Document:

EX-10.1

 Exhibit 10.1 

IDERA PHARMACEUTICALS, INC. 
 CONVERTIBLE PREFERRED STOCK AND WARRANT PURCHASE AGREEMENT 

November 9, 2012 
 This Convertible Preferred Stock and Warrant Purchase Agreement (this “AGREEMENT”) is entered into as of the date set forth above by and among Idera Pharmaceuticals, Inc., a Delaware corporation
(the “COMPANY”), and the undersigned purchasers (each a “PURCHASER” and collectively, the “PURCHASERS”) set forth on the Schedule of Purchasers attached hereto as Exhibit A (the “SCHEDULE OF
PURCHASERS”). The parties hereby agree as follows: 
 ARTICLE 1 

AUTHORIZATION AND SALE OF SECURITIES 
 1.1 Authorization. The Company has duly authorized the sale and issuance to the Purchasers, at the Closing (as defined in Section 2.1 below) and pursuant to the terms and conditions hereof, of
(i) up to 424,242 shares (the “SHARES”) of its Series E Convertible Preferred Stock, par value $0.01 per share (the “SERIES E PREFERRED STOCK”), and (ii) warrants to purchase up to 8,484,840 shares of its common stock,
par value $0.001 per share (the “COMMON STOCK”) in the form attached hereto as Exhibit B (the “WARRANTS”). The Series E Preferred Stock shall have the rights, privileges, preferences and restrictions set forth in the
Certificate of Designations, Preferences and Rights of Series E Preferred Stock attached hereto as Exhibit C (the “CERTIFICATE OF DESIGNATIONS”). The Company has, or before the Closing will have adopted and filed the Certificate of
Designations with the Secretary of State of the State of Delaware. 
 1.2 Sale of Securities. Subject to the terms and
conditions hereof, at the Closing the Company will issue and sell to each Purchaser, and each Purchaser agrees, severally and not jointly, to purchase from the Company, the number of Shares set forth opposite such Purchaser’s name on the
Schedule of Purchasers, at a purchase price of $14.00 per share, and Warrants to purchase the number of shares of Common Stock set forth opposite such Purchaser’s name on the Schedule of Purchasers, at a purchase price of $0.125 per Warrant
Share, and for the aggregate purchase price set forth thereon. Payment of the purchase price for the Shares and the Warrants will be made by the Purchasers by wire transfer in same day funds. 

ARTICLE 2 

CLOSING 

2.1 Closing. Subject to the terms and conditions of this Agreement, the closing (the “CLOSING”) of the sale and purchase
of the Shares and the Warrants under this Agreement shall take place at the offices of WilmerHale, 60 State Street, Boston, MA 02109 (or remotely via the exchange of documents and signatures) on the date of this Agreement (the “CLOSING
DATE”). At the Closing: 

 (A) the Company and the Purchasers shall execute and deliver the Registration Rights
Agreement in the form attached hereto as Exhibit D (the “REGISTRATION RIGHTS AGREEMENT” and together with this Agreement and the Warrants, the “TRANSACTION DOCUMENTS”); 

(B) the Company shall deliver to the Purchasers certificates, as of the most recent practicable dates, (i) as to the corporate good
standing of the Company issued by the Secretary of State of the State of Delaware and (ii) as to the due qualification of the Company as a foreign corporation issued by the Secretary of State of the Commonwealth of Massachusetts; 

(C) the Company shall deliver to the Purchasers the certificate of incorporation of the Company, as amended and in effect as of the
Closing Date (including the Certificate of Designations), certified by the Secretary of the State of the State of Delaware; 

(D) the Company shall deliver to the Purchasers a Certificate of the Secretary of the Company attesting as to (i) the bylaws of the
Company; (ii) the signatures and titles of the officers of the Company executing this Agreement or any of the other agreements to be executed and delivered by the Company at the Closing; and (iii) resolutions of the Board of Directors of
the Company (the “BOARD”) authorizing and approving all matters in connection with this Agreement and the transactions contemplated hereby; 
 (E) WilmerHale, counsel for the Company, shall deliver to the Purchasers an opinion, dated the Closing Date, in substantially the form attached hereto as Exhibit E; 

(F) the Company shall deliver to each of the Purchasers a certificate for the number of Shares set forth opposite such Purchaser’s
name under the heading “Shares” on the Schedule of Purchasers and Warrants to purchase the number of shares of Common Stock set forth opposite such Purchaser’s name under the heading “Warrants” on the Schedule of Purchasers,
in each case registered in the name of such Purchaser; and 
 (G) each Purchaser shall pay to the Company, by wire transfer of
immediately available funds the aggregate purchase price set forth opposite such Purchaser’s name under the heading “Purchase Price” on the Schedule of Purchasers for the Shares and the Warrants being purchased by such Purchaser at
the Closing. The Closing shall not be deemed to occur, and all such payments by any Purchaser shall be deemed to be held in escrow, until all Purchasers listed on the Schedule of Purchasers have tendered to the Company the payment indicated thereon.

 ARTICLE 3 
 REPRESENTATIONS AND WARRANTIES OF THE COMPANY 
 The Company hereby
represents and warrants to each Purchaser as of the date hereof that except as set forth in the Exchange Act Reports (as defined in Section 3.13): 
 3.1 Organization and Qualification. The Company is a corporation duly incorporated, validly existing and in good standing under the laws of the State of Delaware. The Company is qualified to do
business as a foreign corporation in each jurisdiction in which the failure to so qualify would have a Material Adverse Effect. For purposes of this Agreement, the term “MATERIAL ADVERSE EFFECT” shall mean a material adverse effect upon
the business, financial condition, properties or results of operations of the Company. 

  
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 3.2 Authorized Capital Stock. Immediately prior to Closing, the Company will have
(i) authorized 140,000,000 shares of Common Stock, of which 27,641,229 shares of Common Stock were outstanding as of October 15, 2012 and (ii) authorized 5,000,000 shares of Preferred Stock, $0.01 par value per share (“PREFERRED
STOCK”), of which 1,500,000 shares have been designated Series A Convertible Preferred Stock, 655 shares of which are outstanding, 200,000 shares have been designated Series C Junior Participating Preferred Stock, none of which are outstanding,
1,124,260 shares have been designated Series D Convertible Preferred Stock, 1,124,260 shares of which are outstanding, and 424,242 shares have been designated Series E Preferred Stock. The issued and outstanding shares of the Common Stock and
Preferred Stock have been duly authorized and validly issued, are fully paid and nonassessable, have been issued in compliance in material respects with all federal and state securities laws, were not issued in violation of any preemptive rights or
other rights to subscribe for or purchase securities granted by the Company, and conform (except with respect to the number of authorized, issued and outstanding shares) in all material respects to the description thereof contained in the Exchange
Act Reports or in any Registration Statement on Form 8-A filed with the Securities and Exchange Commission (the “COMMISSION” or the “SEC”) by the Company. Except as disclosed in the Exchange Act Reports (including options granted
under plans described in the Exchange Act Reports), the Company does not have outstanding any options to purchase, or any preemptive rights or other rights to subscribe for or to purchase, any securities or obligations convertible into, or any
contracts or commitments requiring the Company to issue or sell, shares of its capital stock or any such options, rights, convertible securities or obligations. 
 3.3 Issuance, Sale and Delivery of the Shares. The Shares, when issued, delivered and paid for in the manner set forth in this Agreement, will be validly issued, fully paid and nonassessable and
free and clear of all pledges, liens, and encumbrances imposed by the Company (other than restrictions on transfer under state and/or federal securities laws). The Common Stock issuable upon conversion of the Shares (the “CONVERSION
SHARES”) or upon exercise of the Warrants (the “WARRANT SHARES,” and collectively with the Shares, the Warrants and the Conversion Shares, the “SECURITIES”), have been duly reserved for issuance, and when issued, delivered
and, in the case of the Warrant Shares, paid for, will be validly issued, fully paid and nonassessable and free and clear of all pledges, liens, and encumbrances imposed by the Company (other than restrictions on transfer under state and/or federal
securities laws). Except as set forth in that certain Convertible Preferred Stock and Warrant Purchase Agreement, dated November 4, 2011, between the Company and the purchasers named therein, no preemptive rights or other rights to subscribe
for or purchase from the Company exist with respect to the issuance and sale of the Securities by the Company pursuant to this Agreement. Except as disclosed in the Exchange Act Reports, no stockholder of the Company has any right (which has not
been waived or has not expired by reason of lapse of time following notification of the Company’s intent to file the registration statement to be filed by it pursuant to the Registration Rights Agreement (the “REGISTRATION
STATEMENT”)) to require the Company to register the sale of any shares owned by such stockholder under the Securities Act of 1933, as amended (the “SECURITIES ACT”) in the Registration Statement. 

  
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 3.4 Due Execution, Delivery and Performance of this Agreement. The Company has full
legal right, corporate power and authority to enter into the Transaction Documents and consummate the transactions contemplated hereby and thereby. The Transaction Documents have been duly authorized, executed and delivered by the Company. The
execution and delivery of the Transaction Documents by the Company and the consummation by the Company of the transactions contemplated herein and therein: (i) will not violate any provision of the certificate of incorporation or bylaws of the
Company, (ii) will not result in the creation of any lien, charge, security interest or encumbrance upon any assets of the Company pursuant to the terms or provisions of, and will not conflict with, result in the breach or violation of, or
constitute, either by itself or upon notice or the passage of time or both, a default under any agreement, lease, franchise, license, permit or other instrument to which the Company is a party or by which the Company or any of its properties are
bound, except, in each case, for any lien, charge, security interest, encumbrance, conflict, breach, violation or default which would not have a Material Adverse Effect, or (iii) conflict with or result in the violation of any statute or any
judgment, decree, order, rule or regulation of any court or any regulatory body, administrative agency or other governmental body applicable to the Company or any of its properties except for any such conflict or violation which would not have a
Material Adverse Effect. Assuming the accuracy of the representations made by the Purchasers in Article 4, no consent, approval, authorization or other order of any court, regulatory body, administrative agency or other governmental body is required
for the execution and delivery by the Company of the Transaction Documents or the consummation by the Company of the transactions contemplated by the Transaction Documents, except for the filing of the Certificate of Designations, compliance with
the blue sky laws and federal securities laws, the listing of the Conversion Shares and the Warrant Shares on the Nasdaq Global Market and the filing of the Registration Statement. Upon the execution and delivery of the Transaction Documents, and
assuming the valid execution thereof by the Purchasers, each Transaction Document will constitute a valid and binding obligation of the Company, enforceable against it in accordance with their respective terms, except as enforceability may be
limited by applicable bankruptcy, insolvency, reorganization, moratorium, fraudulent conveyance or similar laws affecting creditors’ and contracting parties’ rights generally and except as enforceability may be subject to general
principles of equity (regardless of whether such enforceability is considered in a proceeding in equity or at law) and except to the extent enforcement of the indemnification obligations of the Company set forth in the Registration Rights Agreement
may be limited by federal or state securities laws or the public policy underlying such laws. 
 3.5 Accountants. The firm
of Ernst & Young LLP, which has expressed its opinion with respect to the financial statements to be included or incorporated by reference in the Registration Statement and the prospectus which forms a part thereof, is an independent
accountant as required by the Securities Act. 
 3.6 No Defaults. The Company is not in violation or default of any
provision of its certificate of incorporation or bylaws, or in breach of or default with respect to any provision of any agreement, judgment, decree, order, lease, franchise, license, permit or other instrument to which it is a party or by which it
or any of its properties are bound except for any violation or default that would not have a Material Adverse Effect. 

  
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 3.7 Contracts. There is no material contract or agreement required by the Securities
Exchange Act of 1934, as amended (the “EXCHANGE ACT”) to be described in or filed as an exhibit to the Exchange Act Reports which is not described or filed therein as required. Any contracts filed as exhibits to the Exchange Act Reports
that are material to the Company are in full force and effect on the date hereof (except to the extent they have expired by their terms subsequent to the date of the Exchange Act Reports). 

3.8 No Actions. Except as disclosed in the Exchange Act Reports, (1) there are no legal or governmental actions, suits or
proceedings pending and (2) to the Company’s knowledge, there are no inquiries or investigations pending, or any legal or governmental actions, suits, or proceedings threatened in writing, against the Company or of which property owned or
leased by the Company is or may be the subject (it being understood that the interaction between the Company and the United States Food and Drug Administration and such comparable governmental bodies relating solely to the clinical development and
product approval process shall not be deemed proceedings for purposes of this representation), or related to environmental or discrimination matters, which actions, suits or proceedings, individually or in the aggregate, would have a Material
Adverse Effect. No labor disturbance by the employees of the Company exists or, to the Company’s knowledge, is imminent which would have a Material Adverse Effect. The Company is not party to or named as subject to the provisions of any
injunction, judgment, decree or order of any court, regulatory body, administrative agency or other governmental body specifically naming the Company that would have a Material Adverse Effect. 

3.9 No Material Change. Since June 30, 2012, and except as described in the Exchange Act Reports or as disclosed to the
Purchasers: 
 (A) the Company has not incurred any material liabilities or obligations, indirect, or contingent, or entered into
any material oral or written agreement or other transaction, which was not incurred or entered into in the ordinary course of business; 
 (B) the Company has not sustained any material loss or interference with its business or properties from fire, flood, windstorm, accident or other calamity not covered by insurance; 

(C) except for dividends on shares of the Company’s Series D Convertible Preferred Stock paid in accordance with the Series D
Certificate of Designations, Preferences and Rights of Series D Preferred Stock (the “SERIES D CERTIFICATE OF DESIGNATIONS”), the Company has not paid or declared any dividends or other distributions with respect to its capital stock and
the Company is not in default in the payment of principal or interest on any outstanding debt obligations; 
 (D) there has not
been any material change or amendment to a contract filed as an exhibit to an Exchange Act Report that is material to the Company; 
 (E) there has not been any sale, assignment or transfer of all or substantially all of the Company’s rights in any patents, trademarks, copyrights, trade secrets or other intangible assets or other
material assets, except a sale, assignment or transfer made in the ordinary course of business that is not material to the assets, properties, financial condition, operating results or business of the Company; 

  
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 (F) there has not been any waiver by the Company of a material debt owed to it; 

(G) there has not been any material change in any compensation arrangement or agreement with any officer or director; 

(H) there has not been any agreement or commitment by the Company to do any of the acts described in subsections (A) through
(G) above; and 
 (I) there has not been any event which has caused a Material Adverse Effect other than continued
incurrence of operating losses incurred in the ordinary course of the Company’s business. 
 3.10 Intellectual
Property. Except as disclosed in the Exchange Act Reports, (i) to the Company’s knowledge, the Company owns or has the right to use the inventions, patent applications, patents, trademarks (both registered and unregistered), trade
names, copyrights and trade secrets used by it in or necessary for the conduct of the Company’s business (collectively, the “COMPANY INTELLECTUAL PROPERTY”), except where such failure to own or have the right to use such intellectual
property would not have a Material Adverse Effect; and (ii) (a) to the Company’s knowledge, there are no third parties who have any ownership rights to any Company Intellectual Property that would preclude the Company from conducting
its business as currently conducted and have a Material Adverse Effect, except for the ownership rights of the owners of the Company Intellectual Property licensed by the Company; (b) to the Company’s knowledge, there are currently no
sales of any products or any other uses that would constitute an infringement by third parties of any Company Intellectual Property, which infringement would have a Material Adverse Effect; (c) there is no pending or, to the Company’s
knowledge, threatened action, suit, proceeding or claim by others challenging the rights of the Company in or to any Company Intellectual Property, which action, suit, proceeding or claim would have a Material Adverse Effect; (d) there is no
pending or, to the Company’s knowledge, threatened action, suit, proceeding or claim by others challenging the validity or scope of any Company Intellectual Property, which action, suit, proceeding or claim would have a Material Adverse Effect;
and (e) there is no pending or, to the Company’s knowledge, threatened action, suit, proceeding or claim by others that the Company infringes or otherwise violates any patent, trademark, copyright, trade secret or other proprietary right
(an “INTELLECTUAL PROPERTY RIGHT”) of others, which action, suit, proceeding or claim would have a Material Adverse Effect. To the knowledge of the Company, the Company does not infringe any Intellectual Property Rights of any other
person. The Company has not entered into any consent agreements, forbearance to sue or settlement agreements with respect to the validity of the Company’s ownership or right to use Company Intellectual Property. The Company has complied, in all
material respects, with its contractual obligations relating to the protection of the Company Intellectual Property used pursuant to licenses. All former or current employees, officers and consultants of the Company have entered into agreements with
the Company providing for the assignment of inventions to the Company, except where the failure to have entered into an agreement with an employee, officer or consultant would not have a Material Adverse Effect. 

  
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 3.11 Compliance. The Company is conducting its business in compliance with all
applicable laws, rules and regulations of the jurisdictions in which it is conducting its business, including, without limitation, all applicable local, state and federal environmental laws and regulations, except where failure to be so in
compliance would not have a Material Adverse Effect. 
 3.12 Investment Company. The Company is not an “investment
company” or an “affiliated person” of, or “promoter” or “principal underwriter” for an investment company, within the meaning of the Investment Company Act of 1940, as amended. 

3.13 Disclosure. The information contained in the following documents did not, as of the date of the applicable document, include
any untrue statement of a material fact or omit to state any material fact required to be stated therein or necessary to make the statements therein, in the light of the circumstances in which they were made, not misleading, as of their respective
dates: 
 (A) the Company’s Annual Report on Form 10-K for the year ended December 31, 2011; 

(B) the Company’s Quarterly Reports on Form 10-Q for the quarters ended March 31, 2012 and June 30, 2012; 

(C) all other documents, if any, filed by the Company with the Commission since December 31, 2011 pursuant to the reporting
requirements of the Exchange Act (together with Sections 3.13(A) and (B), the “EXCHANGE ACT REPORTS”). 
 3.14
Reporting Company; Form S-3. The Company is subject to the reporting requirements of the Exchange Act and since June 30, 2011 has timely filed all reports required thereby. As of their respective filing dates, all Exchange Act Reports
complied in all material respects with the requirements of the Exchange Act. The Company is eligible to register the Conversion Shares and the Warrant Shares for resale by the Purchaser on a registration statement on Form S-3 under the Securities
Act. 
 3.15 Use of Proceeds. The Company intends to use the proceeds from the sale of the Securities for research and
clinical development activities, the manufacturing and commercialization of its product candidates, working capital and general corporate purposes, including to fund the analysis of the data from the Company’s ongoing phase 2 trial of IMO-3100,
the conduct of a phase 1 trial of IMO-8400 and the preparation for the further advancement of the Company’s autoimmune disease program in at least two indications. 
 3.16 Related Party Transactions. No transaction has occurred between or among the Company and its affiliates, officers or directors or any affiliate or affiliates of any such officer or director
that is required to have been described in the Exchange Act Reports under Item 404 of Regulation S-K as required by the Exchange Act or otherwise and is not so described in the Exchange Act Reports. 

  
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 3.17 Governmental Permits, Etc. The Company has all franchises, licenses,
certificates and other authorizations from such federal, state or local government or governmental agency, department or body that are currently required for the operation of the business of the Company as currently conducted, except where the
failure to possess currently such franchises, licenses, certificates and other authorizations would not have a Material Adverse Effect. The Company has not received any written notice of proceedings relating to the revocation or modification of any
such permit. 
 3.18 Financial Statements. The financial statements of the Company and the related notes contained in the
Exchange Act Reports (collectively, the “FINANCIAL STATEMENTS”) present fairly in all material respects the financial position of the Company as of the dates indicated, and the results of operations and cash flows for the periods therein
specified, subject, in the case of unaudited financial statements for interim periods, to normal year-end audit adjustments. The Financial Statements (including the related notes) have been prepared in accordance with United States generally
accepted accounting principles (“GAAP”), applied on a consistent basis throughout the periods therein specified, except that unaudited financial statements are subject to normal year-end audit adjustments and may not contain all footnotes
required by GAAP. Since September 30, 2012, the Company has not incurred liabilities, contingent or otherwise outside the ordinary course of business which individually or in the aggregate, are material to the financial condition or operating
results of the Company. 
 3.19 Listing. The Common Stock is presently listed on the Nasdaq Global Market. Except as set
forth in the Exchange Act Reports, the Company has not, in the two years preceding the date hereof, received any written notice from the Nasdaq Global Market to the effect that the Company is not in compliance with the maintenance requirements of
such exchange. 
 3.20 Sarbanes-Oxley Act; Accounting Controls. The Company is in compliance in all material respects with
all provisions of the Sarbanes-Oxley Act of 2002 which are applicable to it. The Company maintains a system of internal accounting controls that the Company reasonably believes is sufficient to provide reasonable assurance that (i) transactions
are executed in accordance with management’s general or specific authorization; (ii) transactions are recorded as necessary to permit preparation of financial statements in conformity with generally accepted accounting principles and to
maintain accountability for assets; (iii) access to assets is permitted only in accordance with management’s general or specific authorization; and (iv) the recorded accountability for assets is compared with existing assets at
reasonable intervals and appropriate action is taken with respect to any differences. 
 3.21 Securities Law Exemptions.
Assuming the accuracy of the representations and warranties of the Purchasers contained in Article 4 hereof, the offer, sale and issuance of the Securities are exempt from the registration requirements of the Securities Act, and the registration,
permit or qualification requirements of any applicable state securities laws. Neither the Company nor any person acting on its behalf has taken any action to sell, offer for sale or solicit offers to buy any securities of the Company that would
reasonably be expected to subject the offer, issuance or sale of the Securities, as contemplated by this Agreement, to the registration requirements of Section 5 of the Securities Act. 

3.22 No Integrated Offering. Neither the Company, nor any of its affiliates, nor any person acting on its or their behalf, has
directly or indirectly made any offers or sales of any security or solicited any offers to buy any security under circumstances that would cause this offering of Securities to be integrated with any prior or contemporaneous offering of securities of
the Company for purposes of the Securities Act or any applicable state securities law or any applicable stockholder approval provisions. 

  
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 3.23 No Brokers. The Company has taken no action which would give rise to any claim
by any person for brokerage commissions, finder’s fees or similar payments by any Purchaser relating to this Agreement or the transactions contemplated hereby, other than fees that may be owed to Piper Jaffray & Co. and JMP Group Inc.
as disclosed to the Purchasers. 
 3.24 Tax Matters. The Company has timely prepared and filed all material tax returns
required to have been filed by the Company with all appropriate governmental agencies and timely paid all taxes shown thereon. The charges, accruals and reserves on the books of the Company in respect of taxes for all fiscal periods are adequate in
all material respects, and there are no material unpaid assessments against the Company nor, to the Company’s knowledge, any basis for the assessment of any additional taxes, penalties or interest for any fiscal period or audits by any federal,
state or local taxing authority except for any assessment which would not have a Material Adverse Effect. All material taxes and other assessments and levies that the Company is required to withhold or to collect for payment have been duly withheld
and collected and paid to the proper governmental entity or third party when due. There are no tax liens or claims pending or, to the Company’s knowledge, threatened against the Company or any of its assets or properties. 

3.25 Application of Takeover Protections. The Company has taken all necessary action, if any, in order to render inapplicable any
control share acquisition, business combination, poison pill (including any distribution under a rights agreement) or other similar anti-takeover provision under the Company’s certificate of incorporation (or similar charter documents) or the
laws of its state of incorporation that is or could become applicable to the Purchasers as a result of the Purchasers and the Company fulfilling their obligations or exercising their rights under the Transaction Documents, including without
limitation as a result of the Company’s issuance of the Securities and the Purchasers’ ownership of the Securities. 

3.26 Insurance Coverage. The Company maintains in full force and effect insurance coverage and the Company reasonably believes such
insurance coverage is adequate. 
 ARTICLE 4 
 REPRESENTATIONS AND WARRANTIES OF PURCHASER 
 Each Purchaser hereby
represents and warrants as follows: 
 4.1 This Agreement and the Registration Rights Agreement have been duly and validly
authorized, executed and delivered on behalf of such Purchaser and are valid and binding agreements of such Purchaser enforceable against such Purchaser in accordance with their terms except as enforceability may be limited by applicable bankruptcy,
insolvency, reorganization, moratorium, fraudulent conveyance or similar laws affecting creditors’ and contracting parties’ rights generally and except as enforceability may be subject to general principles of equity (regardless of whether
such enforceability is considered in a proceeding in equity or at law) and except to the extent enforcement of the Purchaser’s indemnification obligations set forth in the Registration Rights Agreement may be limited by federal or state
securities laws or the public policy underlying such laws. 
  

  
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 4.2 The Purchaser represents and warrants to, and covenants with, the Company that:
(i) the Purchaser is knowledgeable, sophisticated and experienced in making, and is qualified to make, decisions with respect to investments in securities representing an investment decision like that involved in the purchase of the Securities,
including investments in securities issued by the Company and comparable entities, and has had the opportunity to request, receive, review and consider all information it deems relevant in making an informed decision to purchase the Securities;
(ii) the Purchaser is acquiring the Securities set forth in Article 1 above in the ordinary course of its business and for its own account for investment only and with no present intention of distributing any of such Securities or any
arrangement or understanding with any other persons regarding the distribution of such Securities (this representation and warranty not limiting the Purchaser’s right to sell pursuant to the Registration Statement or in compliance with the
Securities Act and the rules and regulations promulgated thereunder, or the Purchaser’s right to indemnification under the Registration Rights Agreement); (iii) the Purchaser has not been organized, reorganized or recapitalized
specifically for the purpose of investing in the Securities; (iv) the Purchaser has completed or caused to be completed, or will complete and deliver to the Company within five Business Days (as defined below) after the Closing, the
Registration Statement Questionnaire attached hereto as part of Exhibit F, for use in preparation of the Registration Statement, and the answers thereto are true and correct as of the date such Registration Statement Questionnaire is
delivered to the Company and will be true and correct as of the effective date of the Registration Statement and the Purchaser will notify the Company promptly of any material change in any such information provided in the Registration Statement
Questionnaire until such time as the Purchaser has sold all of its Securities or until the Company is no longer required to keep the Registration Statement effective; (v) the Purchaser has had an opportunity to discuss this investment with
representatives of the Company and ask questions of them; (vi) the Purchaser is an “accredited investor” within the meaning of Rule 501(a) of Regulation D promulgated under the Securities Act; (vii) the Purchaser agrees to notify
the Company promptly of any change in any of the foregoing information until such time as the Purchaser has sold all of its Securities or the Company is no longer required to keep the Registration Statement effective; and (viii) the Purchaser
will not, directly or indirectly, offer, sell, pledge, transfer or otherwise dispose of (or solicit any offers to buy, purchase or otherwise acquire to take a pledge of) any of the Shares except in compliance with the Securities Act, the Rules and
Regulations, and applicable state securities laws. The term “BUSINESS DAY” means a day, other than a Saturday or Sunday, on which banks in New York City are open for the general transaction of business. 

4.3 The Purchaser understands that the Securities are being offered and sold to it in reliance upon specific exemptions from the
registration requirements of the Securities Act, the Rules and Regulations and state securities laws and that the Company is relying upon the truth and accuracy of, and the Purchaser’s compliance with, the representations, warranties,
agreements, acknowledgments and understandings of the Purchaser set forth herein in order to determine the availability of such exemptions and the eligibility of the Purchaser to acquire the Securities. 

  
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 4.4 The Purchaser understands that its investment in the Securities involves a significant
degree of risk, including a risk of total loss of the Purchaser’s investment, and the Purchaser has full cognizance of and understands all of the risk factors related to the Purchaser’s purchase of the Securities. The Purchaser understands
that the market price of the Common Stock has been volatile and that no representation is being made as to the future value of the Common Stock. The Purchaser has the knowledge and experience in financial and business matters as to be capable of
evaluating the merits and risks of an investment in the Securities and has the ability to bear the economic risks of an investment in the Securities. 
 4.5 The Purchaser understands that no United States federal or state agency or any other government or governmental agency has passed upon or made any recommendation or endorsement of the Securities.

 4.6 The Purchaser’s principal executive offices are at the address set forth below the Purchaser’s name on the
Schedule of Purchasers. 
 4.7 The Purchaser further represents and warrants to, and covenants with, the Company that
(i) the Purchaser is in compliance with Executive Order 13224 and the regulations administered by the U.S. Department of the Treasury (“TREASURY”) Office of Foreign Assets Control, (ii) the Purchaser, its parents, subsidiaries,
affiliated companies, officers, directors and partners, and to the Purchaser’s knowledge, its shareholders, owners, employees, and agents, are not on the List of Specially Designated Nationals and Blocked Persons maintained by Treasury and have
not been designated by Treasury as a financial institution of primary money laundering concern, (iii) to the Purchaser’s knowledge after reasonable investigation, all of the funds to be used to acquire the Securities are derived from
legitimate sources and are not the product of illegal activities, and (iv) the Purchaser is in compliance with all other applicable U.S. anti-money laundering laws and regulations and has implemented, if applicable, an anti-money laundering
compliance program in accordance with the requirements of the Bank Secrecy Act, as amended by the USA PATRIOT Act, Pub. L. 107-56. 
 4.8 If the Purchaser is not a U.S. person (as defined in Securities Act Rule 902(k)), he, she or it further makes the representations and warranties set forth in this Section 4.8. 

(A) Such Purchaser is not a U.S. person and is not acquiring the Securities for the account or benefit of any U.S. person. 

(B) Such Purchaser will not offer or sell the Securities to a U.S. person or to for the account or benefit of a U.S. person prior to the
expiration of the six-month period after the date on which such Purchaser purchased such Securities. 
 (C) Such Purchaser
understands and acknowledges that the Securities have not been registered under the Securities Act and are being offered and transferred in reliance upon the exemptions provided in Regulation S of the Securities Act and the rules and regulations
adopted thereunder. Accordingly, the Securities may not be offered or sold in the U.S. or to U.S. persons unless the securities are registered under the Securities Act, or an exemption for the regulation requirements is available. Furthermore,
hedging transactions involving the Securities may not be conducted unless in compliance with the Securities Act. 

  
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 (D) Such Purchaser acknowledges and agrees that, notwithstanding anything in this Agreement
to the contrary, the Company shall, and shall instruct its transfer agent to, refuse to register any transfer of Securities Act that is not made in accordance with the provisions of Regulation S, pursuant to registration under Securities Act or
pursuant to an available exemption from registration required under the Securities Act. 
 ARTICLE 5 

COVENANTS 

5.1 Form D; Form 8-K. The Company shall file with the SEC a Form D with respect to the Securities as required under Regulation D.
Within four trading days after the Closing Date, the Company shall file a Form 8-K (or include in a Form 10-Q information) concerning this Agreement and the transactions contemplated hereby, which Form 8-K (or Form 10-Q) shall attach this Agreement,
the Registration Rights Agreement, the Certificate of Designations and the “form of Warrant” as exhibits to such Form 8-K (or Form 10-Q). 
 5.2 Preemptive Rights. 
 (A) In the event that, on or prior to the earlier
of (i) the third anniversary of the Closing Date and (ii) with respect to any Purchaser the day that such Purchaser holds a number of Shares (including shares of Common Stock issued upon conversion of the Shares) which is less than 50% of
the number of Shares purchased by such Purchaser pursuant to this Agreement and set forth opposite such Purchaser’s name on the Schedule of Purchasers (such number of Shares being subject to adjustment for stock splits, dividends, combinations,
recapitalizations, reclassifications and other similar events), the Company proposes to sell and issue securities of the Company in a private placement and not pursuant to an effective registration statement filed under the Securities Act (an
“ADDITIONAL FINANCING”) each Purchaser shall have the option to purchase, on the same terms and conditions offered by the Company to the other purchasers of such securities in such Additional Financing, up to that percentage of the
securities sold in such Additional Financing equal to (x) the number of shares of Common Stock then held by such Purchaser (including shares of Common Stock then issuable upon conversion of any shares of Preferred Stock then held by such
Purchaser) as compared to (y) the total number of shares of Common Stock then outstanding (including all shares of Common Stock then issuable upon conversion of all shares of Preferred Stock) (such percentage being such Purchaser’s
“ADDITIONAL FINANCING PRO RATA AMOUNT”); provided, however, that if a Purchaser’s Additional Financing Pro Rata Amount as calculated exceeds 19.99% (prior to the date the stockholders of the Company approve the Nasdaq Proposal (as
defined by and in accordance with Section 5.11(B)) or 35% (effective upon the date that the stockholders of the Company approve the Nasdaq Proposal), such Purchaser’s Additional Financing Pro Rata Amount shall be 19.99% or 35%, as the case
may be. 
 (B) In the event that on or prior to the earlier of (i) the third anniversary of the Closing Date and
(ii) with respect to any Purchaser the day before the date that such Purchaser holds a number of Shares which is less than 50% of the number of Shares purchased by such Purchaser pursuant to this Agreement and set forth opposite such
Purchaser’s name on the Schedule of Purchasers (such number of Shares being subject to adjustment for stock splits, dividends, combinations, recapitalizations, reclassifications and other similar events), the Company proposes to (x) enter
into a loan financing for the purpose of raising capital and not for the purpose of purchasing equipment (a “LOAN FINANCING”), or (y) sell and issue convertible debt securities or preferred stock of the Company that ranks senior to
the Series D Preferred Stock or the Series E Preferred Stock in a private placement and not pursuant to an effective registration statement filed under the Securities Act (together with a Loan Financing, a “SENIOR FINANCING,” and, together
with an Additional Financing, an “ADDITIONAL TRANSACTION”), each such Purchaser shall have the option to participate in a Loan Financing or purchase securities in other Senior Financings, on the same terms and conditions offered by the
Company to the other participants or purchasers of securities in such Senior Financings, up to that percentage (such percentage being such Purchaser’s “ADDITIONAL TRANSACTION PRO RATA AMOUNT”) of the amount of the Loan Financing or of
the securities sold in such Senior Financing equal to the product of: 

  
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 i. a fraction, the numerator of which equals the number of Shares then held by the
Purchaser and the denominator of which equals the total number of Shares issued to Purchasers by the Company; and 
 ii. if the
closing date of the Senior Financing is on or prior to (i) the first anniversary of the Closing Date, 50%, (ii) the second anniversary of the Closing Date, 40%, or (iii) the third anniversary of the Closing Date, 30%. 

(C) The terms of any Senior Financing may provide that the participants in such Senior Financing, other than any Purchasers participating
in such Senior Financing, shall have the right to exercise control over any matter requiring action by or on behalf of all participants in such Senior Financing without the consent of any Purchaser. 

(D) If the Board determines in good faith that the participation in the Senior Financing by the Purchasers pursuant to the preemptive
rights set forth in Section 5.2(B) would jeopardize the consummation of such Senior Financing on terms acceptable to the Board, then the Company will have no obligation to offer the Purchasers the opportunity to participate in such Senior
Financing pursuant to Section 5.2(B). 
 (E) To the extent that a Purchaser is entitled to preemptive rights pursuant to
both of Section 5.2(A) and Section 5.2(B) with respect to a Senior Financing, the preemptive right providing such Purchaser with the greater percentage participation right (based on Additional Financing Pro Rata Amount as compared to the
Additional Transaction Pro Rata Amount) shall apply. 
 (F) Promptly after the Company determines to engage in an Additional
Transaction, the Company shall deliver a written notice (the “OFFER NOTICE”) to the Purchasers stating (i) its bona fide intention to offer securities in an Additional Transaction, (ii) the number of such securities to be offered
or amount to be borrowed in the Loan Financing, (iii) the price and terms, to the extent known, upon which it proposes to offer such securities or borrow such funds, and (iv) the anticipated closing date of the Additional Transaction. The
Company shall promptly notify each Purchaser of (i) the determination of the price and terms upon which it proposes to offer such securities, to the extent not set forth in the Offer Notice, and (ii) any material change in any of the
information set forth in the Offer Notice or in the price or other terms previously communicated to such Purchaser. 

  
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 (G) No Purchaser may participate in an Additional Transaction, in whole or in part, unless
it (i) delivers to the Company, on or prior to the date 10 days after the date of delivery of the Offer Notice a written notice of acceptance (an “ACCEPTANCE NOTICE”) providing a representation letter certifying that such Purchaser is
an accredited investor within the meaning of Rule 501 under the Securities Act and indicating the portion of the Purchaser’s Additional Financing Pro Rata Amount or Additional Transaction Pro Rata Amount, as applicable, that such Purchaser
elects to purchase and (ii) deposits in a U.S. escrow account on terms satisfactory to the Company the amount that the Purchaser proposes to invest pursuant to the preemptive rights set forth in this Section 5.2 (the “ESCROW
DEPOSIT”) concurrently with delivering an Acceptance Notice indicating the amount or number of securities to be purchased by the Purchaser; provided, that if the Company does not intend to sign the definitive documentation for such Additional
Transaction within ten days of the date such Acceptance Notice is due pursuant to clause (i) of this Section 5.2(G), the Purchaser must make the Escrow Deposit no later than five days after a request from the Company for the Purchaser to
make such Escrow Deposit. 
 (H) Any issuance of Exempted Securities (as defined in the Series D Certificate of Designations)
shall not be Additional Transactions for purposes of this Section 5.2 and the Purchasers shall have no rights hereunder with respect to the issuance of Exempted Securities; provided, however, that any issuance described in clause (vi) of
the definition of Exempted Securities that constitutes a Senior Financing shall not be exempted from Section 5.2(B). 
 (I)
No Purchaser shall have any right to purchase securities of the Company hereunder, and the Company shall have no obligation to a Purchaser hereunder, if (1) the Company has used its reasonable best efforts to ensure that the sale of such
securities to such Purchaser will not violate the Securities Act or the Exchange Act and, despite such efforts, the Company reasonably determines in good faith that the sale of such securities to such Purchaser cannot be made without the violation
of any rule or regulation promulgated thereunder or (2) the Company reasonably determines in good faith that the sale of such securities to such Purchaser cannot be made without requiring the approval of the Company’s stockholders for a
reason that is related to such Purchaser (or to the Purchasers as a group) and is not related to the participation of other participants in the Additional Transaction, including, without limitation, the application of Nasdaq Listing Rule 5635(b).

 5.3 Expenses. The Company shall pay to Pillar Pharmaceuticals II, L.P. (“PILLAR”) at the Closing upon
delivery to the Company of an invoice, reimbursement for the out-of-pocket expenses reasonably incurred by Pillar or its advisors in connection with the negotiation, preparation, execution and delivery of the Transaction Documents and the other
agreements to be executed in connection herewith, and therewith, including, without limitation, reasonable due diligence and attorneys’ fees and expenses related to the transactions contemplated by the Transaction Documents (the
“EXPENSES”); provided, however, the maximum amount of Expenses for which the Company shall be responsible pursuant to this Section shall be $200,000 and the balance of the expenses of Pillar and the other Purchasers shall be borne by
Pillar and the other Purchasers. 

  
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 5.4 Listing. The Company will use its reasonable best efforts to continue the listing
and trading of its Common Stock, including the Conversion Shares and Warrant Shares, on the NYSE MKT (formerly known as the American Stock Exchange), the New York Stock Exchange, the Nasdaq Global Market, the Nasdaq Capital Market, the Nasdaq Global
Select Market or other equivalent U.S. national exchange or automated trading market (a “PERMITTED EXCHANGE”), and to comply with the reporting, filing and other obligations under the bylaws or rules thereof, provided, however, that in the
event the Company uses its reasonable best efforts but is unsuccessful in maintaining the listing of its Common Stock on the Nasdaq Global Market due to the matters referenced in the letter dated June 4, 2012 from the Nasdaq Global Market as
described in the Exchange Act Reports, then, in light of the Company’s belief that the it is in the best interests of the Company that the Common Stock be listed on a Permitted Exchange, the Company shall use its reasonable best efforts to seek
re-listing of its Common Stock on a Permitted Exchange. 
 5.5 Securities Laws; No Integrated Offerings. The Company shall
not make any offers or sales of any security under circumstances that would cause the offer and sale of the Securities hereunder to violate the Securities Act or the rules or regulations promulgated thereunder or cause the offer and sale of the
Securities to be subject to any stockholder approval provision applicable to the Company or its securities. 
 5.6 No Short
Sales. Each Purchaser agrees that beginning on the date hereof until the earlier of (i) the first anniversary of the date hereof or (ii) the date at which the Shares held by such Purchaser have been converted into Common Stock, it will
not enter into any Short Sales. For purposes of this Section 5.6, a “Short Sale” by a Purchaser means a sale of Common Stock that is marked as a short sale and that is executed at a time when such Purchaser has no equivalent
offsetting long position in the Common Stock. For purposes of determining whether a Purchaser has an equivalent offsetting long position in the Common Stock, all Common Stock that would be issuable upon exercise in full of all options then held by
such Purchaser (assuming that such options were then fully exercisable, notwithstanding any provisions to the contrary, and giving effect to any exercise price adjustments scheduled to take effect in the future) shall be deemed to be held long by
such Purchaser. 
 5.7 Standstill Provision. Each Purchaser hereby agrees that, to the extent that and for so long as the
total number of shares of Common Stock beneficially owned by the Purchaser and its affiliates and any other persons whose beneficial ownership of Common Stock would be aggregated with each Purchaser for purposes of Section 13(d) of the Exchange
Act exceeds 15%, unless specifically invited in writing by the Company to do so, neither the Purchaser nor its affiliates will, or will cause or knowingly permit any of its or their directors, officers, partners, managers, employees, investment
bankers, attorneys, accountants or other advisors or representatives to, in any manner, directly or indirectly: 
 (A) effect or
seek, initiate, offer or propose (whether publicly or otherwise) to effect, or cause or participate in or in any way advise or, assist any other person to effect or seek, initiate, offer or propose (whether publicly or otherwise) to effect or cause
or participate in, any acquisition of any securities (or beneficial ownership thereof) or assets of the Company; any tender or exchange 

  
 - 15 -

 
offer, merger, consolidation or other business combination involving the Company; any recapitalization, restructuring, liquidation, dissolution or other extraordinary transaction with respect to
the Company; or any “solicitation” of “proxies” (as such terms are used in the proxy rules of the Commission) or consents to vote any voting securities of the Company. Notwithstanding the foregoing, nothing in this clause
(A) shall prevent or limit the ability of any director of the Company that is affiliated with a Purchaser to (i) acquire, exercise or dispose of any stock options or other equity securities of the Company received as compensation for
serving as a director or (ii) perform his or her duties as a director of the Company; 
 (B) form, join or in any way
participate in a “group” (as defined under the Exchange Act) with respect to any securities of the Company; 
 (C)
otherwise act, alone or in concert with others, to seek to control or influence the management, Board or policies of the Company; 
 (D) take any action which could reasonably be expected to force the Company to make a public announcement regarding any of the types of matters set forth in this Section 5.7; 

(E) nominate or otherwise support the election of any person as a director of the Company except as approved by the Board; provided, that
this covenant is not intended to prevent any Purchaser or its affiliates from voting any shares of capital stock it holds (other than the Excess Shares) in favor of the election of a person not nominated by the Board as long as such Purchaser or any
of its affiliates have no arrangements with the nominee or the stockholder that nominated the nominee and are not otherwise in breach of this Section 5.7; or 
 (F) enter into any agreements, discussions or arrangements with any third party with respect to any of the foregoing. 
 Notwithstanding the foregoing, the Company hereby agrees that the purchase by a Purchaser of securities of the Company after the date hereof and pursuant to Section 5.2 of this Agreement shall not be
a violation of this Section 5.7. 
 5.8 Voting Rights. 

(A) Each Purchaser hereby agrees that, to the extent that and for so long as the total number of shares of Common Stock beneficially owned
by the Purchaser and its affiliates and any other persons whose beneficial ownership of Common Stock would be aggregated with the Purchaser for purposes of Section 13(d) of the Exchange Act exceeds 19.99% (prior to the date the stockholders of
the Company approve the Nasdaq Proposal) or 25% (effective upon the date that the stockholders of the Company approve the Nasdaq Proposal), in any election of directors and in any other vote to be taken by the stockholders of the Company (whether
taken at an annual or special meeting of stockholders or by written action), it and its affiliates will vote any Excess Shares (as defined below) held in the same manner as and in the same proportion to the votes cast by the other holders of the
Company’s Common Stock or other voting securities. 

  
 - 16 -

 (B) Each Purchaser hereby constitutes and appoints as the proxies of the party and hereby
grants a power of attorney to the officers of the Company, and each of them, with full power of substitution, with respect to clause (A) above, and hereby authorizes each of them to represent and to vote, if and only if the Purchaser
(i) fails to vote or (ii) attempts to vote (whether by proxy, in person or by written consent), in a manner which is inconsistent with the terms of clause (A), all of such Purchaser’s Excess Shares in accordance with the terms of
clause (A). Each of the proxy and power of attorney granted pursuant to the immediately preceding sentence is given in consideration of the agreements and covenants of the Company and the parties in connection with the transactions contemplated by
this Agreement and, as such, each is coupled with an interest and shall be irrevocable unless and until this Agreement terminates or expires. Each Purchaser hereby revokes any and all previous proxies or powers of attorney with respect to the Excess
Shares and shall not hereafter, unless and until this Agreement terminates or expires, purport to grant any other proxy or power of attorney with respect to any of such Excess Shares, deposit any of such Excess Shares into a voting trust or enter
into any agreement (other than this Agreement), arrangement or understanding with any person, directly or indirectly, to vote, grant any proxy or give instructions with respect to the voting of any of such Excess Shares, in each case, with respect
to clause (A) above. 
 (C) Each Purchaser agrees to refrain from exercising (and hereby affirmatively waives) any
dissenters’ rights or rights of appraisal under applicable law at any time with respect to any Sale of the Corporation (as defined in the Certificate of Designations) to the extent such Sale of the Corporation has been approved by the Board.

 (D) For purposes of this Section 5.8, “Excess Shares” means for any Purchaser the number of shares of voting
stock held by the Purchaser and its affiliates equal to (i) the total number of shares of Common Stock held by the Purchaser and its affiliates (including the Conversion Shares and shares of Common Stock issuable upon conversion of other series
of Preferred Stock held by the Purchaser and its affiliates), less (ii) 19.99% (prior to the date the stockholders of the Company approve the Nasdaq Proposal) or 25% (effective upon the date that the stockholders of the Company approve the
Nasdaq Proposal) of the total number of shares of Common Stock then outstanding (including all Conversion Shares and all other shares of Common Stock then issuable upon conversion of other series of Preferred Stock then outstanding). 

5.9 Reservation of Common Stock. The Company shall at all times reserve and keep available out of its authorized but unissued
shares of Common Stock, solely for the purpose of providing for the conversion of the Series E Preferred Stock and the exercise of the Warrants, such number of shares of Common Stock as shall from time to time equal 100% of the number of shares
sufficient to permit the conversion of the Series E Preferred Stock and the exercise of the Warrants issued pursuant to this Agreement in accordance with their respective terms, without regard to any exercise limitations contained therein.

 5.10 Delivery of Certificates. In connection with any conversion of the Shares by a Purchaser, the Company shall use
its best efforts to issue to such Purchaser the applicable certificate or certificates for the Conversion Shares within three Business Days of receipt of all documents and information needed to effect such conversion and issue such certificates.

  
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 5.11 Proxy Statement. 

(A) The Company shall use its best efforts to file a preliminary proxy statement with the SEC with respect to its next annual meeting of
stockholders that will, among other things, seek the Stockholder Approval (as defined below) and include a recommendation of the Board that the stockholders approve such matters as are included in the Stockholder Approval (unless the Board
determines in good faith, that its fiduciary duties require it to do otherwise). 
 (B) As used in this Agreement, the term
“STOCKHOLDER APPROVAL” shall mean the approval at a meeting of stockholders of the Company of the following matters: (i) the issuance and sale by the Company to the Purchasers (together with all prior issuances and sales to Pillar
Pharmaceuticals I, L.P.) of a number of shares of Common Stock (or securities convertible into or exercisable for Common Stock) that is greater than 19.99% of the total number of issued and outstanding shares of Common Stock and of the outstanding
voting power of securities of the Company after such issuance and sale in accordance with Nasdaq Listing Rule 5635(b) (the “NASDAQ PROPOSAL”), (ii) an amendment to the certificate of incorporation and bylaws of the Company, as
necessary, to eliminate the classification of the Board, and (iii) an amendment to the Series D Certificate of Designations in the form attached hereto as Exhibit G; provided, however, that the Company shall not, and shall have no
obligation to, submit the matters contemplated by this clause (iii) to the stockholders of the Company if there are no shares of Series D Preferred Stock then outstanding. In order to be approved at a meeting of the stockholders of the Company:

 (a) the Nasdaq Proposal shall require (y) the affirmative vote of the holders of a majority of the combined voting power
of the outstanding shares of Common Stock and Series D Convertible Preferred Stock, voting as a single class, calculated on an as converted to Common Stock basis, present or represented in person or by proxy and voting at the special meeting and
(z) the affirmative vote of the holders (other than Pillar, the Company and their respective affiliates) of a majority of the combined voting power of the outstanding shares of Common Stock and Series D Convertible Preferred Stock, voting as a
single class, calculated on an as converted to Common Stock basis, held by such holders; 
 (b) the matters described in clause
(ii) above shall require the affirmative vote of the holders of at least 75% of the combined voting power of the outstanding shares of Common Stock and Series D Convertible Preferred Stock, voting as a single class, calculated on an as
converted to Common Stock basis; and 
 (c) the matters described in clause (iii) above shall require (y) the
affirmative vote of the holders of a majority of the combined voting power of the outstanding shares of Common Stock and Series D Convertible Preferred Stock, voting as a single class, calculated on an as converted to Common Stock basis, present or
represented in person or by proxy and voting at the special meeting and (z) the affirmative vote of the holders of a majority of the outstanding shares of the Series D Convertible Preferred Stock, voting separately as a series. 

  
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 ARTICLE 6 
 RESTRICTIONS ON TRANSFERABILITY OF SECURITIES 
 6.1 Restrictions on
Transferability. 
 (A) Subject to Section 6.1(B) and to any requirements of Regulation S that may be applicable to
non-U.S. persons, the Securities shall not be sold, transferred, assigned or hypothecated unless (i) there is an effective registration statement under the Securities Act covering such Securities, (ii) the sale is made in accordance with
Rule 144 under the Securities Act, or (iii) the Company receives an opinion of counsel for the holder of the Securities reasonably satisfactory to the Company stating that such sale, transfer, assignment or hypothecation is exempt from the
registration requirements of the Securities Act, and each such case upon all other conditions specified in this Section 6.1. Furthermore, with respect to Securities that were initially sold by the Company in reliance on Regulation S, hedging
transactions involving such Securities may not be conducted unless in compliance with the Securities Act. Notwithstanding the provisions of the preceding sentence, no registration statement or opinion of counsel shall be required for any transfer of
any Securities by a Purchaser that is a partnership, a limited liability company or a corporation to (a) a partner of such partnership, a member of such limited liability company or a stockholder of such corporation, (b) an entity that
controls, or is controlled by, or is under common control with such partnership, limited liability company or corporation, or (c) the estate of any such partner, member or stockholder (collectively, clauses (a) through (c) the
“PERMITTED TRANSFEREES”); provided, that in each of the foregoing cases the proposed transferee of the Securities held by the Purchaser agrees in writing to take and hold such Securities subject to the provisions and upon the conditions
specified in this Article 6. 
 (B) Notwithstanding anything to the contrary set forth in this Agreement, without the prior
written consent of the Company, Pillar may not sell or transfer any Securities to a person, entity or group (within the meaning of Section 13(d) of the Exchange Act) in one or more transactions if such sale or transfer would, in the aggregate,
result in the transfer to such person, entity or group Securities representing, or exercisable for stock of the Company representing, more than 5% of the then outstanding combined voting power of the outstanding securities of the Company (other than
a sale or transfer to a Permitted Transferee who agrees in writing to be bound by such restrictions or in connection with a resale of such Securities in connection with an underwritten public offering that has been approved by the Board).

 (C) Any transfer not made in compliance with the requirements of this Section 6.1 shall be null and void ab initio, shall
not be recorded on the books of the Company or its transfer agent and shall not be recognized by the Company. Each Purchaser acknowledges and agrees that any breach of this Section 6.1 by a Purchaser would result in substantial harm to the
Company and its stockholders for which monetary damages alone could not adequately compensate. Therefore, each Purchaser unconditionally and irrevocably agrees that the Company shall be entitled to seek protective orders, injunctive relief and other
remedies available at law or in equity (including without limitation, seeking specific performance or the rescission of purchases, sales and other transfers of Securities not made in compliance with this Section 6.1). 

  
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 6.2 Restrictive Legends. Each certificate representing the Securities, and any other
securities issued in respect of the Securities upon any stock split, stock dividend, recapitalization, merger, consolidation or similar event (except as otherwise permitted by the provisions of this Article 6), shall be stamped or otherwise
imprinted with the following legends (as applicable with respect to the second and third legends set forth below) in substantially the following forms: 
 “THE SECURITIES REPRESENTED BY THIS CERTIFICATE HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED, OR THE SECURITIES LAWS OF ANY STATE OF THE UNITED STATES OR IN ANY OTHER
JURISDICTION.” 
 U.S. Investors: “THE SECURITIES REPRESENTED HEREBY MAY NOT BE OFFERED, SOLD OR OTHERWISE TRANSFERRED,
PLEDGED OR HYPOTHECATED IN THE ABSENCE OF AN EFFECTIVE REGISTRATION STATEMENT FOR THE SECURITIES UNDER APPLICABLE SECURITIES LAWS UNLESS OFFERED, SOLD OR OTHERWISE TRANSFERRED, PLEDGED OR HYPOTHECATED PURSUANT TO AN AVAILABLE EXEMPTION FROM THE
REGISTRATION REQUIREMENTS OF THOSE LAWS.” 
 Non-U.S. Investors: “THE SECURITIES REPRESENTED HEREBY MAY NOT BE OFFERED,
SOLD OR OTHERWISE TRANSFERRED, PLEDGED OR HYPOTHECATED EXCEPT IN COMPLIANCE WITH REGULATION S UNDER THE SECURITIES ACT, AND IN THE ABSENCE OF AN EFFECTIVE REGISTRATION STATEMENT FOR THE SECURITIES UNDER APPLICABLE SECURITIES LAWS UNLESS OFFERED,
SOLD OR OTHERWISE TRANSFERRED, PLEDGED OR HYPOTHECATED PURSUANT TO AN AVAILABLE EXEMPTION FROM THE REGISTRATION REQUIREMENTS OF THOSE LAWS. HEDGING TRANSACTIONS INVOLVING THE SECURITIES REPRESENTED HEREBY MAY NOT BE CONDUCTED UNLESS IN COMPLIANCE
WITH THE SECURITIES ACT.” 
 “THE SECURITIES REPRESENTED BY THIS CERTIFICATE MAY BE TRANSFERRED ONLY IN ACCORDANCE WITH
THE TERMS OF AN AGREEMENT BETWEEN THE COMPANY AND THE STOCKHOLDER, A COPY OF WHICH IS ON FILE WITH THE SECRETARY OF THE COMPANY.” 
 6.3 Removal of Legend and Transfer Restrictions. The foregoing legends (other than the last legend) shall be removed from the certificates representing such Securities, at the request of the holder
thereof, at such time as (a) a period of at least one year, as determined in accordance with paragraph (d) of Rule 144 under the Securities Act, as elapsed since the later of the date the Securities were acquired from the Company or an
affiliate of the Company, and (b) the Securities become eligible for resale pursuant to Rule 144(b)(1)(i) under the Securities Act. 

  
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 ARTICLE 7 
 MISCELLANEOUS 
 7.1 Survival of Representations, Warranties and
Agreements. Notwithstanding any investigation made by any party to this Agreement, all covenants, agreements, representations and warranties made by the Company and the Purchasers herein shall survive the execution of this Agreement, the
delivery to the Purchasers of the Shares and Warrants being purchased and the payment therefor. 
 7.2 Notices. All
notices required or permitted hereunder shall be in writing and shall be deemed effectively given: (i) upon delivery to the party to be notified, (ii) when received by email or confirmed facsimile, or (iii) one Business Day after
deposit with a nationally recognized overnight carrier, specifying next Business Day delivery, with written verification of receipt. All communications shall be sent to the Company and the Purchasers as follows or at such other addresses as the
Company or the Purchasers may designate upon 10 days’ advance written notice to the other party: 
 (A) if to the Company,
to: 
 Idera Pharmaceuticals, Inc. 
 167 Sidney Street 
 Cambridge, MA 02139 

Attention: Chief Executive Officer 
 Facsimile: (617) 679-5592 
 Email: sagrawal@iderapharma.com 

with a copy to: 

Wilmer Cutler Pickering Hale and Dorr LLP 
 60 State Street 
 Boston, Massachusetts 02109 

Attention: Stuart Falber 
 Facsimile: (617) 526-5000 Email: stuart.falber@wilmerhale.com 
 (B) if to a
Purchaser, at its address as set forth on the Schedule of Purchasers to this Agreement. 
 7.3 Changes. This Agreement may
not be modified or amended except pursuant to an instrument in writing signed by the Company and the Purchasers holding a majority of the Shares then outstanding. No provision hereunder may be waived other than in a written instrument executed by
the waiving party. 

  
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 7.4 Headings. The headings of the various sections of this Agreement have been
inserted for convenience of reference only and shall not be deemed to be part of this Agreement. 
 7.5 Severability. In
case any provision contained in this Agreement should be invalid, illegal or unenforceable in any respect, the validity, legality and enforceability of the remaining provisions contained herein shall not in any way be affected or impaired thereby.

 7.6 Governing Law. This Agreement shall be governed by and construed in accordance with the laws of the State of
Delaware without regard to principles of conflicts of law. 
 7.7 Counterparts. This Agreement may be executed in two or
more counterparts, each of which shall constitute an original, but all of which, when taken together, shall constitute but one instrument, and shall become effective when one or more counterparts have been signed by each party hereto and delivered
(including by facsimile) to the other parties. 
 7.8 Entire Agreement. This Agreement, the Registration Rights Agreement
and the instruments referenced herein contain the entire understanding of the parties with respect to the matters covered herein and therein and, except as specifically set forth herein or therein, neither the Company nor the Purchasers make any
representation, warranty, covenant or undertaking with respect to such matters. 
 7.9 Assignment. Except as otherwise
expressly provided herein, the provisions hereof shall inure to the benefit of, and be binding upon, the parties hereto and their respective permitted successors, assigns, heirs, executors and administrators. This Agreement and the rights of a
Purchaser hereunder may not be assigned by the Purchaser without the prior written consent of the Company, except such consent shall not be required in cases of assignments by a Purchaser as permitted under Section 6.1, provided that such
assignee agrees in writing to be bound by the terms of this Agreement. Notwithstanding the foregoing, the rights set forth in Sections 5.2 and 5.11 may not be assigned or transferred. 

7.10 Further Assurances. Each party agrees to cooperate fully with the other parties and to execute such further instruments,
documents and agreements and to give such further written assurance as may be reasonably requested by any other party to evidence and reflect the transactions described herein and contemplated hereby and to carry into effect the intents and purposes
of this Agreement. 
 7.11 Confidentiality. Each Purchaser agrees that it will keep confidential and will not disclose or
divulge any confidential, proprietary or secret information which such Purchaser may obtain from the Company pursuant to reports, notices and other materials submitted by the Company to such Purchaser pursuant to this Agreement, otherwise pursuant
to the Registration Rights Agreement, unless (a) such information is known, or until such information becomes known, to the public or (b) such information is required to be disclosed in legal proceedings (such as by deposition,
interrogatory, request for documents, subpoena, civil investigation demand, filing with any governmental authority or similar process), provided, however, that before making any use or disclosure in reliance on this clause (b) the Purchaser
shall give the Company at least 15 days’ prior written notice (or such shorter period as required by law) 

  
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specifying the circumstances giving rise thereto and will furnish only that portion of the non-public information which is legally required and will exercise its best efforts to obtain reliable
assurance that confidential treatment will be accorded any non-public information so furnished. 
 7.12 Use of Purchaser
Name. Except as may be required by applicable law or regulation and as may be required in the Registration Statement, the Company shall not use any Purchaser’s name or the name of any of its affiliates in any advertisement, announcement,
press release or other similar public communication in connection with the offering of the Securities contemplated hereby unless it has received the prior written consent of such Purchaser for the specific use contemplated or as otherwise required
by applicable law or regulation. 
 [REMAINDER OF THIS PAGE INTENTIONALLY LEFT BLANK] 

  
 - 23 -

 IN WITNESS WHEREOF, the parties hereto have executed this Agreement as of the date first set
forth above. 
  

			
	IDERA PHARMACEUTICALS, INC.
		
	By:	 	/s/ Sudhir Agrawal
		 	Sudhir Agrawal
		 	Chairman, Chief Executive Officer and President

  
 - 24 -

 IN WITNESS WHEREOF, the parties hereto have executed this Agreement as of the date first set
forth above. 
  

			
	PURCHASER:
	
	PILLAR PHARMACEUTICALS II, L.P.
		
	By:	 	/s/ Youssef El Zein
	 Name:
	 	Youssef El Zein
	 Title:
	 	General Partner

  
 - 25 -

 IN WITNESS WHEREOF, the parties hereto have executed this Agreement as of the date first set
forth above. 
  

							
	PURCHASER
	
	PARTICIPATIONS BESANCON
			
		 	By:	 	Pillar Invest Corporation, as attorney-in-fact
				
		 		 	By:	 	/s/ Youssef El Zein
		 		 	Name:	 	Youssef El Zein
		 		 	Title:	 	as attorney-in-fact per power signed on November
9th, 2012

  
 - 26 -

 EXHIBIT A 
 Schedule of Purchasers 
  

													
	 	  	Shares	 	  	Warrants	 	  	Purchase Price	 
				
	 Pillar Pharmaceuticals II, L.P.

Address:
 Pillar Invest Offshore SAL Starco Center, Bloc B, Third Floor
 Omar Daouk Street
 Beirut 2020-3313

Lebanon
  

Tel: +961 1 363 362

Fax: +961 1 379 378

Email: pillar@pillarinvest.com
	  	 	313,341	  	  	 	6,266,820	  	  	$	5,170,126.50	  
				
	 Participations Besancon

Address:
 Pillar Invest Offshore SAL
 Starco Center, Bloc B,
Third
 Floor

Omar Daouk Street

Beirut 2020-3313
 Lebanon
  
 Tel: +961 1 363 362
 Fax: +961 1 379 378

Email: pillar@pillarinvest.com
	  	 	110,901	  	  	 	2,218,020	  	  	$	1,829,866.50	  
				
	 Total:
	  	 	424,242	  	  	 	8,484,840	  	  	$	6,999,993.00	  

 EXHIBIT B 
 Form of Warrant 

 EXHIBIT C 
 Certificate of Designations 

 EXHIBIT D 
 Registration Rights Agreement 

 EXHIBIT E 
 Legal Opinion 

 EXHIBIT F 
 Registration Statement Questionnaire 

 EXHIBIT G 
 Amendment to Series D Certificate of DesignationsEX-10.2

 Exhibit 10.2 

IDERA PHARMACEUTICALS, INC. 
 REGISTRATION RIGHTS AGREEMENT 
 REGISTRATION RIGHTS AGREEMENT (this
“AGREEMENT”), dated as of November 9, 2012, by and among IDERA PHARMACEUTICALS, INC., a corporation organized under the laws of the State of Delaware (the “COMPANY”), and each of the persons or entities listed on Exhibit
A hereto (the “PURCHASERS”). 
 WHEREAS: 
 In connection with the Convertible Preferred Stock and Warrant Purchase Agreement, dated as of even date herewith, by and among the Company and the Purchasers (the “STOCK PURCHASE AGREEMENT”),
the Company has agreed, upon the terms and subject to the conditions contained therein, to issue and sell to the Purchasers (i) shares (the “SHARES”) of the Company’s Series E convertible preferred stock, par value $0.01 per
share (the “PREFERRED STOCK”), and (ii) warrants (the “WARRANTS”) to acquire shares of the Company’s common stock, par value $0.001 per share (the “COMMON STOCK”). The shares of Common Stock issuable upon
exercise of or otherwise pursuant to the Warrants are referred to herein as the “WARRANT SHARES.” 
 To induce the
Purchasers to execute and deliver the Stock Purchase Agreement, the Company has agreed to provide certain registration rights under the Securities Act of 1933, as amended, and the rules and regulations thereunder, or any similar successor statute
(collectively, the “SECURITIES ACT”), and applicable state securities laws. 
 NOW, THEREFORE, in consideration of the
premises and the mutual covenants contained herein and other good and valuable consideration, the receipt and sufficiency of which are hereby acknowledged, the Company and the Purchasers hereby agree as follows: 

1. DEFINITIONS. 
 A. As used in
this Agreement, the following terms shall have the following meanings: 
 i. “PURCHASERS” means the Purchasers and any
transferees or assignees who agree to become bound by the provisions of this Agreement in accordance with Section 10 hereof. 
 ii. “REGISTER,” “REGISTERED,” and “REGISTRATION” refer to a registration effected by preparing and filing a Registration Statement or Statements in compliance with the
Securities Act and pursuant to Rule 415 under the Securities Act or any successor rule providing for offering securities on a continuous basis (“RULE 415”), and the declaration or ordering of effectiveness of such Registration Statement by
the United States Securities and Exchange Commission (the “SEC”). 

 iii. “REGISTRABLE SECURITIES” means (a) the shares of Common Stock issued or
issuable upon the conversion of the Shares (the “CONVERSION SHARES”), (b) the Warrant Shares and (c) any shares of capital stock issued or issuable, from time to time (with any adjustments), in respect of the Conversion Shares or
the Warrant Shares by virtue of any stock split, stock dividend, recapitalization or similar event; provided, however, that shares of Common Stock that are Registrable Securities shall cease to be Registrable Securities upon the earliest of
(A) the date such shares become eligible for sale pursuant to Rule 144(b)(1)(i) under the Securities Act; provided that a period of at least one year, as determined in accordance with paragraph (d) of Rule 144 under the Securities
Act, has elapsed since the later of the date such shares were acquired from the Company or an affiliate of the Company, (B) the date that such shares are sold (I) pursuant to a registration statement, (II) to or through a broker, dealer or
underwriter in a public securities transaction and/or (III) in a transaction exempt from the registration and prospectus delivery requirements of the Securities Act such that all transfer restrictions and restrictive legends with respect thereto, if
any, are removed upon the consummation of such sale, or (C) any sale or transfer to any person or entity which by virtue of Section 10 of this Agreement is not entitled to the rights provided by this Agreement. Wherever reference is made
in this Agreement to a request or consent of holders of a certain percentage of Registrable Securities, the determination of such percentage shall include shares of Common Stock issuable upon conversion of the Shares or exercise of the Warrants,
even if such conversion or exercise has not been effected. 
 iv. “REGISTRATION STATEMENT” means a registration
statement of the Company under the Securities Act (including without limitation the Initial Registration Statement, the New Registration Statement and any Remainder Registration Statements, each, as defined below). 

v. “SEC GUIDANCE” means (i) any publicly-available written or oral guidance, comments, requirements or requests of the SEC
staff (ii) any written or oral guidance, requirements or requests by the SEC staff to the Company and (iii) the Securities Act. 
 B. Capitalized terms used herein and not otherwise defined herein shall have the respective meanings set forth in the Stock Purchase Agreement. 
 2. REGISTRATION. 
 A. MANDATORY REGISTRATION. 

i. The Company shall file with the SEC and use its reasonable best efforts to cause to become effective a Registration Statement on Form
S-3 (or, if Form S-3 is not then available, on such form of Registration Statement as is then available to effect a registration of all of the Registrable Securities) covering the resale of the Registrable Securities on or prior to February 7,
2013 (the “INITIAL REGISTRATION STATEMENT”). The Initial Registration Statement filed hereunder, to the extent allowable under the Securities Act, shall state that such Initial Registration Statement also covers such indeterminate number
of additional shares of Common Stock as may become issuable upon conversion of the Shares or exercise of the Warrants to prevent dilution resulting from stock splits, stock dividends or similar transactions. 

  
 - 2 -

 ii. Notwithstanding the registration obligations set forth in this Section 2, in the
event the SEC informs the Company that all of the Registrable Securities cannot, as a result of the application of Rule 415, be registered for resale as a secondary offering on a single registration statement, the Company shall promptly inform each
of the Purchasers and use its commercially reasonable efforts to (a) file amendments to the Initial Registration Statement as required by the SEC and/or (b) withdraw the Initial Registration Statement and file a new registration statement
(a “NEW REGISTRATION STATEMENT”), in either case covering the maximum number of Registrable Securities permitted to be registered by the SEC, on Form S-3 or such other form available to register for resale the Registrable Securities as a
secondary offering; provided, however, that prior to filing such amendment or New Registration Statement, the Company shall be obligated to use its commercially reasonable efforts to advocate with the SEC for the registration of all of the
Registrable Securities in accordance with the SEC Guidance, including without limitation, Compliance and Disclosure Interpretation 612.09 of the rules adopted under the Securities Act. 

iii. Notwithstanding any other provision of this Agreement, if any SEC Guidance sets forth a limitation on the number of Registrable
Securities permitted to be registered on a particular Registration Statement as a secondary offering (and notwithstanding that the Company used commercially reasonable efforts to advocate with the SEC for the registration of all or a greater number
of Registrable Securities), unless otherwise directed in writing by a holder as to its Registrable Securities, the number of Registrable Securities to be registered on such Registration Statement will first be reduced by (a) Registrable
Securities not acquired pursuant to the Stock Purchase Agreement (whether pursuant to registration rights or otherwise), (b) second by Registrable Securities that are Warrant Shares (applied, in the case that some Warrant Shares may be
registered, to the holders on a pro rata basis based on the total number of unregistered Warrant Shares held by such holders), and (c) third by Registrable Securities that are Shares or Conversion Shares (applied, in the case that some Shares
and Conversion Shares may be registered, to the holders on a pro rata basis based on the total number of unregistered Shares and Conversion Shares held by such holders, subject to a determination by the SEC that the Shares and Conversion Shares of
certain holders must be reduced first based on the number of Shares and Conversion Shares held by such holders). 
 iv. In the
event the Company amends the Initial Registration Statement or files a New Registration Statement, as the case may be, under clause ii. above, the Company will use its commercially reasonable efforts to file with the SEC, as promptly as allowed by
the SEC or the SEC Guidance provided to the Company or to registrants of securities in general, one or more registration statements on Form S-3 or such other form available to register for resale those Registrable Securities that were not registered
for resale on the Initial Registration Statement, as amended, or the New Registration Statement (the “REMAINDER REGISTRATION STATEMENTS”). 
 B. PAYMENTS BY THE COMPANY. 
 i. If the Initial Registration Statement or the New
Registration Statement, as the case may be, is not declared effective by the SEC on or before March 30, 2013 (the “REGISTRATION DEADLINE”) or, (ii) if, after a Registration Statement has been declared effective by the SEC, sales
of any of the Registrable Securities covered by such Registration Statement cannot be made pursuant to such Registration Statement because such Registration Statement has been suspended (by reason of a stop order or the Company’s failure to
update the Registration Statement or otherwise) except as a result of a permitted Suspension under Section 9, then the Company will make payments to the Purchasers in such amounts and at such times as shall be determined pursuant

  
 - 3 -

 
to this Section 2(B), as liquidated damages and not as a penalty for such delay in or reduction of their ability to sell the Registrable Securities (which remedy shall constitute the
Purchasers exclusive monetary remedy). In such event, the Company shall pay to each Purchaser an amount equal to the product of (i) the aggregate purchase price of the Shares then held by such Purchaser which are not able to be sold pursuant to
a Registration Statement for such reasons (the “AGGREGATE SHARE PRICE”), multiplied by (ii) one hundredths (.01), for each thirty (30) day period, (A) after the Registration Deadline and prior to the date the Initial
Registration Statement or the New Registration Statement, as the case may be, is declared effective by the SEC, and (B) during which sales of any Registrable Securities covered by a Registration Statement cannot be made pursuant to any such
Registration Statement after the Registration Statement has been declared effective; provided, however, that there shall be excluded from each such period any delays which are attributable to changes (other than corrections of Company
mistakes with respect to information previously provided by the Purchasers) required by the Purchasers in the Registration Statement with respect to information relating to the Purchasers, including, without limitation, changes to the plan of
distribution. Such amounts shall be paid in cash within five (5) trading days after the end of each thirty (30) day period that gives rise to such obligation. 
 ii. Notwithstanding the foregoing, in no event shall the Company be obligated to make payments hereunder (a) to more than one Purchaser in respect of the same Registrable Securities for the same
period of time or (b) to any one Purchaser in an aggregate amount that exceeds 10% of the Aggregate Share Price paid by such Purchaser for such Shares. All liquidated damages hereunder shall apply on a daily pro-rata basis for any portion of a
30-day period prior to the cure of any of the events specified in (A) or (B) of this Section 2(B). 
 iii. The
Company shall not be liable for liquidated damages under this Agreement as to any Registrable Securities which are not permitted by the SEC to be included in the Initial Registration Statement or the New Registration Statement due solely to SEC
Guidance relating to the inclusion of such Registrable Securities in a Registration Statement from the time that it is determined that such Registrable Securities are not permitted to be registered. In such case, the liquidated damages shall be
calculated to only apply to the Registrable Securities which are permitted in accordance with SEC Guidance relating to the inclusion of such Registrable Securities in a Registration Statement to be included in such Initial Registration Statement or
such New Registration Statement. 
 3. OBLIGATIONS OF THE COMPANY. 
 In connection with the registration of the Registrable Securities, the Company shall have the following obligations: 
 A. The Company shall prepare and file with the SEC such amendments (including post-effective amendments) and supplements to each Registration Statement and the prospectus used in connection with each
Registration Statement as may be necessary to keep each such Registration Statement effective pursuant to Rule 415 at all times until no Registrable Securities thereunder remain outstanding (the “REGISTRATION PERIOD”), and, during such
period, comply with the provisions of the Securities Act in order to 

  
 - 4 -

 
enable the disposition of all Registrable Securities of the Company covered by the Registration Statement until such time as all of such Registrable Securities have been disposed of in accordance
with the intended methods of disposition by the seller or sellers thereof as set forth in the Registration Statement. 
 B. In
connection with the effectiveness of each Registration Statement, the Company shall furnish to each Purchaser whose Registrable Securities are included in the Registration Statement within three trading days of the date of effectiveness of the
Registration Statement or any amendment thereto, a notice stating that the Registration Statement or amendment has been declared effective; and such number of copies of a prospectus, including a preliminary prospectus, and all amendments and
supplements thereto and such other documents as such Purchaser may reasonably request in order to facilitate the disposition of the Registrable Securities owned by such Purchaser. 

C. The Company shall use its reasonable best efforts to (i) register and qualify the Registrable Securities covered by Registration
Statements under such other securities or “blue sky” laws of such jurisdictions in the United States as each Purchaser who holds Registrable Securities being offered reasonably requests, (ii) prepare and file in those jurisdictions
such amendments (including post-effective amendments) and supplements to such registrations and qualifications as may be necessary to maintain the effectiveness thereof during the Registration Period, (iii) take such other actions as may be
necessary to maintain such registrations and qualifications in effect at all times during the Registration Period, and (iv) take all other actions reasonably necessary or advisable to qualify the Registrable Securities for sale in such
jurisdictions; provided, however, that the Company shall not be required in connection therewith or as a condition thereto to (a) qualify to do business in any jurisdiction where it would not otherwise be required to qualify but for this
Section 3(C), (b) subject itself to general taxation in any such jurisdiction, (c) file a general consent to service of process in any such jurisdiction, (d) provide any undertakings that cause the Company undue expense or
burden, or (e) make any change in its charter or by-laws, which in each case the Board of Directors of the Company determines to be contrary to the best interests of the Company and its stockholders. 

D. The Company shall notify each Purchaser who holds Registrable Securities of the time when a supplement to any prospectus forming a part
of a Registration Statement has been filed and of any request by the SEC for the amending or supplementing of such Registration Statement or prospectus. If the Company has delivered a Prospectus and after having done so the prospectus is amended to
comply with the requirements of the Securities Act, the Company shall promptly notify each Purchaser who holds Registrable Securities covered by such prospectus and, if requested, such Purchasers shall immediately cease making offers of Registrable
Securities pursuant to such prospectus and return all copies of such prospectus to the Company. The Company shall promptly provide the Purchasers with revised prospectuses and, following receipt of the revised prospectuses, the Purchasers shall be
free to resume making offers of the Registrable Securities. 
 E. The Company shall provide a transfer agent and registrar, which
may be a single entity, for the Registrable Securities not later than the effective date of the Initial Registration Statement or the New Registration Statement, as applicable. 

  
 - 5 -

 F. The Company shall cooperate with the Purchasers who hold Registrable Securities to
facilitate the timely preparation and delivery of certificates representing Registrable Securities to be offered pursuant to the Registration Statements and enable such certificates to be in such denominations or amounts, as the case may be, as
Purchasers may reasonably request and registered in such names as the Purchasers may request. 
 G. At the reasonable request of
the Purchasers holding a majority in interest of the Registrable Securities covered by a Registration Statement, the Company shall prepare and file with the SEC such amendments (including post effective amendments) and supplements to such
Registration Statement and the prospectus used in connection with such Registration Statement as may be necessary in order to change the plan of distribution set forth in such Registration Statement. 

H. The Company shall use its reasonable best efforts to cause all Registrable Securities registered pursuant to this Agreement to be
listed on each securities exchange or trading system on which similar securities issued by the Company are then listed. 
 4. OBLIGATIONS OF THE
PURCHASERS. In connection with the registration of the Registrable Securities, the Purchasers shall have the following obligations: 
 A. It shall be a condition precedent to the obligations of the Company under Sections 2 and 3 with respect to the Registrable Securities of a particular Purchaser that such Purchaser shall furnish to the
Company such information regarding itself, the Registrable Securities held by it and the intended method of disposition of the Registrable Securities held by it as shall be reasonably required to effect the registration of such Registrable
Securities and shall execute such documents in connection with such registration as the Company may reasonably request. At least five (5) trading days prior to the first anticipated filing date of the Initial Registration Statement or the New
Registration Statement, as the case may be, the Company shall notify each Purchaser of the information the Company requires from each such Purchaser. 
 B. Each Purchaser, by such Purchaser’s acceptance of the Registrable Securities, agrees to cooperate with the Company as reasonably requested by the Company in connection with the preparation and
filing of each Registration Statement hereunder, unless such Purchaser has notified the Company in writing of such Purchaser’s election to exclude all of such Purchaser’s Registrable Securities from such Registration Statement. 

C. Each Purchaser agrees that, upon receipt of any notice from the Company of the happening of any event of the kind described in Sections
3(D) or 9, such Purchaser will immediately discontinue disposition of Registrable Securities pursuant to the Registration Statement covering such Registrable Securities until such Purchaser’s receipt of the copies of the supplemented or amended
prospectus contemplated by Sections 3(D) or 9. 
 5. EXPENSES OF REGISTRATION. All reasonable expenses incurred by the Company or the Purchasers
in connection with registrations, filings or qualifications pursuant to Sections 2 and 3 above, including, without limitation, all registration, listing and qualifications fees, printers and accounting fees, the fees and disbursements of counsel for
the Company and the fees and disbursements of one counsel selected by the Purchasers, shall be borne by the Company, excluding underwriting discounts, selling commissions and similar costs which shall be borne by the Purchasers. 

  
 - 6 -

 6. INDEMNIFICATION. In the event any Registrable Securities are included in a Registration Statement under
this Agreement: 
 A. To the extent permitted by law, the Company will indemnify, hold harmless and defend (i) each
Purchaser who holds such Registrable Securities, and (ii) the directors, officers, partners, members, employees and agents of such Purchaser and each person who controls any Purchaser within the meaning of Section 15 of the Securities Act
or Section 20 of the Securities Exchange Act of 1934, as amended (the “EXCHANGE ACT”), if any, (each, an “INDEMNIFIED PERSON”), against any joint or several losses, claims, damages, liabilities or expenses (collectively,
together with actions, proceedings or inquiries by any regulatory or self-regulatory organization, whether commenced or threatened, in respect thereof, “CLAIMS”) to which any of them may become subject insofar as such Claims arise out of
or are based upon: (i) any untrue statement or alleged untrue statement of a material fact in a Registration Statement or the omission or alleged omission to state therein a material fact required to be stated or necessary to make the
statements therein not misleading, (ii) any untrue statement or alleged untrue statement of a material fact contained in any preliminary prospectus if used prior to the effective date of such Registration Statement, or contained in the final
prospectus (as amended or supplemented, if the Company files any amendment thereof or supplement thereto with the SEC) or the omission or alleged omission to state therein any material fact necessary to make the statements made therein, in light of
the circumstances under which the statements therein were made, not misleading, or (iii) any violation or alleged violation by the Company of the Securities Act, the Exchange Act, any other law, including, without limitation, any state
securities law, or any rule or regulation thereunder relating to the offer or sale of the Registrable Securities (the matters in the foregoing clauses (i) through (iii), collectively, “VIOLATIONS”). Subject to the restrictions set
forth in Section 6(C) with respect to the number of legal counsel, the Company shall reimburse the Purchasers and each other Indemnified Person, promptly as such expenses are incurred and are due and payable, for any reasonable legal fees or
other reasonable expenses incurred by them in connection with investigating or defending any such Claim. Notwithstanding anything to the contrary contained herein, the obligations of the Company contained in this Section 6(A): (i) shall
not apply to a Claim arising out of or based upon (A) a Violation which occurs in reliance upon and in conformity with information furnished in writing to the Company by such Indemnified Person expressly for use in the Registration Statement or
any such amendment thereof or supplement thereto, (B) the failure of a Purchaser to comply with Section 4(C) or (C) the use by a Purchaser in connection with any sale or sales of Registrable Securities of a prospectus containing any
untrue statement or omission of a material fact following notification by the Company that such prospectus contains an untrue statement or omission of a material fact and receipt by the Purchaser of a corrected prospectus; and (ii) shall not
apply to amounts paid in settlement of any Claim if such settlement is effected without the prior written consent of the Company, which consent shall not be unreasonably withheld. Such indemnity shall remain in full force and effect regardless of
any investigation made by or on behalf of the Indemnified Person and shall survive the transfer of the Registrable Securities by the Purchasers pursuant to Section 10 hereof. 

  
 - 7 -

 B. Each Purchaser who holds such Registrable Securities agrees severally and not jointly to
indemnify, hold harmless and defend, to the same extent and in the same manner set forth in Section 6(A), the Company, each of its directors, each of its officers who signs the Registration Statement, its employees, agents and each person, if
any, who controls the Company within the meaning of Section 15 of the Securities Act or Section 20 of the Exchange Act, and any other stockholder selling securities pursuant to the Registration Statement or any of its directors or officers
or any person who controls such stockholder within the meaning of the Securities Act or the Exchange Act (collectively and together with an Indemnified Person, an “INDEMNIFIED PARTY”), against any Claim to which any of them may become
subject, under the Securities Act, the Exchange Act or otherwise, insofar as such Claim arises out of or is based upon any Violation, in each case to the extent (and only to the extent) that such Violation occurs in reliance upon and in conformity
with written information furnished to the Company by such Purchaser expressly for use in connection with such Registration Statement; and subject to Section 6(C) such Purchaser will reimburse any legal or other expenses (promptly as such
expenses are incurred and are due and payable) reasonably incurred by them in connection with investigating or defending any such Claim; provided, however, that (I) the obligations of a Purchaser contained in this Section 6(B) shall not
apply to amounts paid in settlement of any Claim if such settlement is effected without the prior written consent of such Purchaser, which consent shall not be unreasonably withheld, and (II) the Purchaser shall be liable under this Agreement
(including this Section 6(B) and Section 7) for only that amount as does not exceed the gross proceeds actually received by such Purchaser as a result of the sale of Registrable Securities pursuant to such Registration Statement. Such
indemnity shall remain in full force and effect regardless of any investigation made by or on behalf of such Indemnified Party and shall survive the transfer of the Registrable Securities by the Purchasers pursuant to Section 10 hereof.

 C. Promptly after receipt by an Indemnified Person or Indemnified Party under this Section 6 of notice of the threat or
commencement of any action (including any governmental action), such Indemnified Person or Indemnified Party shall, if a Claim in respect thereof is to made against any indemnifying party under this Section 6, deliver to the indemnifying party
a written notice of the commencement thereof, and the indemnifying party shall have the right to participate in, and, to the extent the indemnifying party so desires, jointly with any other indemnifying party similarly noticed, to assume control of
the defense thereof with counsel mutually satisfactory to the indemnifying party and the Indemnified Person or the Indemnified Party, as the case may be; provided, however, that such indemnifying party shall not be entitled to assume such defense
and an Indemnified Person or Indemnified Party shall have the right to retain its own counsel with the fees and expenses to be paid by the indemnifying party, if, in the reasonable opinion of counsel retained by the indemnifying party, the
representation by such counsel of the Indemnified Person or Indemnified Party and the indemnifying party would be inappropriate due to actual or potential conflicts of interest between such Indemnified Person or Indemnified Party and any other party
represented by such counsel in such proceeding or the actual or potential defendants in, or targets of, any such action include both the Indemnified Person or the Indemnified Party and the indemnifying party and any such Indemnified Person or
Indemnified Party reasonably determines, based upon the reasonable opinion of counsel, that there may be legal defenses available to such Indemnified Person or Indemnified Party which are in conflict with those available to such indemnifying party.
The indemnifying party shall pay for only one separate legal counsel for the Indemnified Persons or the Indemnified Parties, as applicable, and such legal counsel shall be selected by Purchasers holding a majority-in-interest of the Registrable
Securities included in the Registration Statement to which the Claim relates (with the approval of the Purchasers if it holds Registrable Securities included in such Registration Statement), if the Purchasers are entitled to indemnification
hereunder, or by the Company, if the Company is entitled to indemnification hereunder, as applicable. The failure to deliver written notice to the indemnifying party within a reasonable time of the commencement of any such action shall not relieve
such indemnifying party of any liability to the Indemnified Person or Indemnified Party under this Section 6, except to the extent that the indemnifying party is actually prejudiced in its ability to defend such action. 

  
 - 8 -

 D. The Indemnified Party shall cooperate fully with the indemnifying party in connection
with any negotiation or defense of any such action or claim by the indemnifying party and shall furnish to the indemnifying party all information reasonably available to the Indemnified Party which relates to such action or claim. 

E. No indemnifying party shall, except with the consent of each Indemnified Party (which consent shall not be unreasonably withheld),
consent to entry of any judgment or enter into any settlement which does not include the giving by the claimant to such Indemnified Party a release from all liability in respect to such claim or litigation. 

7. CONTRIBUTION. To the extent any indemnification by an indemnifying party required by the terms of this Agreement is prohibited or limited by law, the
indemnifying party, in lieu of indemnifying the Indemnified Party, agrees to contribute with respect to any amounts for which it would otherwise be liable under Section 6 up to the amount paid or payable by the indemnifying party as a result of
the Claims in such proportion as is appropriate to reflect the relative fault of the indemnifying party, on the one hand, and the Indemnified Person or Indemnified Party, as the case may be, on the other hand, with respect to the Violation giving
rise to the applicable Claim; provided, however, that (i) no contribution shall be made under circumstances where the maker would not have been liable for indemnification under the fault standards set forth in Section 6, (ii) no
person guilty of fraudulent misrepresentation (within the meaning of Section 11(f) of the Securities Act) shall be entitled to contribution from any seller of Registrable Securities who was not guilty of such fraudulent misrepresentation, and
(iii) contribution (together with any indemnification or other obligations under this Agreement) by any seller of Registrable Securities shall be limited in amount to the amount of gross proceeds received by such seller from the sale of such
Registrable Securities. The relative fault of the Company and the Purchasers shall be determined by reference to, among other things, whether the untrue or alleged untrue statement of material fact related to information supplied by the Company or
the Purchasers and the parties’ relative intent, knowledge, access to information and opportunity to correct or prevent such statement or omission. 

  
 - 9 -

 8. REPORTS UNDER THE EXCHANGE ACT. With a view to making available to the Purchasers the benefits of Rule
144 promulgated under the Securities Act or any other similar rule or regulation of the SEC that may at any time permit each Purchaser to sell securities of the Company to the public, so long as the Registration Statement is effective and such
Purchaser holds Registrable Securities, without registration (“RULE 144”), the Company agrees to: 
 i. file with the
SEC in a timely manner and make and keep available all reports and other documents required of the Company under the Securities Act and the Exchange Act so long as the Company remains subject to such requirements and the filing and availability of
such reports and other documents is required for the applicable provisions of Rule 144; and 
 ii. furnish to each Purchaser so
long as such Purchaser owns Registrable Securities, promptly upon request, (i) a written statement by the Company that it has complied with the reporting requirements of Rule 144, the Securities Act and the Exchange Act, (ii) a copy of the
most recent annual or quarterly report of the Company and such other reports and documents so filed by the Company, and (iii) such other information as may be reasonably requested to permit the Purchasers to sell such securities under Rule 144
without registration. 
 9. SUSPENSION OF USE OF PROSPECTUS. Subject to Section 2(B), the Company may, by written notice to the Purchasers,
(i) delay the filing of, or effectiveness of, a Registration Statement; or (ii) suspend such Registration Statement after effectiveness and require that the Purchasers immediately cease sales of Registrable Securities pursuant to such
Registration Statement, if (a) the Company reasonably believes that there is or may be in existence material nonpublic information or events involving the Company, the failure of which to be disclosed in the prospectus included in the
registration statement would result in a Violation, and (b) the Company shall furnish to the Purchasers a certificate signed by the Chairman of the Board of Directors of the Company stating that in the good faith judgment of the Board of
Directors of the Company, it would have a material adverse effect on the Company (which for this purpose shall include a material adverse effect on a pending transaction) to disclose such material nonpublic information or events in the prospectus
included in the registration statement (a “SUSPENSION”). The Company shall not disclose such information or events to any Purchaser. If the Company requires the Purchasers to cease sales of Registrable Securities pursuant to a Suspension,
the Company shall, as promptly as practicable following the termination of the circumstance which entitled the Company to do so, take such actions as may be necessary to reinstate the effectiveness of the Registration Statements covering such
Registrable Securities, and/or give written notice to the Purchasers authorizing them to resume sales pursuant to the Registration Statements. If, as a result thereof, the prospectuses included in the Registration Statements have been amended to
comply with the requirements of the Securities Act, the Company shall enclose such revised prospectuses with the notice to the Purchasers given pursuant hereto, and the Purchasers shall make no offers or sales of Registrable Securities pursuant to
the Registration Statements other than by means of such revised prospectus. The Company shall not cause a Suspension on more than two occasions during any twelve (12) month period or for more than thirty (30) days per such occasion.

 10. ASSIGNMENT OF REGISTRATION RIGHTS. The rights of the Purchasers hereunder, including the right to have the Company register Registrable
Securities pursuant to this Agreement, shall be automatically assignable by each Purchaser to any affiliate of the Purchaser to which all or any portion of the Registrable Securities are transferred if: (i) the Purchaser agrees in writing with
the transferee or assignee to assign such rights, and a copy of such agreement is furnished to the Company after such assignment, (ii) the Company is furnished with written notice of (a) the name and address of such transferee or assignee,
and (b) the securities with respect to which such registration rights are being transferred or assigned, (iii) the transferee or assignee agrees in writing for the benefit of the Company to be bound by all of the provisions contained
herein, and (iv) such transfer shall have been made in accordance with the applicable requirements of the Stock Purchase Agreement and the Warrants, as applicable. 

  
 - 10 -

 11. AMENDMENT OF REGISTRATION RIGHTS. Provisions of this Agreement may be amended and the observance thereof
may be waived (either generally or in a particular instance and either retroactively or prospectively), only with written consent of the Company and Purchasers who hold a majority in interest of the Registrable Securities; provided, however, that no
consideration shall be paid to a Purchaser by the Company in connection with an amendment hereto unless each Purchaser similarly affected by such amendment receives a pro-rata amount of consideration from the Company. Unless a Purchaser otherwise
agrees, each amendment hereto must similarly affect each Purchaser. Any amendment or waiver effected in accordance with this Section 11 shall be binding upon each Purchaser and the Company. 

12. MISCELLANEOUS. 
 A. A person
or entity is deemed to be a holder of Registrable Securities whenever such person or entity owns of record such Registrable Securities. If the Company receives conflicting instructions, notices or elections from two or more persons or entities with
respect to the same Registrable Securities, the Company shall act upon the basis of instructions, notice or election received from the registered owner of such Registrable Securities. 

B. All notices required or permitted hereunder shall be in writing and shall be deemed effectively given: (i) upon delivery to the
party to be notified, (ii) when received by email or confirmed facsimile, or (iii) one (1) business day after deposit with a nationally recognized overnight carrier, specifying next business day delivery, with written verification of
receipt. All communications shall be sent to the Company and the Purchasers as follows or at such other addresses as the Company or the Purchasers may designate upon ten (10) days’ advance written notice to the other party: 

If to the Company: 
 Idera Pharmaceuticals, Inc. 
 167 Sidney Street 

Cambridge, MA 02139 
 Attn: Chief Executive Officer 
 Fax: (617)-679-5592 

Email: sagrawal@iderapharma.com 
 with a copy simultaneously transmitted by like means to: 
 Wilmer Cutler Pickering
Hale and Dorr LLP 
 60 State Street 
 Boston, Massachusetts 02109 
 Attn: Stuart Falber 

Fax: (617) 526-5000 
 Email: stuart.falber@wilmerhale.com 

  
 - 11 -

 If to a Purchaser, at its address as set forth on the Schedule of Purchasers attached to the
Stock Purchase Agreement. 
 C. Failure of any party to exercise any right or remedy under this Agreement or otherwise, or delay
by a party in exercising such right or remedy, shall not operate as a waiver thereof. 
 D. This Agreement shall be governed by
and construed in accordance with the laws of the State of Delware without regard to principles of conflicts of law. 
 E. This
Agreement, the Stock Purchase Agreement (including all schedules and exhibits thereto) and the Warrants constitute the entire agreement among the parties hereto with respect to the subject matter hereof and thereof. There are no restrictions,
promises, warranties or undertakings, other than those set forth or referred to herein and therein. This Agreement, the Stock Purchase Agreement and the Warrants supersede all prior agreements and understandings among the parties hereto with respect
to the subject matter hereof and thereof. 
 F. Subject to the requirements of Section 10 hereof, this Agreement shall inure
to the benefit of and be binding upon the successors and assigns of each of the parties hereto. 
 G. The headings in this
Agreement are for convenience of reference only and shall not limit or otherwise affect the meaning hereof. 
 H. This Agreement
may be executed in two or more counterparts, each of which shall be deemed an original but all of which shall constitute one and the same agreement. This Agreement, once executed by a party, may be delivered to the other party hereto by facsimile
transmission of a copy of this Agreement bearing the signature of the party so delivering this Agreement. 
 I. Each party shall
do and perform, or cause to be done and performed, all such further acts and things, and shall execute and deliver all such other agreements, certificates, instruments and documents, as the other party may reasonably request in order to carry out
the intent and accomplish the purposes of this Agreement and the consummation of the transactions contemplated hereby. 
 J. All
consents, approvals and other determinations to be made by the Purchasers pursuant to this Agreement shall be made by the Purchasers holding a majority in interest of the Registrable Securities (determined as if all Shares and Warrant Shares then
outstanding had been converted into or exercised for Registrable Securities) held by all Purchasers. 
 K. Each party to this
Agreement has participated in the negotiation and drafting of this Agreement. As such, the language used herein shall be deemed to be the language chosen by the parties hereto to express their mutual intent, and no rule of strict construction will
be applied against any party to this Agreement. 

  
 - 12 -

 L. For purposes of this Agreement, the term “Business Day” means any day other
than a Saturday or Sunday or a day on which banking institutions in the State of New York are authorized or obligated by law, regulation or executive order to close, and the term “Trading Day” means any day on which the Nasdaq Global
Market, or if the Common Stock is not then traded on the Nasdaq Global Market the principal securities exchange or trading market where the Common Stock is then listed or traded, is open for trading. 

[REMAINDER OF PAGE INTENTIONALLY LEFT BLANK] 

  
 - 13 -

 IN WITNESS WHEREOF, the parties have caused this Agreement to be duly executed as of the
date first above written. 
  

			
	IDERA PHARMACEUTICALS, INC.
		
	By:	 	/s/ Sudhir Agrawal
	Name:	 	Sudhir Agrawal
	Its:	 	Chairman, Chief Executive Officer and President

 [SIGNATURE PAGE TO REGISTRATION RIGHTS AGREEMENT] 

  
 - 14 -

 PURCHASERS: 

 

					
	PILLAR PHARMACEUTICALS II, L.P.
		
	By:	 	/s/ Youssef El Zein
		 	 Name:
	 	Youssef El Zein
		 	 Title:
	 	General Partner

  

							
	PARTICIPATIONS BESANCON
			
		 	By:	 	Pillar Invest Corporation, as attorney-in-fact
				
		 		 	By: 	 	/s/ Youssef El Zein
		 		 	Name:	 	Youssef El Zein
		 		 	Title:	 	as per power of attorney of November 9th, 2012

 [SIGNATURE PAGE TO REGISTRATION RIGHTS AGREEMENT] 

  
 - 15 -

 EXHIBIT A 
 Purchasers 
 Pillar Pharmaceuticals II, L.P. 

Participations Besancon 

  
 - 16 -

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