Document:

exv10w38

Exhibit
10.38

AMENDMENT TO THE CONSULTING SERVICES AGREEMENT

This Amendment, effective the 16th day of December, 2008, (“Amendment Date”) is by and
between Idera Pharmaceuticals, Inc., a Delaware corporation, having an place of business
at 167 Sidney Street, Cambridge, Massachusetts 02139 (hereinafter referred to as “Idera”) and
Karr Pharma Consulting, LLC, having a place of business at 707 Dominion Drive, St. Louis,
Missouri 63131 (hereinafter referred to as the “Consultant”). Idera and Consultant may be referred
to herein individually as a “Party” and collectively as the “Parties.”

Background

The Parties entered into a Consulting Services Agreement (“Agreement”), dated January 1, 2008
(“Effective Date”), which set forth certain terms and conditions for the Consultant to perform
services for Idera.

The Parties now desire to amend the Agreement to extend the term through December 31, 2009.

Now, Therefore, the Parties hereby agree as follows:

Section 2 of the Agreement shall be amended and restated in its entirety as follows:

TERM. This Agreement shall commence on the Effective Date and shall continue until December 31,
2009 (such period, as it may be extended, being referred to as the “Consultation Period”), unless
sooner terminated in accordance with the provisions of Section 4.

All other terms and conditions of the Agreement shall remain in full force and effect.

IN WITNESS WHEREOF, the Parties have executed this Amendment as of the Amendment Date.

	 	 	 	 	 	 	 	 	 	 	 
	Idera Pharmaceuticals, Inc.	 	 	 	Karr Pharma Consulting, LLC	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	By:

	 	/s/ Louis J. Arcudi, III	 	 	 	By:
	 	/s/ Robert W. Karr, M.D.	 	 
	 

	 	 
	 	 	 	 	 	 	 	 
	 

	 	Louis J. Arcudi, III
	 	 	 	 	 	Robert W. Karr, M.D.	 	 
	 

	 	Chief Financial Officer	 	 	 	 	 	 	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	Date:

	 	12/16/2008	 	 	 	Date:	 	12/16/2008exv10w55

Exhibit 10.55

Execution Version

Confidential Materials omitted and filed separately with the

Securities and Exchange Commission. Asterisks denote omissions.

Amendment To The License Agreement

This Amendment, effective the 12th day of February, 2009, (“Amendment Date”) is by and between
Idera Pharmaceuticals, Inc., having a place of business located at 167 Sidney Street, Cambridge,
Massachusetts 02139 (“Idera”) and Merck KGaA, a general partnership limited by shares organized
under German law having a place of business at Frankfurter Strasse 250, 64293 Darmstadt, Germany
(“Merck”). Idera and Merck may be referred to collectively as “Parties.”

Background

The Parties entered into a License Agreement dated 18 December 2007 (“License Agreement”), which
sets forth certain terms and conditions for the Parties to research, develop and commercialize
immune modulatory oligonucleotides in the field of cancer.

The Parties now desire to amend the License Agreement to allow Idera to continue to act as the
sponsor (as such term is defined in 21 CFR § 312.3(b), hereinafter “Sponsor”) of certain clinical
trials until such time as Merck has filed an Investigational New Drug application with the US Food
and Drug Administration and assumes the Sponsor role under the Merck IND.

Now, Therefore, the Parties hereby agree as follows:

1. Section 1.17, definition of “Development Costs” is hereby amended and restated in its entirety
as follows:

     “Development Costs” means those Out-of-Pocket Expenses incurred by Licensor after the
Effective Date that are directly and solely attributable to the achievement of work or activities
performed by or on behalf of Licensor after the Effective Date toward the completion of the
On-Going Trials or the Future Trials.

2. Section 3.4, of the License Agreement, Licensor Support in the Development, is hereby amended
and restated in its entirety as follows:

3.4(a). Licensor Support in the Development. For a period of [**] starting from Effective
Date, Licensor shall make its employees that are knowledgeable on the Compound or Follow-On
Compound, its properties and functions, reasonably available to Merck, at Licensor’s
facilities, for scientific and technical explanations, advice and support, that may
reasonably be required by Merck, relating to the Development and registration of the
Compound, Follow-On Compound and the Licensed Products (the “Development Support”). The
Development Support shall be provided by Licensor [**] during such first [**] following the
Effective Date. Thereafter, during the remaining [**] period, Merck shall reimburse
Licensor for Licensor’s reasonable Out-of-Pocket Expenses incurred in providing the
Development Support should Merck require any of such Development Support, subject however to
Licensor providing Merck with documented evidence of such Out-of-Pocket Expenses having been
incurred.

					
	 	 	 	 	 
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3.4(b). Licensor Sponsorship and Conduct of Clinical Trials. Notwithstanding Section 2.3
and 3.4(a), during the Interim Period Licensor agrees to remain the Sponsor for the On-Going
Trials and for additional Clinical Trials that the Parties agree to conduct during the
Interim Period, including the study in [**] (“Future Trials” and together with the On-Going
Trials, collectively, the “TLR9 Agonist Trials”). For purposes of this Agreement, the
“Interim Period” means that period of time commencing on the Effective Date and ending on
the date that is the earlier of (i) the date on which the FDA has approved the IND submitted
by Merck for conducting clinical trials with Licensor’s TLR9 agonists (the “Merck TLR9
Agonists IND”) and Merck has assumed the role of Sponsor for all on-going TLR9 Agonist
Trials or (b) the date that is [**] from the Effective Date. The following provisions shall
apply during the Interim Period in connection with the conduct of the TLR9 Agonist Trials:

	 	(1)	 	Such trials shall be conducted under Licensor’s IND Application
Number[**] or IND Application Number [**].
	 
	 	(2)	 	Licensor’s acts shall be in compliance with Section 3.2.
	 
	 	(3)	 	The Parties shall establish an agreement for each TLR9 Agonist
Trial that sets forth each Party’s responsibilities (the “Charter Agreements”).
	 
	 	(4)	 	The Charter Agreements shall, at a minimum, identify a process
for developing and executing the protocol for each TLR9 Agonist Trial and set
forth a trial budget to be paid by Merck, which shall include after [**] the
reimbursement by Merck of Licensor’s internal costs, up to an agreed upon limit
and at an agreed upon rate to be set forth in the budget attached to the
respective Charter Agreement and pre-approved Development Costs in conducting
such trial (each a “Trial Budget”).
	 
	 	(5)	 	Merck shall have responsibility for determining if any Future
Trial is to be conducted and for defining objectives of any Future Trial.
	 
	 	(6)	 	Merck shall seek Licensor’s input on each Future Trial.
	 
	 	(7)	 	If requested by Merck during the Interim Period, Licensor
agrees to initiate and conduct the [**] Trial during the Interim Period,
subject to the terms of a mutually agreed Charter Agreement, unless Licensor,
in its reasonable discretion, determines that it is unable to conduct such
trial, wherein such determination takes into account [**] under the relevant
Charter Agreement.
	 
	 	(8)	 	For each Future Trial [**] that Merck desires to initiate
during the Interim Period, Licensor agrees to initiate and conduct such Future
Trial during the Interim Period, subject to the terms of a mutually agreed
Charter Agreement, unless Licensor, in its sole discretion, determines that it
is unable to conduct such trial. Such inability determination shall take into
[**] under the relevant Charter Agreement.
	 
	 	(9)	 	Licensor shall have the right to take, at its sole discretion
after appropriate discussions with Merck under the Charter Agreements, any
actions it reasonably deems necessary or desirable to fulfill the regulatory
requirements appropriate to the role of Sponsor for any or all TLR9 Agonist
Trials.
	 
	 	(10)	 	For the avoidance of doubt, if the Initiation of a Future Trial
by Idera would qualify as a milestone payment triggering event as set forth in
Section 5.2 if

					
	 	 	 	 	 
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	 	 	 	such Initiation had been undertaken by Merck, such milestone shall be
considered achieved as if Merck achieved such milestone and all payments
resulting therefrom shall be due and payable by Merck to Idera according to
the Agreement.
	 
	 	(11)	 	Notwithstanding Section 3.4(b)(10), the Parties agree that the
Initiation of the [**] Trial shall in no event be considered [**].
	 
	 	(12)	 	Licensor’s acts pursuant to the provisions of this Section
3.4(b) shall not be considered a breach of Section 2.6 or Section 3.1.
	 
	 	(13)	 	Merck’s acts pursuant to the provisions of this Section 3.4(b),
as well as the fact that Merck [**], shall not be considered a breach of
Section 3.2 or Section 3.9.
	 
	 	(14)	 	Licensor has entered into a contract with [**] pursuant to
which [**] is to perform certain labeling, storage, packing and distribution
activities related to [**] on behalf of Licensor. During the Interim Period
and in accordance with Merck’s direction, Licensor shall manage the labeling,
packing and distribution of [**] vials of [**] via [**] for purposes of (i)
completion of transfer of the manufacturing technology as provided for under
this License Agreement, (ii) the On-Going Trials and (iii) any Future Trials.
Licensor shall not be responsible for manufacturing any amounts of [**] in
addition to the [**] vials referenced in this clause (14). To the extent that
Licensor follows the direction given by Merck pursuant to this clause (14),
Merck shall be accountable for the allocation of such vials to the transfer of
the manufacturing technology activities, the On-Going Trials and any Future
Trials
	 
	 	(15)	 	With respect to each TLR9 Agonist Trial, Licensor shall own the
corresponding clinical data generated by that Trial (the “Clinical Data”) until
such time as Merck shall [**]. Merck shall have a fully paid, royalty free,
exclusive license to use, disclose and copy the Clinical Data related to such
Trial to bring about the purposes of this License Agreement, the Charter
Agreements and the filing of the Merck TLR9 Agonists IND. Licensor shall retain
the right to use, disclose and copy (i) any and all Clinical Data during the
Interim Period as necessary to comply with applicable laws, rules and
regulations and to publish in accordance with Section 7.2 of the License
Agreement, (ii) any safety data in connection with contractual
pharmacovigilance obligations to third parties and (iii) the final study report
for [**] to the extent necessary to comply with [**]. In connection with the
foregoing and to the fullest extent permitted by law, Licensor shall authorize
any contract research organization, data management company or central
laboratory providing services in respect of a TLR9 Agonist Trial to
concurrently disclose the related Clinical Data to Merck or Merck’s designee.
In respect of Clinical Data for a TLR9 Agonist Trial generated by a Third-Party
vendor other than a contracts research organization, data management company or
central laboratory, Licensor shall promptly and timely disclose Clinical Data
to Merck after receipt thereof from such Third-Party vendor. Without additional
action or payment of an additional fee, ownership of the Clinical Data will
transfer from

					
	 	 	 	 	 
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	 	 	 	Licensor to Merck at the end of the Interim Period; provided, that Licensor
shall have a fully paid, royalty free, non-exclusive license to use and
disclose (i) the Clinical Data for purposes of any required regulatory
filings in connection with a TLR9 Agonist Trial or to respond to any
regulatory inquiries related to the period when Licensor was Sponsor of such
Trial and (ii) any safety data that are generated from a TLR9 Agonist Trial
for Licensor’s and its collaborators’ and their affiliates’ regulatory
purposes.
	 
	 	(16)	 	Licensor agrees that during such time that Licensor is owner of
any Clinical Data, such ownership rights shall be subject to and to the extent
applicable, limited by, the terms of this License Agreement, including Section
7.2(c).
	 
	 	(17)	 	Strategic Development Committee.

	 	(i)	 	The Parties shall establish a committee for the
purpose of reviewing and exchanging information regarding the general
direction and progress of the TLR9 Agonist Trials during the Interim
Period (the “Strategic Development Committee” or “SDC”). Each Party
shall designate two (2) individuals to be its authorized
representatives on the Strategic Development Committee (each a “SDC
Representative”). Merck shall also appoint one of the SDC
Representatives it has designated as the chair of the Strategic
Development Committee (the “SDC Chair”). The initial SDC
Representatives and chairperson are set forth on Schedule 3.4(b).
Each Party may change its SDC Representatives, or Merck may change its
designee for the SDC Chair, as the case may be, from time to time,
effective upon notice to the other Party of such change. Additional
representatives or consultants may from time to time, by mutual consent
of the Parties, be invited to attend SDC meetings. Except as expressly
set forth in clauses (ii) and (iii) below, the SDC shall function
solely as a forum for reviewing and exchanging information regarding
the progress and overall direction of the TLR9 Agonist Trials and not
as a decision-making body. The SDC shall meet in accordance with a
schedule established by the SDC Chair (taking in consideration the
availability of the SDC Representatives), but no less frequently than
once a month during the Interim Period and as needed to address an
Unresolved Issue as provided under clauses (ii) and (iii) below. Such
meetings will occur via teleconference, videoconference or in-person,
as determined by the SDC Chair. For an in-person SDC meeting held more
than fifty (50) miles outside of Boston, Massachusetts, Merck will
reimburse Licensor, in accordance with and subject to its corporate
travel and expense policies, for the reasonable travel expenses
incurred by Licensor’s SDC Representatives in connection with their
attendance of such meeting outside of Boston. The SDC Chair shall
ensure that relevant results of such SDC meetings are recorded and
approved by all SDC Representatives.

					
	 	 	 	 	 
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	 	(ii)	 	A specific study team comprised of
representatives designated by both Licensor and Merck will be formed in
respect of each TLR9 Agonist Trial (each a “Study Team”). With respect
to each TLR9 Agonist Trial, the applicable Study Team will be charged
with certain decision-making responsibilities related to that Trial as
set forth in the Trial’s Charter Agreement. Each Charter Agreement
will set out the procedures pursuant to which an unresolved issue,
requiring the unanimous consent of the Study Team members, may be
brought before the Strategic Development Committee (each an “Unresolved
Issue”). In the event that the SDC Representatives receive written
notice of an Unresolved Issue together with a summary thereof and the
action to be decided upon (an “Issue Summary”), the SDC Representatives
shall discuss the Unresolved Issue and shall meet with respect thereto
if one or more of them believes a meeting or meetings to be useful. If
the SDC Representatives do not resolve the matter within thirty (30)
days following receipt by them of the Issue Summary (or such lesser or
longer period as they may agree is appropriate for their discussions),
then the SDC Chair shall, after due and reasonable consideration and
subject to clause (iii) below, make the final decision regarding the
Unresolved Issue unless such issue is a Safety Issue as defined below.
In that case, Licensor’s SDC Representatives shall, after due and
reasonable consideration, including consultation with the safety team
representatives assigned to the relevant Study, make the final decision
regarding such Safety Issue. Licensor’s SDC Representatives shall
promptly inform the SDC Chair in writing of any final decisions
regarding Safety Issues reached in accordance with this clause (ii).
For purposes of this clause (ii), a Safety Issue is (A) any strategy
decision regarding a TLR9 Agonist Trial (including a decision to
terminate any such Trial) or material change to a TLR9 Agonist Trial
protocol that is under consideration which arises from safety findings
or other safety matters related to a Compound or (B) any change to a
TLR9 Agonist Trial protocol that could reasonably be expected to
significantly alter the foreseeable risks or discomforts to a TLR9
Agonist Trial subject. The SDC Chair shall provide the applicable
Study Team written notice, with a copy to all other SDC
Representatives, of any final decision regarding an Unresolved Issue
reached by the Strategic Development Committee pursuant to this clause
(ii).

	 	(iii)	 	Notwithstanding any of the foregoing, the SDC
Chair shall not make a final determination regarding an Unresolved
Issue the implementation of which could reasonably be expected to have
a material adverse effect on Licensor due to any liabilities or
obligations under laws, rules or regulations applicable to Licensor as
Sponsor of the relevant TLR9 Agonist Trial (a “Sponsor

					
	 	 	 	 	 
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	 	 	 	MAE”). For purposes of the foregoing, (A) during the course of
Strategic Development Committee discussions regarding an Unresolved
Issue, each of the Parties should endeavor to discuss specific
proposals to resolve the relevant issue and Licensor shall endeavor
in good faith to identify any aspect of a proposal the implementation
of which could reasonably be expected to result in a Sponsor MAE and
(B) the Merck SDC Representatives shall provide Licensor written
notice of any proposed final determination (“Proposed Final
Determination”) to be made hereunder (“Final Determination Notice”)
before its implementation. A Licensor’s SDC Representative shall
notify the Merck SDC Representatives in writing within five (5)
Business Days of receipt of a Final Determination Notice if in
Licensor’s reasonable opinion, a Proposed Final Determination could
result in a Sponsor MAE. In the absence of any such notice within
such five Business Day period, the Proposed Final Determination shall
become final and shall be implemented by written notification to the
applicable Study Team. In the event a Licensor’s SDC Representative
delivers such notice with respect to a Proposed Final Determination,
Merck shall not take any steps to implement the Proposed Final
Determination and may submit to Licensor SDC Representatives another
Proposed Final Determination that will be subject to this clause
(iii).

3. Section 9.1, Indemnification by Merck, shall be amended and restated in its entirety as
follows:

9.1 Indemnification by Merck. Merck shall indemnify, defend and hold Licensor and its
Affiliates and each of the respective employees, officers, directors and agents (the
“Licensor Indemnitees”) harmless from and against any and all liability, damage, loss,
cost or expense (including reasonable attorneys’ fees) to the extent arising out of
Third Party claims or suits related to (a) Merck’s acts or omissions, during the Interim
Period, in connection with the On-Going Trials or the Future Trials, (b) the
Development, manufacture, use or Commercialization of a Compound, Follow-On Compound or
Licensed Product by or on behalf of Merck, its Affiliates or Sublicensees, (c) the use,
handling or storage of any Licensor Materials by or on behalf of Merck, its Affiliates
or Sublicensees, (d) Merck’s performance of its obligations under this Agreement, (e)
breach by Merck of its representations, warranties or covenants set forth in this
Agreement; provided, however, that Merck’s obligations pursuant to this Section 9.1
shall not apply to the extent such claims or suits (i) result from the negligence or
willful misconduct of any of the Licensor Indemnitees or (ii) arise out of a breach by
Licensor of its representations, warranties or covenants set forth in this Agreement.

					
	 	 	 	 	 
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4. Section 9.2, Indemnification by Licensor, shall be amended and restated in its entirety
as follows:

9.2. Indemnification by Licensor. Licensor shall indemnify, defend and hold Merck
and its Affiliates and each of their respective agents, employees, officers and
directors (the “Merck Indemnitees”) harmless from and against any and all liability,
damage, loss, cost or expense (including reasonable attorney’s fees) to the extent
arising out of Third Party claims or suits related to (a) Licensor’s acts or omissions,
subject to the delegation of responsibilities to Merck or its Affiliates under any
applicable Charter Agreement, in conducting the On-Going Trials or the Future Trials
prior to and during the Interim Period, (b) the Development, manufacture, use or
Commercialization of Compounds or Follow-On Compounds by or on behalf of Licensor, its
Affiliates or licensees, (c) Licensor’s performance of its obligations under this
Agreement, (d) breach by Licensor of its representations, warranties or covenants set
forth in this Agreement, or (e) the matters set forth in [**]; provided, however, that
Licensor’s obligations pursuant to this Section 9.2 shall not apply to the extent such
claims or suits (i) result from the negligence or willful misconduct of any of the Merck
Indemnitees or (ii) arise out of a breach by Merck of its representations, warranties or
covenants set forth in this Agreement.

5. Section 9.5, Insurance, shall be amended and restated in its entirety as follows:

9.5 Insurance. During the Interim Period and with respect to each TLR9 Agonist Trial,
Licensor shall obtain and maintain, occurrence-form, product liability insurance with a
clinical trials endorsement, or clinical trials insurance, in an amount that is agreed
by Licensor and Merck as reasonable and customary in the United States pharmaceutical
and biotechnology industries for companies engaged in comparable activities. Merck
agrees to reimburse Licensor for the cost incurred by Licensor in obtaining such
insurance, up to the amount set forth as insurance expense payable or reimbursable by
Merck set forth in the applicable Trial Budget. After the Interim Period, until
expiration or termination of the Term, each Party shall bear its own costs of obtaining
and maintaining occurrence-form, product liability insurance with a clinical trials
endorsement, or clinical trials insurance (including self-insured arrangements), in
amounts that are reasonable and customary in the United States pharmaceutical and
biotechnology industry for companies engaged in comparable activities. It is understood
and agreed that this insurance shall not be construed to limit either Party’s liability
with respect to its indemnification obligations hereunder. Each Party will, except to
the extent self insured as permitted under this Section 9.5, provide to the other Party
upon request a certificate evidencing the insurance such Party is required to obtain and
keep in force under this Section 9.5. To the extent possible under each Party’s
respective insurance plans, each Party will notify the other Party at least thirty (30)
days prior to the expiration or cancellation of such insurance, or any reduction in
coverage thereunder.

6. The Schedules to the License Agreement are hereby amended with the addition of Schedule
3.4(b) attached hereto.

					
	 	 	 	 	 
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7. All other terms and conditions of the License Agreement shall remain in full force and
effect.

[SIGNATURE PAGE FOLLOWS]

					
	 	 	 	 	 
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IN WITNESS WHEREOF, the Parties have executed this Amendment as of the Amendment Date.

	 	 	 	 	 
	Idera Pharmaceuticals, Inc.	 	 
	 
	 	 	 	 
	By:

	 	/s/ Louis Arcudi, III
	 	 
	 

	 	 	 	 
	Name:

	 	Louis Arcudi, III	 	 
	Title:

	 	Chief Financial Officer	 	 
	Date:

	 	11 Feb 2009	 	 
	 

	 	 	 	 
	 
	 	 	 	 
	Merck KGaA	 	 
	 
	 	 	 	 
	By:

	 	/s/ Dr. Claudia [illegible]	 	 
	 

	 	 	 	 
	Name:

	 	Dr. Claudia [illegible]	 	 
	Title:
	 	 	 	 
	Date:

	 	13 Feb 2009	 	 
	 

	 	 	 	 
	 
	 	 	 	 
	By:

	 	/s/ Jens Eckhardt	 	 
	 

	 	 	 	 
	Name:

	 	Jens Eckhardt	 	 
	Title:

	 	Legal Counsel	 	 
	Date:

	 	13 Feb 2009	 	 
	 

	 	 	 	 

					
	 	 	 	 	 
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Schedule 3.4(b)

Strategic Development Committee Members

Idera SDC Representatives: [**]

Merck SDC Representative: [**]

Merck SDC Representative/SDC Chair: [**]

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