Document:

exv10w2

Exhibit 10.2

IDERA PHARMACEUTICALS, INC.

REGISTRATION RIGHTS AGREEMENT

     REGISTRATION RIGHTS AGREEMENT (this “AGREEMENT”), dated as of November 4, 2011, 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 D 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.

     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. 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 2, 2012. The Registration Statement filed hereunder, to the
extent allowable under the Securities Act, shall state that such Registration Statement also covers
such indeterminate number of additional shares of Common Stock as may become issuable upon
conversion of the Preferred Stock or exercise of the Warrants to prevent dilution resulting from
stock splits, stock dividends or similar transactions.

     B. PAYMENTS BY THE COMPANY. If the Registration Statement is not declared effective by the
SEC on or before March 4, 2012 (the “REGISTRATION DEADLINE”) or, (ii) if, after the Registration
Statement has been declared effective by the SEC, sales of any of the Registrable Securities 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
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). The Company shall pay to

- 2 -

 

each Purchaser an amount equal to the product of (i) the aggregate purchase price of the Shares
then held by such Purchaser (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
Registration Statement filed pursuant to Section 2(A) is declared effective by the SEC, and (B)
during which sales of any Registrable Securities 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. 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 Purchase 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).

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 the Registration Statement and the prospectus used in connection
with the Registration Statement as may be necessary to keep the Registration Statement effective
pursuant to Rule 415 at all times until no Registrable Securities remain outstanding (the
“REGISTRATION PERIOD”), and, during such period, comply with the provisions of the Securities Act
in order to 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 the 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 the Registration Statement 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

- 3 -

 

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 such Registration Statement has been filed and of
any request by the Commission 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 and, if requested, such Purchasers shall
immediately cease making offers of Registrable Securities and return all prospectuses 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 Registration Statement.

     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 Statement 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, the Company shall prepare and file with the SEC such amendments (including
post effective amendments) and supplements to a 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:

- 4 -

 

     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 Registration Statement, 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 the 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. 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

- 5 -

 

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.

     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

- 6 -

 

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.

     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 -

 

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.

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, the Registration Statement; or (ii)
suspend the Registration Statement after effectiveness and require that the Purchasers immediately
cease sales of Registrable Securities pursuant to the 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 (as defined
below) 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

- 8 -

 

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 Statement and/or give written notice to the Purchasers authorizing them to
resume sales pursuant to the Registration Statement. If, as a result thereof, the prospectus
included in the Registration Statement has been amended to comply with the requirements of the
Securities Act, the Company shall enclose such revised prospectus 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 Statement 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.

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.

- 9 -

 

     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

     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
Commonwealth of Massachusetts 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.

- 10 -

 

     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.

     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]

- 11 -

 

     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: Chief Executive Officer and
President 	 
	 

- 12 -

 

PURCHASER:

	 	 	 	 	 
	 	PILLAR PHARMACEUTICALS I, L.P.

 	 
	 	By:  	/s/ Youssef El Zein
 	 
	 	 	Name:  	Youssef El Zein 	 
	 	 	Title:  	Director 	 
	 

- 13 -

 

EXHIBIT A

Purchasers

Pillar Pharmaceuticals I, L.P.

- 14 -exv10w3

Exhibit 10.3

THIS WARRANT AND THE SHARES OF COMMON STOCK ISSUED UPON ITS

EXERCISE ARE SUBJECT TO THE RESTRICTIONS ON

TRANSFER SET FORTH IN SECTION 5 OF THIS WARRANT 

			
	 	 	 
	Warrant No. ___
	 	Number of Shares:______________

(subject to adjustment)

Original Issue Date: November __ 2011

Common Stock Purchase Warrant

(Void after November __, 2016)

     Idera Pharmaceuticals, Inc., a Delaware corporation (the “Company”), for value received,
hereby certifies that ______________________, or its registered assigns (the “Registered Holder”),
is entitled, subject to the terms and conditions set forth below, to purchase from the Company, at
any time or from time to time on or after the date of issuance and on or before 5:00 p.m. (Boston
time) on November __, 2016, _________ shares of Common Stock, $0.001 par value per share, of the
Company (“Common Stock”), at a purchase price of $_______ per share. The shares purchasable upon
exercise of this Warrant, and the purchase price per share, each as adjusted from time to time
pursuant to the provisions of this Warrant, are hereinafter referred to as the “Warrant Shares” and
the “Purchase Price,” respectively.

     1. Exercise.

          (a) Exercise for Cash. The Registered Holder may, at its option, elect to exercise
this Warrant, in whole or in part and at any time or from time to time, by surrendering this
Warrant, with the purchase form appended hereto as Exhibit I duly executed by or on behalf
of the Registered Holder, at the principal office of the Company, or at such other office or agency
as the Company may designate, accompanied by payment in full, in lawful money of the United States,
of the Purchase Price payable in respect of the number of Warrant Shares purchased upon such
exercise.

          (b) Cashless Exercise.

               (i) During such periods as there is not an effective registration statement under the
Securities Act of 1933, as amended (the “Securities Act”), registering, and no current prospectus
available for, the resale by the Registered Holder of any Warrant Shares (except to the extent due
to any actions or inactions of the Registered Holders under the Registration Rights Agreement dated
as of November 4, 2011 by and among the Company and the Purchasers (as defined therein)), the
Registered Holder may, at its option, elect to exercise this Warrant, in whole or in part, on a
cashless basis, by surrendering this Warrant, with the purchase form appended hereto as Exhibit
I duly executed by or on behalf of the Registered
Holder, at the principal office of the Company, or at such other office or agency as the
Company may designate, by canceling a portion of this Warrant in payment of the Purchase Price
payable in respect of the number of Warrant Shares purchased upon such exercise. In the event of
an

 

 

exercise pursuant to this subsection 1(b), the number of Warrant Shares issued to the Registered
Holder shall be determined according to the following formula:

	 	 	 	 	 

	X

	= 	 Y(A-B)
 

A

	 	 

	 	 	 

	Where: X =

	 	the number of Warrant Shares that shall be issued to the
Registered Holder;
	 
	 	 
	Y =

	 	the number of Warrant Shares for which this Warrant is being exercised
(which shall include both the number of Warrant Shares issued to the Registered Holder
and the number of Warrant Shares subject to the portion of the Warrant being cancelled
in payment of the Purchase Price);
	 
	 	 
	A =

	 	the Fair Market Value (as defined below) of one share of Common Stock; and
	 
	 	 
	B =

	 	the Purchase Price then in effect.

               (ii) The Fair Market Value per share of Common Stock shall be determined as follows:

                    (A) If the Common Stock is listed on a national securities exchange, or another nationally
recognized trading system as of the Exercise Date, the Fair Market Value per share of Common Stock
shall be deemed to be the average of the high and low reported sale prices per share of Common
Stock thereon on the trading day immediately preceding the Exercise Date (provided that if
no such price is reported on such day, the Fair Market Value per share of Common Stock shall be
determined pursuant to clause (B)).

                    (B) If the Common Stock is not listed on a national securities exchange or another nationally
recognized trading system as of the Exercise Date, the Fair Market Value per share of Common Stock
shall be deemed to be the amount most recently determined by the Board of Directors of the Company
(the “Board”) to represent the fair market value per share of the Common Stock (including without
limitation a determination for purposes of granting Common Stock options or issuing Common Stock
under any plan, agreement or arrangement with employees of the Company); and, upon request of the
Registered Holder, the Board (or a representative thereof) shall, as promptly as reasonably
practicable but in any event not later than 10 days after such request, notify the Registered
Holder of the Fair Market Value per share of Common Stock and furnish the Registered Holder with
reasonable documentation of the Board’s determination of such Fair Market Value. Notwithstanding
the foregoing, if the Board has not made such a determination within the three-month period prior
to the Exercise Date, then (A) the Board shall make, and shall provide or cause to be provided to
the Registered Holder notice of, a determination of the Fair Market Value per share of the Common
Stock
within 15 days of a request by the Registered Holder that it do so, and (B) the exercise of
this Warrant pursuant to this subsection 1(b) shall be delayed until such determination is made and
notice thereof is provided to the Registered Holder.

- 2 -

 

          (c) Exercise Date. Each exercise of this Warrant shall be deemed to have been
effected immediately prior to the close of business on the day on which this Warrant shall have
been surrendered to the Company as provided in subsection 1(a) or 1(b) above (the “Exercise Date”).
At such time, the person or persons in whose name or names any certificates for Warrant Shares
shall be issuable upon such exercise as provided in subsection 1(d) below shall be deemed to have
become the holder or holders of record of the Warrant Shares represented by such certificates.

          (d) Issuance of Certificates. The Company, at its expense, shall use its best
efforts, as soon as practicable after the exercise of this Warrant in whole or in part, and in any
event within three (3) business days thereafter, to cause to be issued in the name of, and
delivered to, the Registered Holder, or as the Registered Holder (upon payment by the Registered
Holder of any applicable transfer taxes) may direct:

               (i) a certificate or certificates for the number of full Warrant Shares to which the
Registered Holder shall be entitled upon such exercise plus, in lieu of any fractional share to
which the Registered Holder would otherwise be entitled, cash in an amount determined pursuant to
Section 3 hereof; and

               (ii) in case such exercise is in part only, a new warrant or warrants (dated the date hereof)
of like tenor, calling in the aggregate on the face or faces thereof for the number of Warrant
Shares equal (without giving effect to any adjustment therein) to the number of such shares called
for on the face of this Warrant minus the number of Warrant Shares for which this Warrant was so
exercised (which, in the case of an exercise pursuant to subsection 1(b), shall include both the
number of Warrant Shares issued to the Registered Holder pursuant to such partial exercise and the
number of Warrant Shares subject to the portion of the Warrant being cancelled in payment of the
Purchase Price).

          (e) Exercise Limitation. Notwithstanding anything to the contrary contained herein,
the Company shall not effect any exercise of this Warrant and the Registered Holder shall not be
entitled to exercise this Warrant for a number of Warrant Shares in excess of that number of
Warrant Shares which, upon giving effect to such exercise, would cause (i) the aggregate number of
shares of Common Stock beneficially owned by a holder of Series D Preferred Stock and its
affiliates and any other persons whose beneficial ownership of Common Stock would be aggregated
with the holder’s for purposes of Section 13(d) of the Securities Exchange Act of 1934, as amended
(the “Exchange Act”), to exceed 19.99% of the total number of issued and outstanding shares of
Common Stock of the Company following such exercise, or (b) the combined voting power of the
securities of the Company beneficially owned by a holder of Series D Preferred Stock and its
affiliates and any other persons whose beneficial ownership of Common Stock would be aggregated
with the holder’s for purposes of Section 13(d) of the Exchange Act to exceed 19.99% of the
combined voting power of all of the securities of the Company then outstanding following such
exercise, unless, in either case, the Company obtains the requisite stockholder approval under
NASDAQ Marketplace Rule 5635(b), in which case, the
Issuance Limitation under this Section 1(e) shall no longer apply to the Registered Holder.
For purposes of this Section 1(e), the aggregate number of shares of Common Stock or voting
securities beneficially owned by the Registered Holder and its affiliates and any other persons
whose beneficial ownership of Common Stock would be aggregated with the Registered

- 3 -

 

Holder’s for
purposes of Section 13(d) of the Exchange Act shall include the shares of Common Stock issuable
upon the exercise of this Warrant with respect to which such determination is being made, but shall
exclude the number of shares of Common Stock which would be issuable upon (i) exercise of the
remaining unexercised and non-cancelled portion of this Warrant by the Registered Holder and (ii)
exercise or conversion of the unexercised, non-converted or non-cancelled portion of any other
securities of the Company that do not have voting power (including without limitation any
securities of the Company which would entitle the holder thereof to acquire at any time Common
Stock, including without limitation any debt, preferred stock, right, option, warrant or other
instrument that is at any time convertible into or exercisable or exchangeable for, or otherwise
entitles the holder thereof to receive, Common Stock), subject to a limitation on conversion or
exercise analogous to the limitation contained herein beneficially owned by the Registered Holder
or any of its affiliates and other persons whose beneficial ownership of Common Stock would be
aggregated with the Registered Holder’s for purposes of Section 13(d) of the Exchange Act.

     2. Adjustments.

          (a) Adjustments to Purchase Price for Diluting Issues. In the event that the Series D
Conversion Price (as defined in the Certificate of Designations, Preferences and Rights of the
Series D Convertible Preferred Stock of the Company (the “Certificate of Designations”)) shall be
adjusted pursuant to Section 4.4.4 of the Certificate of Designations, the Purchase Price hereunder
shall, automatically and concurrently with the adjustment to the Series D Conversion Price, be
adjusted in the same manner and same proportion as the Series D Conversion Price is so adjusted.

          (b) Adjustment for Stock Splits and Combinations. If the Company shall at any time or
from time to time after the Original Issue Date effect a subdivision of the outstanding Common
Stock, the Purchase Price then in effect immediately before that subdivision shall be
proportionately decreased. If the Company shall at any time or from time to time after the
Original Issue Date combine the outstanding shares of Common Stock, the Purchase Price then in
effect immediately before the combination shall be proportionately increased. Any adjustment under
this paragraph shall become effective at the close of business on the date the subdivision or
combination becomes effective.

          (c) Adjustment for Certain Dividends and Distributions. In the event the Company at
any time, or from time to time after the Original Issue Date shall make or issue, or fix a record
date for the determination of holders of Common Stock entitled to receive, a dividend or other
distribution payable in additional shares of Common Stock, then and in each such event the Purchase
Price then in effect immediately before such event shall be decreased as of the time of such
issuance or, in the event such a record date shall have been fixed, as of the close of business on
such record date, by multiplying the Purchase Price then in effect by a fraction:

                    (A) the numerator of which shall be the total number of shares of Common Stock issued and
outstanding immediately prior to the time of such issuance or the close of business on such record
date, and

- 4 -

 

                    (B) the denominator of which shall be the total number of shares of Common Stock issued and
outstanding immediately prior to the time of such issuance or the close of business on such record
date plus the number of shares of Common Stock issuable in payment of such dividend or
distribution;

provided, however, that if such record date shall have been fixed and such dividend
is not fully paid or if such distribution is not fully made on the date fixed therefor, the
Purchase Price shall be recomputed accordingly as of the close of business on such record date and
thereafter the Purchase Price shall be adjusted pursuant to this paragraph as of the time of actual
payment of such dividends or distributions.

          (d) Adjustment in Number of Warrant Shares. When any adjustment is required to be
made in the Purchase Price pursuant to subsections 2(b) or 2(c), the number of Warrant Shares
purchasable upon the exercise of this Warrant shall be changed to the number determined by dividing
(i) an amount equal to the number of shares issuable upon the exercise of this Warrant immediately
prior to such adjustment, multiplied by the Purchase Price in effect immediately prior to such
adjustment, by (ii) the Purchase Price in effect immediately after such adjustment.

          (e) Adjustments for Other Dividends and Distributions. In the event the Company at
any time or from time to time after the Original Issue Date shall make or issue, or fix a record
date for the determination of holders of Common Stock entitled to receive, a dividend or other
distribution payable in securities of the Company (other than shares of Common Stock) or in cash or
other property (other than regular cash dividends paid out of earnings or earned surplus,
determined in accordance with generally accepted accounting principles), then and in each such
event provision shall be made so that the Registered Holder shall receive upon exercise hereof, in
addition to the number of shares of Common Stock issuable hereunder, the kind and amount of
securities of the Company, cash or other property which the Registered Holder would have been
entitled to receive had this Warrant been exercised on the date of such event and had the
Registered Holder thereafter, during the period from the date of such event to and including the
Exercise Date, retained any such securities receivable during such period, giving application to
all adjustments called for during such period under this Section 2 with respect to the rights of
the Registered Holder.

          (f) Adjustment for Reorganization. If there shall occur any reorganization,
recapitalization, reclassification, consolidation or merger involving the Company in which the
Common Stock is converted into or exchanged for securities, cash or other property (other than a
transaction covered by subsections 2(b), 2(c) or 2(e)) (collectively, a “Reorganization”), then,
following such Reorganization, the Registered Holder shall receive upon exercise hereof the kind
and amount of securities, cash or other property which the Registered Holder would have been
entitled to receive pursuant to such Reorganization if such exercise had taken place immediately
prior to such Reorganization. In any such case, appropriate adjustment (as determined in good
faith by the Board) shall be made in the application of the provisions set forth herein with
respect
to the rights and interests thereafter of the Registered Holder, to the end that the
provisions set forth in this Section 2 (including provisions with respect to changes in and other
adjustments of the Purchase Price) shall thereafter be applicable, as nearly as reasonably may be,
in relation to any securities, cash or other property thereafter deliverable upon the exercise of
this Warrant.

- 5 -

 

          (g) Certificate as to Adjustments. Upon the occurrence of each adjustment or
readjustment of the Purchase Price pursuant to this Section 2, the Company at its expense shall, as
promptly as reasonably practicable but in any event not later than 10 days thereafter, compute such
adjustment or readjustment in accordance with the terms hereof and furnish to the Registered Holder
a certificate setting forth such adjustment or readjustment (including the kind and amount of
securities, cash or other property for which this Warrant shall be exercisable and the Purchase
Price) and showing in detail the facts upon which such adjustment or readjustment is based. The
Company shall, as promptly as reasonably practicable after the written request at any time of the
Registered Holder (but in any event not later than 10 days thereafter), furnish or cause to be
furnished to the Registered Holder a certificate setting forth (i) the Purchase Price then in
effect and (ii) the number of shares of Common Stock and the amount, if any, of other securities,
cash or property which then would be received upon the exercise of this Warrant.

     3. Fractional Shares. The Company shall not be required upon the exercise of this
Warrant to issue any fractional shares, but shall pay the value thereof to the Registered Holder in
cash on the basis of the Fair Market Value per share of Common Stock, as determined pursuant to
subsection 1(b)(ii) above.

     4. Redemption of Warrants.

          (a) At any time after November 4, 2013, subject to the terms of this Section 4, the Company
shall have the right to redeem all or a portion of this Warrant for a redemption price (the
“Redemption Price”) equal to the result obtained by multiplying (i) $0.01 by (ii) the number of
Warrant Shares that the Registered Holder is entitled to purchase upon exercise of all or the
portion of this Warrant that is being redeemed (such Redemption Price being subject to adjustment
for stock splits, stock dividends, combinations, recapitalizations, reclassifications, and similar
transactions affecting the Common Stock).

          (b) The Company shall exercise this redemption right by providing at least 30 days’ prior
written notice to the Registered Holder of such redemption (the “Redemption Notice”). Such
Redemption Notice shall be provided to the Registered Holder in accordance with Section 19 of this
Warrant. The Redemption Notice shall specify the time, manner and place of redemption, including
without limitation the date on which this Warrant shall be redeemed (the “Redemption Date”) and the
Redemption Price payable to the Registered Holder (assuming that this Warrant is not exercised on
or prior to the Redemption Date).

          (c) Notwithstanding the foregoing, the Company may not redeem this Warrant or provide the
Redemption Notice to the Registered Holder (i) unless the closing sales price of the Common Stock
for twenty (20) or more trading days in a period of thirty (30) consecutive trading days ending
within thirty (30) days prior to the date the Company provides the Redemption Notice to the
Registered Holder is greater than or equal to $6.51 (subject to adjustment for stock splits, stock
dividends, combinations, recapitalizations, reclassifications,
and similar transactions affecting the Common Stock) and (ii) with respect to any portion of
this Warrant which may not be exercised by the Registered Holder as of the time of the Redemption
Notice under Section 1(e).

- 6 -

 

          (d) This Warrant shall cease to be exercisable and shall be terminated and of no further force
or effect effective at 5:00 p.m. (Boston Time) on the Redemption Date. If the Registered Holder
does not exercise this Warrant on or prior to the Redemption Date, the Registered Holder shall
surrender this Warrant to the Company on the Redemption Date for cancellation. From and after the
Redemption Date, the Registered Holder’s sole right hereunder shall be to receive the Redemption
Price, without interest, upon presentation and surrender of this Warrant for cancellation.

     5. Transfers, etc.

          (a) This Warrant and the Warrant Shares shall not be sold or transferred unless either (i)
they first shall have been registered under the Securities Act, or (ii) the Company first shall
have been furnished with an opinion of legal counsel, reasonably satisfactory to the Company, to
the effect that such sale or transfer is exempt from the registration requirements of the
Securities Act. Notwithstanding the foregoing, no registration or opinion of counsel shall be
required for (i) a transfer by a Registered Holder which is an entity to a wholly owned subsidiary
of such entity, a transfer by a Registered Holder which is a partnership to a partner of such
partnership or a retired partner of such partnership or to the estate of any such partner or
retired partner, or a transfer by a Registered Holder which is a limited liability company to a
member of such limited liability company or a retired member or to the estate of any such member or
retired member, provided that the transferee in each case agrees in writing to be subject
to the terms of this Section 5, or (ii) a transfer made in accordance with Rule 144 under the
Securities Act.

          (b) Each certificate representing Warrant Shares shall bear a legend substantially in the
following form:

“The securities represented by this certificate have not
been registered under the Securities Act of 1933, as
amended, and may not be offered, sold or otherwise
transferred, pledged or hypothecated unless and until such
securities are registered under such Act or an opinion of
counsel satisfactory to the Company is obtained to the
effect that such registration is not required.”

     The foregoing legend shall be removed from the certificates representing any Warrant Shares,
at the request of the holder thereof, at such time as (i) a period of at least one year, as
determined in accordance with paragraph (d) of Rule 144 under the Act, has elapsed since the later
of the date the Warrant Shares were acquired from the Company or an affiliate of the Company, and
(ii) the Warrant Shares become eligible for resale pursuant to Rule 144(b)(1)(i) under the
Securities Act.

          (c) The Company will maintain a register containing the name and address of the Registered
Holder of this Warrant. The Registered Holder may change its address as shown on the warrant
register by written notice to the Company requesting such change.

          (d) Subject to the provisions of Section 5 hereof, this Warrant and all rights hereunder are
transferable, in whole or in part, upon surrender of this Warrant with a properly

- 7 -

 

executed
assignment (in the form of Exhibit II hereto) at the principal office of the Company (or,
if another office or agency has been designated by the Company for such purpose, then at such other
office or agency).

     6. Notices of Record Date, etc. In the event:

          (a) the Company shall take a record of the holders of its Common Stock (or other stock or
securities at the time deliverable upon the exercise of this Warrant) for the purpose of entitling
or enabling them to receive any dividend or other distribution, or to receive any right to
subscribe for or purchase any shares of stock of any class or any other securities, or to receive
any other right; or

          (b) of any capital reorganization of the Company, any reclassification of the Common Stock of
the Company, any consolidation or merger of the Company with or into another corporation (other
than a consolidation or merger in which the Company is the surviving entity and its Common Stock is
not converted into or exchanged for any other securities or property), or any transfer of all or
substantially all of the assets of the Company; or

          (c) of the voluntary or involuntary dissolution, liquidation or winding-up of the Company,

then, and in each such case, the Company will send or cause to be sent to the Registered Holder a
notice specifying, as the case may be, (i) the record date for such dividend, distribution or
right, and the amount and character of such dividend, distribution or right, or (ii) the effective
date on which such reorganization, reclassification, consolidation, merger, transfer, dissolution,
liquidation or winding-up is to take place, and the time, if any is to be fixed, as of which the
holders of record of Common Stock (or such other stock or securities at the time deliverable upon
the exercise of this Warrant) shall be entitled to exchange their shares of Common Stock (or such
other stock or securities) for securities or other property deliverable upon such reorganization,
reclassification, consolidation, merger, transfer, dissolution, liquidation or winding-up. Such
notice shall be sent at least 10 days prior to the record date or effective date for the event
specified in such notice.

     7. Reservation of Stock. The Company will at all times reserve and keep available,
solely for issuance and delivery upon the exercise of this Warrant, such number of Warrant Shares
and other securities, cash and/or property, as from time to time shall be issuable upon the
exercise of this Warrant.

     8. Exchange or Replacement of Warrants.

          (a) Upon the surrender by the Registered Holder, properly endorsed, to the Company at the
principal office of the Company, the Company will, subject to the provisions of Section 5 hereof,
issue and deliver to or upon the order of the Registered Holder, at the Company’s expense, a new
Warrant or Warrants of like tenor, in the name of the Registered Holder or as the Registered Holder
(upon payment by the Registered Holder of any applicable transfer taxes) may direct, calling in the
aggregate on the face or faces thereof for the number of

- 8 -

 

shares of Common Stock (or other
securities, cash and/or property) then issuable upon exercise of this Warrant.

          (b) Upon receipt of evidence reasonably satisfactory to the Company of the loss, theft,
destruction or mutilation of this Warrant and (in the case of loss, theft or destruction) upon
delivery of an indemnity agreement (with surety if reasonably required) in an amount reasonably
satisfactory to the Company, or (in the case of mutilation) upon surrender and cancellation of this
Warrant, the Company will issue, in lieu thereof, a new Warrant of like tenor.

     9. Notices. All notices and other communications from the Company to the Registered
Holder in connection herewith shall be mailed by certified or registered mail, postage prepaid,
sent by email or confirmed facsimile or sent via a reputable nationwide overnight courier service
guaranteeing next business day delivery, to the address last furnished to the Company in writing by
the Registered Holder. All notices and other communications from the Registered Holder to the
Company in connection herewith shall be mailed by certified or registered mail, postage prepaid,
sent by email or confirmed facsimile or sent via a reputable nationwide overnight courier service
guaranteeing next business day delivery, to the Company at its principal office set forth below.
If the Company should at any time change the location of its principal office to a place other than
as set forth below, it shall give prompt written notice to the Registered Holder and thereafter all
references in this Warrant to the location of its principal office at the particular time shall be
as so specified in such notice. All such notices and communications shall be deemed delivered (i)
two business days after being sent by certified or registered mail, return receipt requested,
postage prepaid, (ii) upon receipt of email or confirmed facsimile or (iii) one business day after
being sent via a reputable nationwide overnight courier service guaranteeing next business day
delivery.

     Notices and other communications from the Registered Holder to the Company shall be sent 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

- 9 -

 

     10. No Rights as Stockholder. Until the exercise of this Warrant, the Registered
Holder shall not have or exercise any rights by virtue hereof as a stockholder of the Company.
Notwithstanding the foregoing, in the event (i) the Company effects a split of the Common Stock by
means of a stock dividend and the Purchase Price of and the number of Warrant Shares are adjusted
as of the date of the distribution of the dividend (rather than as of the record date for such
dividend), and (ii) the Registered Holder exercises this Warrant between the record date and the
distribution date for such stock dividend, the Registered Holder shall be entitled to receive, on
the distribution date, the stock dividend with respect to the shares of Common Stock acquired upon
such exercise, notwithstanding the fact that such shares were not outstanding as of the close of
business on the record date for such stock dividend.

     11. Amendment or Waiver. Any term of this Warrant may be amended or waived only by an
instrument in writing signed by the party against which enforcement of the change or waiver is
sought. No waivers of any term, condition or provision of this Warrant, in any one or more
instances, shall be deemed to be, or construed as, a further or continuing waiver of any such term,
condition or provision.

     12. Section Headings. The section headings in this Warrant are for the convenience of
the parties and in no way alter, modify, amend, limit or restrict the contractual obligations of
the parties.

     13. Governing Law. This Warrant will be governed by and construed in accordance with
the internal laws of the Commonwealth of Massachusetts (without reference to the conflicts of law
provisions thereof).

     14. Facsimile Signatures. This Warrant may be executed by facsimile signature.

EXECUTED as of the Date of Issuance indicated above.

	 	 	 	 	 
	 	Idera Pharmaceuticals, Inc.

 	 
	 	By: 	 	 
	 	 	Title: 	 
	 	 	 	 

- 10 -

 

EXHIBIT I

PURCHASE FORM

			
	To:                    
	 	Dated:                    

     The undersigned, pursuant to the provisions set forth in the attached Warrant (No. ___),
hereby elects to purchase (check applicable box):

     Ğ ____ shares of the Common Stock of Idera Pharmaceuticals, Inc. covered by such Warrant; or

     Ğ the maximum number of shares of Common Stock covered by such Warrant pursuant to the
cashless exercise procedure set forth in subsection 1(b).

     The undersigned herewith makes payment of the full purchase price for such shares at the price
per share provided for in such Warrant. Such payment takes the form of (check applicable box or
boxes):

	 	Ğ 	 	 $______ in lawful money of the United States; and/or
	 
	 	Ğ 	 	 the cancellation of such portion of the attached Warrant as is exercisable for
a total of _____ Warrant Shares (using a Fair Market Value of $_____ per share for
purposes of this calculation) ; and/or
	 
	 	Ğ 	 	 the cancellation of such number of Warrant Shares as is necessary, in
accordance with the formula set forth in subsection 1(b), to exercise this Warrant with
respect to the maximum number of Warrant Shares purchasable pursuant to the cashless
exercise procedure set forth in subsection 1(b).

	 	 	 	 	 
	 	Signature:  	 	 
	 
	 	Address:	 	 
	 
	 		 	 

- 11 -

 

EXHIBIT II

ASSIGNMENT FORM

     FOR VALUE RECEIVED, ____________________ hereby sells, assigns and transfers all of the rights
of the undersigned under the attached Warrant (No. ____) with respect to the number of shares of
Common Stock of Idera Pharmaceuticals, Inc. covered thereby set forth below, unto:

	 	 	 	 	 
	Name of Assignee	 	Address	 	No. of Shares
	 

	 	 
	 	 

			
	 	 	 
	Dated:                                                            
	 	Signature:                                                            
	 	 	 
	Signature Guaranteed:	 	 
	 	 	 
	By:                                                                            
     	 	 

The signature should be guaranteed by an eligible guarantor institution (banks, stockbrokers,
savings and loan associations and credit unions with membership in an approved signature guarantee
medallion program) pursuant to Rule 17Ad-15 under the Securities Exchange Act of 1934.

- 12 -

Source: [{"source": "alea-institute/alea-institute/kl3m-data-edgar-agreements/train-00196-of-00352.parquet"}, [{"source": "alea-institute/alea-institute/kl3m-data-edgar-agreements/train-00196-of-00352.parquet"}]]