months ended September 30, 2018
(In thousands)	Beginning		Additions		Deductions		Ending
Contract assets	$	—	$	—	$	—	$	—
Contract liabilities:
Deferred revenue	$	566	$	—	$	(472)	$	94


	Nine months ended September 30, 2017
(In thousands)	Beginning		Additions		Deductions		Ending
Contract assets	$	—	$	—	$	—	$	—
Contract liabilities:
Deferred revenue	$	1,263	$	—	$	(606)	$	657

During the nine months ended September 30, 2018 and 2017, the Company recognized Alliance revenues of $0.5 million and $0.6 million, respectively, as a result of changes in the contract liability balances associated with its contracts with customers. Revenue recognized during each of the nine months ended September 30, 2018 and 2017 were included in the contract liability at the beginning of each respective period. As of September 30, 2018, contract liabilities consisted of deferred revenue related entirely to the Company’s collaboration and license agreement with GSK and were included in Deferred revenue in the accompanying condensed balance sheet.

See Note 8 for additional details regarding the Company’s collaboration arrangements.

Collaboration and License Agreements	9 Months Ended
Collaboration and License Agreements	Sep. 30, 2018
Collaboration and License Agreements
Collaboration and License Agreements	Note 8. Collaboration and License Agreements Collaboration with Vivelix In November 2016, the Company entered into an exclusive license and collaboration agreement with Vivelix pursuant to which the Company granted Vivelix worldwide rights to develop and market IMO-9200, an antagonist of TLR7, TLR8, and TLR9, for non-malignant gastrointestinal disorders (the “GI Field” or “Field” as defined in the Vivelix Agreement), and certain back-up compounds to IMO-9200 (the “Vivelix Agreement”). The Company was previously developing IMO-9200 for potential use in selected autoimmune disease indications. However, the Company determined not to proceed with internal development of IMO-9200 because the large autoimmune disease indications for which IMO-9200 had been developed did not fit within the strategic focus of the Company. Under the terms of the Vivelix Agreement, Vivelix is solely responsible for the development and commercialization of IMO-9200 and any designated back-up compounds. In connection with the Vivelix Agreement, Idera also transferred certain drug material to Vivelix for Vivelix’s use in its development activities. Pursuant to the Vivelix Agreement, Vivelix could request that the Company create, characterize and perform research on back-up compounds (the “Research Program”). Such activity was to be mutually agreed upon and moderated by the Joint Research Committee (“JRC”) established under the Vivelix Agreement. The research period commenced with the execution of the agreement and may last for up to three years. As a result of the Company’s decision to wind-down its discovery operations as described in Note 9, in July 2018, the Company informed Vivelix that no additional research projects will be undertaken by the Company. Note 8. Collaboration and License Agreements (Continued) Vivelix has certain rights under the agreement whereby it may exercise (i) the right of first refusal to develop and commercialize products in any available field (“Right of First Refusal”), (ii) the right of first negotiation to obtain an exclusive license for any compound controlled by Idera that has activity in the field of inflammatory bowel disease (“Right of First Negotiation”) and (iii) the right to request an expanded Field beyond the GI Field (“Expanded Field Option”). Under the terms of the Vivelix Agreement, the Company received an upfront, non-refundable fee of $15 million. In addition, the Company will be eligible for future IMO-9200 related development, regulatory and sales milestone payments totaling up to $140 million, including development and regulatory milestones totaling up to $65 million and sales milestones totaling up to $75 million, and escalating royalties ranging from the mid single-digits to low double-digits of global net sales, which percentages are subject to reduction under agreed upon circumstances. As it relates to back-up compounds, including certain compounds controlled by the Company as of the effective date of the Vivelix Agreement and/or those created at Vivelix’s request under the Research Program, the Company will be eligible for related designation payments and development, regulatory and sales milestone payments totaling up to $52.5 million, including development and regulatory milestones totaling up to $35 million and sales milestones totaling up to $17.5 million and escalating royalties ranging from the mid single-digits to low double-digits of global net sales, which percentages are subject to reduction under agreed upon circumstances. Under the terms of the agreement, the Company has performed research services, as requested by Vivelix and at Vivelix’s expense. To date, Vivelix has not designated any back-up compounds subject to the Research Program, such right which expires on the third anniversary of the end of the Research Period. At the effective date of the Vivelix Agreement, Baker Bros. Advisors LP and certain of its affiliated funds (collectively, “Baker Brothers”) beneficially owned approximately 7.0% of the Company’s outstanding common stock and affiliates of Baker Brothers constituted two of the seven directors on the board of directors of the Company. Baker Brothers also owned a controlling financial interest of Vivelix at the effective date of the Vivelix Agreement and as of December 31, 2017, and affiliates of Baker Brothers constituted two of the four directors on the board of directors of Vivelix. However, the boards of the Company and Vivelix share no common board members. See Note 11 for information on related parties of the Company as of September 30, 2018. Pursuant to the Vivelix Agreement, Vivelix conducted two clinical studies on IMO-9200 in the field of inflammatory bowel diseases. While there were no apparent safety signals identified in either study, there was no apparent benefit associated with IMO-9200 at the doses studied compared with placebo. As a result, Vivelix has decided to terminate ongoing development activities related to IMO-9200. However, a final decision by Vivelix on whether to continue working on IMO-9200 or terminate the Vivelix Agreement has not been made as of November 4, 2018. Accounting Analysis under ASC 606 In evaluating the Vivelix Agreement in accordance with ASC Topic 606, the Company concluded that the contract counterparty, Vivelix, is a customer. The Company identified the following performance obligations as of the inception of agreement: (i) a research and commercialization license for IMO-9200 and back-up compounds to IMO-9200 (the “IMO-9200 License”) and (ii) drug materials transferred, which were both deemed to be distinct. The Company determined that participation in the JRC was immaterial in the context of the contract. Consistent with the guidance under ASC 606-10-25-16A, the Company disregarded immaterial promised goods and services when determining performance obligations. The Company concluded that the IMO-9200 License was distinct within the context of the contract (i.e. separately identifiable) because it has stand-alone value from other promised goods and services as Vivelix could benefit from the IMO-9200 License on a stand-alone basis and sell the compound in the market without any additional involvement or participation from Idera. Additionally, Idera has no further obligations related to the IMO-9200 License. In the event that Vivelix does not make a designated compound payment, the license to back-up compounds reverts back to Idera at the end of the research term at no cost or payment by either party. The services provided under the Research Program relate to the back-up compounds and Vivelix would be able to conduct research and development activities with external third parties, as IMO-9200 is at an advanced enough stage where Idera’s expertise would not be required. Accordingly, the IMO-9200 License is a separate performance obligation. Note 8. Collaboration and License Agreements (Continued) The Company concluded that the drug materials transferred identified at the inception are also distinct within the context of the contract (i.e. separately identifiable) because they have standalone value from other promised goods and services based on their nature. Accordingly, the drug materials transferred are a separate performance obligation. Allocable arrangement consideration at inception of the Vivelix Agreement was comprised of the up-front payment of $15 million. The $15 million was allocated based on the relative stand-alone selling prices of each performance obligation. Allocated revenue associated with the IMO-9200 License was recognized at the inception of the Vivelix Agreement in the fourth quarter of 2016 as Vivelix was granted an exclusive, perpetual license to develop and commercialize IMO-9200 and certain back-up compounds to IMO-9200, subject to certain designation milestone and royalty payments, and the performance obligations of Idera under the agreement were extinguished at that point. Allocable revenue associated with drug materials transferred shortly after the inception of the agreement was recognized upon delivery, also in the fourth quarter of 2016. At inception of the contract, the transaction price included only the $15.0 million up-front consideration received. None of the development and commercialization milestones were included in the transaction price, as all milestone amounts were fully constrained. As part of its evaluation of the constraint, the Company considered numerous factors, including that receipt of the milestones is outside the control of the Company and contingent upon success in future clinical trials and the licensee’s efforts. Similarly, other variable consideration related to services that may be provided under the Research Program and back-up compound designation payments were fully constrained. Any consideration related to sales-based royalties will be recognized when the related sales occur, provided that the reported sales are reliably measurable and the Company has no remaining performance obligations, as such sales were determined to relate predominantly to the license granted to Vivelix and therefore have also been excluded from the transaction price. The Company re-evaluates the transaction price in each reporting period and as uncertain events are resolved or other changes in circumstances occur. Revenue associated with goods and services provided to Vivelix under the Research Program have been immaterial to date and such revenue is recognized as the related performance obligations under each research project are satisfied. See Note 7 for details on revenue recognized in connection with the Company’s collaboration with Vivelix for the three and nine months ended September 30, 2018 and 2017. Collaboration with GSK In November 2015, the Company entered into a collaboration and license agreement with GSK to license, research, develop and commercialize pharmaceutical compounds from the Company’s nucleic acid chemistry technology for the treatment of selected targets in renal disease (the “GSK Agreement”). The initial collaboration term is currently anticipated to last between two and four years. In connection with the GSK Agreement, GSK identified an initial target for the Company to attempt to identify a potential population of development candidates to address such target under a mutually agreed upon research plan, which is estimated to take 36 months to complete. From the population of identified development candidates, GSK may designate one development candidate in its sole discretion to move forward into clinical development. If GSK designates a development candidate, GSK would be solely responsible for the development and commercialization activities for that designated development candidate. The GSK Agreement also provided GSK with the option to select up to two additional targets at any time during the first two years of the GSK Agreement for further research under mutually agreed upon research plans. Upon selecting additional targets, GSK then had the option to designate one development candidate for each additional target, at which time GSK would have sole responsibility to develop and commercialize each such designated development candidate. GSK did not select any additional targets for research through expiry of the option period. In accordance with the GSK Agreement, a Joint Steering Committee (“JSC”) was formed with equal representation from Idera and GSK. The responsibilities of the JSC, include, but are not limited to monitoring the progress of the collaboration, reviewing research plans and dealing with disputes that may arise between the parties. If a dispute cannot be resolved by the JSC, GSK has final decision-making authority. Note 8. Collaboration and License Agreements (Continued) Under the terms of the GSK Agreement, the Company received a $2.5 million upfront, non-refundable, non-creditable cash payment upon the execution of the GSK Agreement. Additionally, the Company was eligible to receive a total of up to approximately $100 million in license, research, clinical development and commercialization milestone payments, of which $9 million of these milestone payments would have been payable by GSK upon the identification of the additional targets, the completion of current and future research plans and the designation of development candidates and $89 million would have been payable by GSK upon the achievement of clinical milestones and commercial milestones. As a result of GSK not selecting additional targets during the two-year option period, the Company is now only eligible to receive a total of up to approximately $20 million in license, research, clinical development and commercialization milestone payments, of which $1 million would be payable by GSK upon the designation of a development candidate from the initial target and $17 million would be payable by GSK upon the achievement of clinical milestones and commercial milestones. In addition, the Company is eligible to receive royalty payments on sales upon commercialization at varying rates of up to 5% on annual net sales, as defined in the GSK Agreement. Accounting Analysis under ASC 606 In evaluating the GSK Agreement in accordance with ASC Topic 606, the Company concluded that the contract counterparty, GSK, is a customer. The Company identified the following performance obligations as of the inception of the agreement: (i) research services, combined with the license for Idera’s proprietary technology related to the initial target (collectively, the “Collaboration License and Research Services”) and (ii) daily options to extend the Collaboration License and Research Services. The Company determined that participation in the JSC and materials transferred were deemed immaterial in the context of the contract. Consistent with the guidance under ASC 606-10-25-16A, the Company disregarded immaterial promised goods and services when determining performance obligations. The Company concluded that the research services related to the initial target and collaboration license to the Company’s proprietary technology related to the initial target were not capable of being distinct as the collaboration license related to the initial target is highly interdependent upon the research services to be provided related to the initial target. As it relates to the assessment of standalone value, the Company determined that GSK cannot fully exploit the value of the collaboration license without receipt of the research services from the Company. The research services involve unique skills and specialized expertise, particularly as it relates to the Company’s proprietary technology, which is not available in the marketplace. Accordingly, GSK must obtain the research services from the Company which significantly limits the ability for GSK to utilize the collaboration license for its intended purpose on a standalone basis. Similarly, the Company concluded that the daily option to extend the collaboration license and the daily option to extend the research services were also highly interdependent as the license has no value to GSK without the accompanying research services using the Company’s proprietary technology. Accordingly, the Collaboration License and Research Services were determined to represent a single performance obligation and the daily options to extend the Collaboration License and Research Services were determined to represent a single performance obligation. Factors considered in this determination included, among other things, the capabilities of the collaborator, whether any other vendor sells the item separately, whether the value of the deliverable is dependent on the other elements in the arrangement, whether there are other vendors that can provide the items and if the customer could use the item for its intended purpose without the other deliverables in the arrangement. Allocable arrangement consideration at inception of the GSK Agreement consisted of the up-front payment of $2.5 million. The $2.5 million was allocated based on the relative stand-alone selling prices of each performance obligation, calculated based on the expected period of time over which the initial license term will be in place, as well as the expected period of time over which the optional renewals occur. The Company will recognize the consideration allocated to the Collaboration License and Research Services over time as GSK is receiving the benefit of the Company’s expertise and know-how on an on-going basis as the research progresses towards the goal of the development candidate designation for the initial target. The exercise of the daily options to extend the Collaboration License and Research Services are treated as a continuation of the contract and allocated consideration is recognized point-in-time upon commencement of each daily exercise. Note 8. Collaboration and License Agreements (Continued) At inception of the contract, the transaction price included only the $2.5 million up-front consideration received. None of the development and commercialization milestones were included in the transaction price, as all milestone amounts were fully constrained. As part of its evaluation of the constraint, the Company considered numerous factors, including that receipt of the milestones is outside the control of the Company and contingent upon success in future clinical trials and the licensee’s efforts. Any consideration related to sales-based royalties will be recognized when the related sales occur, provided that the reported sales are reliably measurable and the Company has no remaining performance obligations, as such sales were determined to relate predominantly to the license granted to GSK and therefore have also been excluded from the transaction price. The Company re-evaluates the transaction price in each reporting period and as uncertain events are resolved or other changes in circumstances occur. The up-front payment of $2.5 million was recorded as deferred revenue in the Company’s balance sheet upon receipt and is currently being recognized as revenue on a straight-line basis over the estimated 36-month research plan period, which approximates the timing in which performance obligations are satisfied. See Note 7 for details on revenue recognized in connection with the Company’s collaboration with GSK for each of the three and nine months ended September 30, 2018 and 2017.

Restructuring Costs

9 Months Ended

Sep. 30, 2018

Restructuring Costs

Restructuring Costs

Note 9. Restructuring Costs

In July 2018, the Company determined to wind-down its discovery operations, reduce the workforce in Cambridge, Massachusetts that supports such operations, and close its Cambridge facility. In connection with the reduction-in-workforce, 18 positions are being eliminated, primarily in the area of discovery, representing approximately 40% of the Company’s employees. Of the 18 positions being eliminated, 15 were effective July 31, 2018 with the remaining expected to be eliminated by December 31, 2018.

Restructuring-related charges for both the three and nine months ended September 30, 2018 totaled $3.0 million and were comprised of (i) one-time termination costs in connection with the reduction in workforce, including severance, benefits and related costs, of approximately $2.4 million; (ii) contract termination costs of approximately $0.2 million in connection with the early lease termination for the Cambridge facility, as further discussed below; (iii) non-cash asset impairments of approximately $0.7 million, which includes $0.5 million of fixed asset impairments and $0.2 million in write-offs of facility-related prepaid expenses; offset by (iv) a non-cash gain of approximately $0.4 million related to the write-off of the remaining deferred rent liability associated with the Cambridge facility lease.


($ in thousands)	Employee Severance and Benefits		Contract Termination Costs		Asset Impairments		Total
Accrued restructuring balance as of December 31, 2017	$	—	$	—	$	—	$	—
Charges incurred (1)		2,436		225		694		3,355
Cash payments		(625)		(61)		—		(686)
Non-cash settlements		(24)		—		(694)		(718)
Accrued restructuring balance as of September 30, 2018	$	1,787	$	164	$	—	$	1,951

(1)

Excludes $0.4 million gain due to the write-off of the remaining deferred rent liability associated with the termination of the Cambridge, Massachusetts facility lease.

As of September 30, 2018, the short-term portion of the accrued restructuring balance, or $1.9 million, is included in “Accrued expenses” in the accompanying condensed balance sheets. See Note 9. The long-term portion of less than $0.1 million is included within “Other liabilities’ in the accompanying condensed balance sheets.

Note 9. Restructuring Costs (Continued)

In connection with the closing of its Cambridge facility, on July 27, 2018, the Company entered into a termination agreement with the landlord terminating the lease agreement, dated October 31, 2006, as amended, between the Company and the landlord effective September 30, 2018. The Company leased its facility at 167 Sidney Street in Cambridge under the lease agreement. Under the terms of the termination agreement, the Company has agreed to pay an early termination fee of $0.2 million. The Company recorded a charge for the $0.2 million early termination fee and a non-cash gain of $0.4 million due to the write-off of the remaining deferred rent liability associated with the lease in the third quarter of 2018. The Company completed the consolidation of its operations to its Exton, Pennsylvania location in the third quarter of 2018.

Stock-Based Compensation

9 Months Ended

Sep. 30, 2018

Stock-Based Compensation

Stock-Based Compensation

Note 10. Stock-Based Compensation

Equity Compensation Plans

2013 Stock Incentive Plan

The Company's board of directors adopted the 2013 Stock Incentive Plan (as amended to date, the “2013 Plan”), which was approved by the Company’s stockholders effective July 26, 2013. The 2013 Plan is intended to further align the interests of the Company and its stockholders with its employees, including its officers, non-employee directors, consultants and advisers by providing equity-based incentives. The 2013 Plan allows for the issuance of up to such number of shares of the Company’s common stock as equal to (i) 3,153,057 shares of common stock; plus (ii) such additional number of shares of common stock (up to 868,372 shares) as is equal to the sum of the number of shares of common stock subject to awards granted under the Company’s 2005 Stock Incentive Plan (the “2005 Plan”) or the Company’s 2008 Stock Incentive Plan (the “2008 Plan” and, together with the 2005 Plan, the “Existing Plans”) which awards expire, terminate or are otherwise surrendered, canceled, forfeited or repurchased by the Company at their original issuance price pursuant to a contractual repurchase right (subject, however, in the case of incentive stock options to any limitations of the Internal Revenue Code).

As of September 30, 2018, options to purchase a total of 2,418,332 shares of common stock were outstanding and up to 941,192 shares of common stock remained available for grant under the 2013 Plan. The Company has not made any awards pursuant to other equity incentive plans, including the Existing Plans, since the Company’s stockholders approved the 2013 Plan. As of September 30, 2018, options to purchase a total of 511,093 shares of common stock were outstanding under these earlier plans.

In addition, as of September 30, 2018, non-statutory stock options to purchase an aggregate of 393,750 shares of common stock were outstanding that were issued outside of the 2013 Plan to certain employees in 2017, 2015 and 2014 pursuant to the Nasdaq inducement grant exception as a material component of new hires’ employment compensation.

2017 Employee Stock Purchase Plan

The Company’s board of directors adopted the 2017 Employee Stock Purchase Plan (the “2017 ESPP”) which was approved by the Company’s stockholders and became effective on June 7, 2017. The 2017 ESPP provides for the issuance of up to 62,500 shares of common stock to participating employees of the Company or its subsidiaries. Participation is limited to employees that would not own 5% or more of the total combined voting power or value of the stock of the Company after the grant. As of September 30, 2018, 38,763 shares remained available for issuance under the 2017 ESPP.

Note 10. Stock-Based Compensation (Continued)

For the nine months ended September 30, 2018 and 2017, the Company issued 18,355 and 16,490 shares of common stock, respectively, under the 2017 ESPP and the Company’s 1995 Employee Stock Purchase Plan and received proceeds of approximately $0.2 million during each period as a result of employee stock purchases.

Accounting for Stock-based Compensation

The Company recognizes non-cash compensation expense for stock-based awards under the Company’s equity incentive plans over an award’s requisite service period, or vesting period, using the straight-line attribution method, based on their grant date fair value determined using the Black-Scholes option-pricing model. The Company also recognizes non-cash compensation for stock purchases made under the 2017 ESPP. The fair value of the discounted purchases made under the Company’s 2017 ESPP is calculated using the Black-Scholes option-pricing model. The fair value of the look-back provision plus the 15% discount is recognized as compensation expense over each plan period.

Total stock-based compensation expense attributable to stock-based payments made to employees and directors and employee stock purchases included in operating expenses in the Company's statements of operations for the three and nine months ended September 30, 2018 and 2017 was as follows:


	Three Months Ended				Nine Months Ended
	September 30,				September 30,
(in thousands)	2018		2017		2018		2017
Stock-based compensation:
Research and development
Employee Stock Purchase Plans	$	11	$	26	$	62	$	68
Equity Incentive Plans		303		563		1,379		5,904
	$	314	$	589	$	1,441	$	5,972
General and administrative
Employee Stock Purchase Plans	$	8	$	18	$	40	$	48
Equity Incentive Plans		981		1,016		2,949		3,145
	$	989	$	1,034	$	2,989	$	3,193
Restructuring costs
Employee Stock Purchase Plans	$	24	$	—	$	24	$	—
	$	24	$	—	$	24	$	—
Total stock-based compensation expense	$	1,327	$	1,623	$	4,454	$	9,165

During the nine months ended September 30, 2018 and 2017, the weighted average fair market value of stock options granted was $7.15 and $8.08, respectively. The following weighted average assumptions apply to the options to purchase 1,091,474 and 520,812 shares of common stock granted to employees and directors during the nine months ended September 30, 2018 and 2017, respectively:


	Nine Months Ended
	September 30,
	2018		2017
Average risk-free interest rate		2.5%		1.7%
Expected dividend yield		—		—
Expected lives (years)		3.8		4.0
Expected volatility		74.0%		86.5%
Weighted average exercise price (per share)	$	12.91	$	12.88

All options granted during the nine months ended September 30, 2018 were granted at exercise prices equal to the fair market value of the common stock on the dates of grant.

Note 10. Stock-Based Compensation (Continued)

Stock Option Activity

The following table summarizes stock option activity for the nine months ended September 30, 2018:


($ in thousands, except per share data)	Stock Options	Weighted-Average Exercise Price		Weighted-Average Remaining Contractual Life (in years)	Aggregate Intrinsic Value
Outstanding at December 31, 2017	2,675,184	$	23.52	6.5	$	5,805
Granted	1,091,474		12.91
Exercised	(858)		12.77
Forfeited	(279,444)		18.16
Expired	(163,181)		47.56
Outstanding at September 30, 2018 (1)	3,323,175	$	19.31	6.7	$	1,249
Exercisable at September 30, 2018	1,958,773	$	22.96	5.0	$	714

(1)

Includes both vested stock options as well as unvested stock options for which the requisite service period has not been rendered but that are expected to vest based on achievement of a service condition.

The fair value of options that vested during the nine months ended September 30, 2018 was $5.1 million. As of September 30, 2018, there was $9.1 million of unrecognized compensation cost related to unvested options, which the Company expects to recognize over a weighted average period of 2.7 years.

Summary of Significant Accounting Policies (Policies)

9 Months Ended

Sep. 30, 2018

Summary of Significant Accounting Policies

Basis of Presentation

Cash and Cash Equivalents

Restricted Cash


	September 30,		December 31,
(In thousands)	2018		2017
Cash and cash equivalents	$	82,462	$	112,629
Restricted cash		311		311
Cash, cash equivalents and restricted cash	$	82,773	$	112,940

Financial Instruments

Revenue Recognition

(i)

identify the contract(s) with a customer;

(ii)

identify the performance obligations in the contract;

(iii)

determine the transaction price;

(iv)

allocate the transaction price to the performance obligations in the contract; and

(v)

recognize revenue when (or as) the entity satisfies a performance obligation.

Note 2. Summary of Significant Accounting Policies (Continued)

Alliance Revenues

In determining the appropriate amount of revenue to be recognized as it fulfills its obligations under each of its agreements, the Company performs the following steps:

(i)

identification of the promised goods or services in the contract;

(ii)

determination of whether the promised goods or services are performance obligations including whether they are distinct in the context of the contract;

(iii)

measurement of the transaction price, including the constraint on variable consideration;

(iv)

allocation of the transaction price to the performance obligations; and

(v)

recognition of revenue when (or as) the Company satisfies each performance obligation.

See Note 8, “Collaboration and License Agreements” for additional details regarding the Company’s collaboration arrangements.

Note 2. Summary of Significant Accounting Policies (Continued)

The Company’s revenue arrangements may include the following:

Merger-related Costs, net

Restructuring Costs

Income Taxes

New Accounting Pronouncements

Recently Adopted Accounting Pronouncements

Recently Issued (Not Yet Adopted) Accounting Pronouncements

Fair Value Measurements (Tables)

9 Months Ended

Sep. 30, 2018

Fair Value Measurements

Schedule of assets and liabilities measured and recorded in financial statements at fair value on a recurring basis



	September 30, 2018
(In thousands)	Total		Level 1		Level 2		Level 3
Assets
Money market funds	$	17,746	$	17,746	$	—	$	—
Total assets	$	17,746	$	17,746	$	—	$	—
Total liabilities	$	—	$	—	$	—	$	—


	December 31, 2017
(In thousands)	Total		Level 1		Level 2		Level 3
Assets
Money market funds	$	66,183	$	66,183	$	—	$	—
Total assets	$	66,183	$	66,183	$	—	$	—
Total liabilities	$	—	$	—	$	—	$	—

Stockholders' Equity (Tables)

9 Months Ended

Sep. 30, 2018

Stockholders' Equity

Schedule of warrants outstanding and exercisable for purchase of common stock


	Number of Shares
	September 30,	December 31,	Weighted-Average
Description	2018	2017	Exercise Price		Expiration Date
Issued in May 2013 financing	—	2,700,791		$ 3.76	May 2018
Issued in May 2013 financing (pre-funded)	1,977,041	1,977,041		$ 0.08	May 2020
Issued in September 2013 financing (pre-funded)	521,997	521,997		$ 0.08	Sep 2020
Issued in February 2014 financing (pre-funded)	269,844	269,844		$ 0.08	Feb 2021
Total	2,768,882	5,469,673

Summary of warrant activity

The table below is a summary of the Company's warrant activity for the nine months ended September 30, 2018:


	Number of	Weighted-Average
	Warrants	Exercise Price
Outstanding at December 31, 2017	5,469,673	$	1.90
Issued	—		—
Exercised (1)	(2,700,791)		3.76
Expired	—		—
Outstanding at September 30, 2018	2,768,882	$	0.08

(1) During the nine months ended September 30, 2018, a related party exercised certain of these warrants as more fully described in Note 11.

- Definition

Tabular disclosure of warrants or rights issued. Warrants and rights outstanding are derivative securities that give the holder the right to purchase securities (usually equity) from the issuer at a specific price within a certain time frame. Warrants are often included in a new debt issue to entice investors by a higher return potential. The main difference between warrants and call options is that warrants are issued and guaranteed by the company, whereas options are exchange instruments and are not issued by the company. Also, the lifetime of a warrant is often measured in years, while the lifetime of a typical option is measured in months. Disclose the title of issue of securities called for by warrants and rights outstanding, the aggregate amount of securities called for by warrants and rights outstanding, the date from which the warrants or rights are exercisable, and the price at which the warrant or right is exercisable.

+ References + Details

Alliance Revenue (Tables)

9 Months Ended

Sep. 30, 2018

Alliance Revenue

Schedule of accompanying statements of operations and comprehensive loss


	Three months ended				Nine months ended
	September 30,				September 30,
(In thousands)	2018		2017		2018		2017
GSK collaboration (1)	$	141	$	141	$	424	$	698
Vivelix collaboration (2)		—		14		56		14
Other (3)		4		9		83		17
Total Alliance revenue	$	145	$	164	$	563	$	729

(1)

(2)

Note 7. Alliance Revenue (Continued)

(3)

Schedule of changes in the Company’s contract assets and liabilities


	Nine months ended September 30, 2018
(In thousands)	Beginning		Additions		Deductions		Ending
Contract assets	$	—	$	—	$	—	$	—
Contract liabilities:
Deferred revenue	$	566	$	—	$	(472)	$	94


	Nine months ended September 30, 2017
(In thousands)	Beginning		Additions		Deductions		Ending
Contract assets	$	—	$	—	$	—	$	—
Contract liabilities:
Deferred revenue	$	1,263	$	—	$	(606)	$	657

Stock-Based Compensation (Tables)

9 Months Ended

Sep. 30, 2018

Stock-Based Compensation

Schedule of stock-based compensation expense attributable to share-based payments made to employees and directors and included in operating expenses


	Three Months Ended				Nine Months Ended
	September 30,				September 30,
(in thousands)	2018		2017		2018		2017
Stock-based compensation:
Research and development
Employee Stock Purchase Plans	$	11	$	26	$	62	$	68
Equity Incentive Plans		303		563		1,379		5,904
	$	314	$	589	$	1,441	$	5,972
General and administrative
Employee Stock Purchase Plans	$	8	$	18	$	40	$	48
Equity Incentive Plans		981		1,016		2,949		3,145
	$	989	$	1,034	$	2,989	$	3,193
Restructuring costs
Employee Stock Purchase Plans	$	24	$	—	$	24	$	—
	$	24	$	—	$	24	$	—
Total stock-based compensation expense	$	1,327	$	1,623	$	4,454	$	9,165

Schedule of weighted average assumptions applied to options


	Nine Months Ended
	September 30,
	2018		2017
Average risk-free interest rate		2.5%		1.7%
Expected dividend yield		—		—
Expected lives (years)		3.8		4.0
Expected volatility		74.0%		86.5%
Weighted average exercise price (per share)	$	12.91	$	12.88

Schedule of information related to outstanding and exercisable options


($ in thousands, except per share data)	Stock Options	Weighted-Average Exercise Price		Weighted-Average Remaining Contractual Life (in years)	Aggregate Intrinsic Value
Outstanding at December 31, 2017	2,675,184	$	23.52	6.5	$	5,805
Granted	1,091,474		12.91
Exercised	(858)		12.77
Forfeited	(279,444)		18.16
Expired	(163,181)		47.56
Outstanding at September 30, 2018 (1)	3,323,175	$	19.31	6.7	$	1,249
Exercisable at September 30, 2018	1,958,773	$	22.96	5.0	$	714

(1)

Summary of Significant Accounting Policies (Details) - USD ($) $ in Thousands	1 Months Ended	3 Months Ended		9 Months Ended
	Jul. 31, 2018	Sep. 30, 2018	Sep. 30, 2017	Sep. 30, 2018	Sep. 30, 2017	Dec. 31, 2017	Dec. 31, 2016
Accounting Policies
Restructuring Charges		$ 3,017		$ 3,017
Cash and cash equivalents		82,462		82,462		$ 112,629
Restricted Cash		311		311		311
Cash, cash equivalents and restricted cash		82,773	$ 64,252	82,773	$ 64,252	112,940	$ 80,978
Tax expense (benefit)		0	$ 0	0	$ 0
Uncertain tax positions		$ 0		$ 0		$ 0
Practical Expedient, Financing Component				true
Cambridge, Massachusetts facility operations
Accounting Policies
Restructuring Charges				$ 3,355
Employee Severance and Benefits \| Cambridge, Massachusetts facility operations
Accounting Policies
Restructuring Charges				2,436
Contract Termination Costs \| Cambridge, Massachusetts facility operations
Accounting Policies
Restructuring Charges				225
Asset Impairments \| Cambridge, Massachusetts facility operations
Accounting Policies
Restructuring Charges				$ 694
BioCryst
Accounting Policies
Fixed expense reimbursement	$ 6,000

Collaboration and License Agreements (Details) $ in Thousands	1 Months Ended		9 Months Ended
	Nov. 30, 2016 USD ($) director	Nov. 30, 2015 USD ($) person	Sep. 30, 2018 USD ($) item	Dec. 31, 2017 USD ($)
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Contract with Customer, Liability, Current			$ 94	$ 566
Total number of board of director seats \| director	7
Number of common board of directors \| director	0
Baker Bros. Advisors LP
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Common stock ownership percentage under the collaboration agreement	7.00%
Number of board director seats held \| director	2
Vivelix
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Remaining performance obligation			$ 0
Total number of board of director seats \| director	4
Number of clinical studies conducted \| item			2
Vivelix \| Up-front Payment Arrangement
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Upfront payment received under collaboration agreement	$ 15,000
Vivelix \| Maximum
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Milestone payments	$ 140,000
Vivelix \| Maximum \| Back-up compounds
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Anticipated initial collaboration term	3 years
Milestone payments	$ 52,500
Vivelix \| Maximum \| Development and Regulatory Milestones
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Milestone payments	65,000
Vivelix \| Maximum \| Development and Regulatory Milestones \| Back-up compounds
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Milestone payments	35,000
Vivelix \| Maximum \| Sales Milestones
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Milestone payments	75,000
Vivelix \| Maximum \| Sales Milestones \| Back-up compounds
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Milestone payments	$ 17,500
GSK Agreement
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Deferred revenue recognition period		36 months
Number of optional additional targets \| person		2
Number of development candidates \| person		1
Remaining performance obligation			$ 0
Revised, increased research period			36 months
GSK Agreement \| Up-front Payment Arrangement
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Upfront payment received under collaboration agreement		$ 2,500
GSK Agreement \| License, Research, Clinical Development and Commercialization
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Milestone payments			$ 20,000
GSK Agreement \| Research and Development Plans and Designation of Development Candidates
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Milestone payments			1,000
GSK Agreement \| Clinical and Commercial Milestones
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Milestone payments		$ 89,000	$ 17,000
GSK Agreement \| Maximum
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Anticipated initial collaboration term		4 years
Maximum royalty percentage on net sales			5.00%
GSK Agreement \| Maximum \| License, Research, Clinical Development and Commercialization
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Milestone payments		$ 100,000
GSK Agreement \| Maximum \| Research and Development Plans and Designation of Development Candidates
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Milestone payments		$ 9,000
GSK Agreement \| Minimum
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Anticipated initial collaboration term		2 years
R&D Services Unit of Accounting \| GSK Agreement \| Up-front Payment Arrangement
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Upfront payment received under collaboration agreement		$ 2,500

Stock-Based Compensation - Stock Option Activity (Details) - USD ($) $ / shares in Units, $ in Thousands	9 Months Ended		12 Months Ended
	Sep. 30, 2018	Sep. 30, 2017	Dec. 31, 2017
Stockholders' Equity
Options, Outstanding, Beginning Balance	2,675,184
Granted	1,091,474
Exercised	(858)
Forfeited	(279,444)
Expired	(163,181)
Options, Outstanding, Ending Balance	3,323,175		2,675,184
Exercisable, Ending Balance	1,958,773
Weighted Average Exercise Price, Beginning Balance	$ 23.52
Granted, Weighted Average Exercise Price	12.91	$ 12.88
Exercised, Weighted Average Exercise Price	12.77
Forfeited, Weighted Average Exercise Price	18.16
Expired, Weighted Average Exercise Price	47.56
Weighted Average Exercise Price, Ending Balance	19.31		$ 23.52
Exercisable, Weighted Average Exercise Price	$ 22.96
Outstanding, Ending balance, Weighted Average Remaining Contractual Term	6 years 8 months 12 days		6 years 6 months
Exercisable Ending Balance, Weighted Average Remaining Contractual Term	5 years
Outstanding, Intrinsic Value, Ending Balance	$ 1,249		$ 5,805
Exercisable, Ending Balance, Intrinsic Value	714
Fair value of options, vested	5,100
Unrecognized compensation cost related to nonvested stock-based compensation	$ 9,100
Weighted average remaining period over which unrecognized compensation expense will be recognized	2 years 8 months 12 days

CONDENSED BALANCE SHEETS (Parenthetical) - $ / shares	Sep. 30, 2018	Dec. 31, 2017
Preferred stock, par value	$ 0.01	$ 0.01
Preferred stock, shares authorized	5,000,000	5,000,000
Common stock, par value	$ 0.001	$ 0.001
Common stock, shares authorized	70,000,000	70,000,000
Common stock, shares issued	27,179,000	24,453,000
Common stock, shares outstanding	27,179,000	24,453,000
Series A Preferred Stock
Preferred stock, shares designated	1,500,000	1,500,000
Preferred stock, shares issued	1,000	1,000
Preferred stock, shares outstanding	1,000	1,000

Business and Organization	9 Months Ended
Business and Organization	Sep. 30, 2018
Business and Organization
Business and Organization	Note 1. Business and Organization Business Overview Idera Pharmaceuticals, Inc. (“Idera” or the “Company”), a Delaware corporation, is a clinical-stage biopharmaceutical company currently focused on the development, and ultimately the commercialization, of therapeutic drug candidates, including our Toll-like receptor (“TLR”) agonist, tilsotolimod (IMO-2125), for oncology. The Company’s business strategy is focused on the clinical development, and ultimately the commercialization, of drug candidates for both oncology and rare disease indications characterized by small, well-defined patient populations with serious unmet medical needs. The Company believes it can develop and commercialize these targeted therapies on its own. To the extent the Company seeks to develop drug candidates for broader disease indications, it has entered into and may explore additional collaborative alliances to support development and commercialization. Agreement and Plan of Merger On January 21, 2018, the Company, BioCryst Pharmaceuticals, Inc., a Delaware corporation (“BioCryst”), Nautilus Holdco, Inc., a Delaware corporation and a direct, wholly owned subsidiary of BioCryst (“Holdco”), Island Merger Sub, Inc., a Delaware corporation and a direct, wholly owned subsidiary of Holdco, and Boat Merger Sub, Inc., a Delaware corporation and a direct, wholly owned subsidiary of Holdco, entered into an Agreement and Plan of Merger (the “Merger Agreement”). The board of directors of each of Idera and BioCryst unanimously approved the Merger Agreement and the transactions contemplated thereby and the required regulatory approvals were received. However, the proposed merger was subject to approval by the stockholders of Idera and BioCryst, and satisfaction of other customary closing conditions, as specified in the Merger Agreement. At a special meeting of BioCryst stockholders held on July 10, 2018, BioCryst’s stockholders voted against the adoption of the Merger Agreement. Following such vote and in accordance with the terms of the Merger Agreement, BioCryst terminated the Merger Agreement. In accordance with the Merger Agreement, BioCryst paid the Company a fixed expense reimbursement amount of $6 million in July 2018 in connection with the termination of the Merger Agreement. The fixed expense reimbursement amount is included in “Merger-related costs, net” in the accompanying condensed statements of operations. Liquidity and Financial Condition As of September 30, 2018, the Company had an accumulated deficit of $652.2 million. The Company expects to incur substantial operating losses in future periods and will require additional capital as it seeks to advance tilsotolimod and any future drug candidates through development to commercialization. The Company does not expect to generate product revenue, sales-based milestones or royalties until the Company successfully completes development of and obtains marketing approval for tilsotolimod or other future drug candidates, either alone or in collaboration with third parties, which the Company expects will take a number of years. In order to commercialize tilsotolimod and any future drug candidates, the Company needs to complete clinical development and comply with comprehensive regulatory requirements. The Company is subject to a number of risks and uncertainties similar to those of other companies of the same size within the biotechnology industry, such as uncertainty of clinical trial outcomes, uncertainty of additional funding and history of operating losses. The Company believes, based on its current operating plan, that its existing cash and cash equivalents will enable the Company to fund its operations into the first quarter of 2020. The Company has and plans to continue to evaluate available alternatives to extend its operations beyond the first quarter of 2020. Note 1. Business and Organization (Continued) Reverse Stock Split As further described in Note 6, on July 27, 2018, the Company effected a 1-for-8 reverse stock split of the Company's outstanding shares of common stock, as authorized at a special meeting of stockholders on June 20, 2018. All share and per share amounts of common stock, options and warrants in the accompanying condensed financial statements and notes thereto have been retroactively adjusted for all periods presented to reflect the reverse stock split.

Related Party Transactions	9 Months Ended
Related Party Transactions	Sep. 30, 2018
Related Party Transactions
Related Party Transactions	Note 11. Related Party Transactions Overview of Related Parties Youssef El Zein, a member of the Company’s Board until his resignation in October 2017, is a director and controlling stockholder of Pillar Invest Corporation (“Pillar Invest”), which is the general partner of Pillar Pharmaceuticals I, L.P. (“Pillar I”), Pillar Pharmaceuticals II, L.P. (“Pillar II”), Pillar Pharmaceuticals III, L.P. (“Pillar III”), Pillar Pharmaceuticals IV, L.P. (“Pillar IV”) and Pillar Pharmaceuticals V, L.P. (“Pillar V”) and a limited partner of Pillar I, Pillar II, Pillar III, Pillar IV and Pillar V. Entities affiliated with Pillar Invest and Participations Besancon (“Besancon”), an investment fund advised by Pillar Invest having no affiliation with Mr. El Zein, Pillar I, Pillar II, Pillar III, Pillar IV, Pillar V or Pillar Invest (collectively, the “Pillar Investment Entities”), owned approximately 9% of the Company's common stock as of September 30, 2018. Julian C. Baker, a member of the Company’s Board until his resignation in September 2018, is a principal of Baker Bros. Advisors, LP. Baker Bros. Advisors, LP and certain of its affiliated funds (collectively, “Baker Brothers”) owned approximately 18% of the Company's common stock as of September 30, 2018. Additionally, one of the Company’s directors, Kelvin M. Neu, was an employee of Baker Bros. Advisors, LP as of September 30, 2018. Pillar Investment Entities During the nine months ended September 30, 2018, Besancon exercised warrants to purchase 150,000 shares of the Company’s common stock at an exercise price of $3.76 per share for a total exercise price of approximately $0.6 million. Baker Brothers During the nine months ended September 30, 2018, Baker Brothers exercised warrants to purchase 2,539,541 shares of the Company’s common stock at an exercise price of $3.76 per share for a total exercise price of approximately $9.5 million. As of September 30, 2018, Baker Brothers held pre-funded warrants to purchase up to 2,768,882 shares of the Company’s common stock at an exercise price of $0.08 per share. Note 11. Related Party Transactions (Continued) Board Fees Paid in Stock Pursuant to the Company’s director compensation program, in lieu of director board and committee fees incurred of $0.1 million during each of the nine months ended September 30, 2018 and 2017, the Company issued 7,067 and 6,538 shares of its common stock, respectively, to certain of its directors. Director board and committee fees are paid in arrears (including fees paid in stock) and the number of shares issued was calculated based on the market closing price of the Company’s common stock on the issuance date.

Net Loss per Common Share	9 Months Ended
Net Loss per Common Share	Sep. 30, 2018
Net Loss per Common Share
Net Loss per Common Share	Note 12. Net Loss per Common Share Basic and diluted net loss per common share applicable to common stockholders is calculated by dividing net loss applicable to common stockholders by the weighted-average number of shares of common stock outstanding during the period, without consideration of common stock equivalents. The Company’s potentially dilutive shares, which include outstanding stock option awards, common stock warrants and convertible preferred stock, are considered to be common stock equivalents and are only included in the calculation of diluted net loss per share when their effect is dilutive. For the three and nine months ended September 30, 2018 and 2017, diluted net loss per common share applicable to common stockholders was the same as basic net loss per common share applicable to common stockholders as the effects of the Company’s potential common stock equivalents are antidilutive. Total antidilutive securities that were excluded from the calculation of diluted net loss per share, due to their anti-dilutive effect, were 6,093,983 and 9,124,279 as of September 30, 2018 and 2017, respectively, and consisted of stock options, preferred stock and warrants.

Subsequent Events	9 Months Ended
Subsequent Events	Sep. 30, 2018
Subsequent Events.
Subsequent Events	Note 13. Subsequent Events The Company considers events or transactions that occur after the balance sheet date but prior to the issuance of the financial statements to provide additional evidence relative to certain estimates or to identify matters that require additional disclosure.

Business and Organization (Details) $ in Thousands	1 Months Ended	9 Months Ended
Business and Organization (Details) $ in Thousands	Jul. 31, 2018 USD ($)	Sep. 30, 2018 USD ($)	Dec. 31, 2017 USD ($)
Accumulated deficit		$ 652,225	$ 604,494
Reverse stock split conversion ratio		0.125
BioCryst
Fixed expense reimbursement	$ 6,000

Summary of Significant Accounting Policies - Tax Cuts and Jobs Act (Details) - USD ($) $ in Millions	3 Months Ended	12 Months Ended
	Dec. 31, 2017	Dec. 31, 2018	Dec. 31, 2017
Corporate federal income tax rate		21.00%
TCJA of 2017 measurement period adjustment	$ 27.6
Maximum
Corporate federal income tax rate			35.00%

Fair Value Measurements - Transfers Between Levels (Details) $ in Thousands	9 Months Ended
	Sep. 30, 2018 USD ($)
Fair Value Measurements
Fair value of assets transfers from level 1 to level 2	$ 0
Fair value of assets transfers from level 2 to level 1	0
Fair value of liabilities transfers from level 1 to level 2	0
Fair value of liabilities transfers from level 2 to level 1	0
Fair value of assets transfers into level 3	0
Fair value of assets transfers out of level 3	0
Fair value of liabilities transfers into level 3	0
Fair value of liabilities transfers out of level 3	$ 0

Fair Value Measurements - Assets and Liabilities at Fair Value on Recurring Basis (Details) - USD ($) $ in Thousands	Sep. 30, 2018	Dec. 31, 2017
Fair Value of Assets and Liabilities Measured at Fair Value on a Recurring Basis
Total Assets	$ 17,746	$ 66,183
Money market funds
Fair Value of Assets and Liabilities Measured at Fair Value on a Recurring Basis
Money market funds	17,746	66,183
Quoted Prices in Active Markets for Identical Assets or Liabilities (Level 1)
Fair Value of Assets and Liabilities Measured at Fair Value on a Recurring Basis
Total Assets	17,746	66,183
Quoted Prices in Active Markets for Identical Assets or Liabilities (Level 1) \| Money market funds
Fair Value of Assets and Liabilities Measured at Fair Value on a Recurring Basis
Money market funds	$ 17,746	$ 66,183

Property and Equipment - Net Property and Equipment at Cost (Details) - USD ($) $ in Thousands	Sep. 30, 2018	Dec. 31, 2017
Property, Plant and Equipment
Total property and equipment, at cost	$ 868	$ 5,932
Less: accumulated depreciation and amortization	627	4,460
Property and equipment, net	241	1,472
Leasehold improvements
Property, Plant and Equipment
Total property and equipment, at cost	104	671
Laboratory equipment and other
Property, Plant and Equipment
Total property and equipment, at cost	$ 764	$ 5,261

Accrued Expenses (Details) - USD ($) $ in Thousands	Sep. 30, 2018	Dec. 31, 2017
Accrued Expenses
Payroll and related costs	$ 1,705	$ 3,108
Clinical and nonclinical trial expenses	4,859	3,495
Professional and consulting fees	497	1,317
Restructuring expenses	1,905
Other	205	80
Total accrued expenses	$ 9,171	$ 8,000

Stockholders’ Equity - Common Stock Warrants (Details)		9 Months Ended
Stockholders’ Equity - Common Stock Warrants (Details)	Jun. 20, 2018 shares	Sep. 30, 2018 $ / shares shares	Jul. 27, 2018 shares	Dec. 31, 2017 $ / shares shares
Class of Warrant or Right
Common stock, shares authorized	280,000,000	70,000,000		70,000,000
Reverse stock split conversion ratio		0.125
Multiplier used for the reverse stock split ratio	2
Number of shares to be exchange in the reverse stock split			8
Number of shares received in the reverse stock split			1
Common stock, par value \| $ / shares		$ 0.001		$ 0.001
Number of Warrants		2,768,882		5,469,673
Warrant exercise price per share \| $ / shares		$ 0.08		$ 1.90
Expiration Date - May 2018
Class of Warrant or Right
Number of Warrants				2,700,791
Warrant exercise price per share \| $ / shares				$ 3.76
Expiration Date - May 2020
Class of Warrant or Right
Number of Warrants		1,977,041		1,977,041
Warrant exercise price per share \| $ / shares				$ 0.08
Expiration Date - September 2020
Class of Warrant or Right
Number of Warrants		521,997		521,997
Warrant exercise price per share \| $ / shares				$ 0.08
Expiration Date - February 2021
Class of Warrant or Right
Number of Warrants		269,844		269,844
Warrant exercise price per share \| $ / shares				$ 0.08
Minimum
Class of Warrant or Right
Reverse stock split conversion ratio	0.25
Maximum
Class of Warrant or Right
Reverse stock split conversion ratio	0.125

Alliance Revenue (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
Alliance Revenue (Details) - USD ($) $ in Thousands	Sep. 30, 2018	Sep. 30, 2017	Sep. 30, 2018	Sep. 30, 2017
Alliance Revenue
Alliance revenue	$ 145	$ 164	$ 563	$ 729
Deferred revenue recognized during the period			500	600
Gsk Collaboration
Alliance Revenue
Alliance revenue	141	141	424	698
Vivelix Collaboration
Alliance Revenue
Alliance revenue		14	56	14
Other
Alliance Revenue
Alliance revenue	$ 4	$ 9	83	$ 17
Additional Research Services
Alliance Revenue
Deferred revenue recognized during the period			$ 100

Restructuring Costs (Details) $ in Thousands	1 Months Ended	3 Months Ended	9 Months Ended
Restructuring Costs (Details) $ in Thousands	Jul. 31, 2018 employee	Sep. 30, 2018 USD ($)	Sep. 30, 2018 USD ($)	Dec. 31, 2017 USD ($)
Restructuring costs
Restructuring Charges		$ 3,017	$ 3,017
Long-term portion of restructuring accrual		63	63	$ 613
Cambridge, Massachusetts facility operations
Restructuring costs
Number of positions eliminated \| employee	18
Percentage of positions eliminated	40.00%
Number of positions eliminated since inception \| employee	15
Restructuring Charges			3,355
Fixed asset impairments		$ 500	500
Non-cash gain due to write-off of remaining deferred rent liability			$ 400

Stock-Based Compensation - Equity Incentive Plans (Details) - shares		9 Months Ended
	Jul. 26, 2013	Sep. 30, 2018	Dec. 31, 2017
Class of Stock
Common stock options outstanding		3,323,175	2,675,184
Options outstanding under earlier plans		511,093
Grant of inducement stock option		393,750
2013 Stock Incentive Plan
Class of Stock
Maximum number of additional common shares	868,372
Common stock options outstanding		2,418,332
Common shares available for grant	3,153,057	941,192

Stock-Based Compensation - Employee Stock Purchase Plans (Details) - USD ($) $ in Millions		9 Months Ended
	Jun. 07, 2017	Sep. 30, 2018	Sep. 30, 2017
2017 Employee Stock Purchase Plan
Class of Stock
Maximum percentage of total combined voting power or value of the stock of the Company after the grant	5.00%
Common shares available for grant	38,763
2017 Employee Stock Purchase Plan \| Maximum
Class of Stock
Common stock shares authorized for issuance under stock purchase plan	62,500
Employee Stock Purchase Plans
Class of Stock
Common stock share issued		18,355	16,490
Proceeds from employee stock purchase plan		$ 0.2

Net Loss per Common Share (Details) - shares	9 Months Ended
Net Loss per Common Share (Details) - shares	Sep. 30, 2018	Sep. 30, 2017
Net Loss per Common Share
Total antidilutive securities	6,093,983	9,124,279