Document:

EX-10.3

 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 AND ARTICLE 6 OF THE PURCHASE AGREEMENT 

 

			
	Warrant No.         	  	 Number of
Shares:                    
 (subject to adjustment)

 Original Issue Date: November     , 2012 

Common Stock Purchase Warrant 
 (Void after November 9, 2017) 
 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 9, 2017,                      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. 
 This
Warrant is one in a series of warrants (the “Series Warrant”) issued pursuant to that certain Convertible Preferred Stock and Warrant Purchase Agreement, dated November 9, 2012, among the Company, the Registered Holder and the other
parties thereto (the “Purchase Agreement”). 
 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 9, 2012 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)). 

  
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 (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. 

(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). 

  
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 (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 the Registered Holder and its affiliates and any other persons whose beneficial ownership of Common Stock would be aggregated with the Registered 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
(ii) the combined voting power of the securities of the Company beneficially owned by the Registered Holder 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 stockholders of the Company approve the
Nasdaq Proposal (as defined by and in accordance with Section 5.11(B) of the Purchase Agreement), in which case, the 19.99% limitation under clause (i) and clause (ii) of this Section 1(e) shall be increased, with respect to the
Registered Holder, to 35% for purposes of both clause (i) and clause (ii) of this Section 1(e). 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 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) 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. 

(b) 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: 

  
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 (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 
 (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. 
 (c) Adjustment in Number of Warrant
Shares. When any adjustment is required to be made in the Purchase Price pursuant to subsections 2(a) or 2(b), 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. 
 (d) 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. 

(e) 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(a), 2(b) or 2(d)) (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. 

  
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 (f) 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 ten (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 ten (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 9, 2014, 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 $____ (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). 

  
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 (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.

 (e) Notwithstanding anything to the contrary set forth in this Section 4, no redemptions may be effected by the Company
pursuant to this Section 4 unless and until such redemption has been approved by a majority in number of the directors of the Company that are not affiliated with any holder of the Series E Preferred Stock or the Series Warrants and were not
elected as a director of the Corporation as a result of being nominated or submitted for consideration by any holder of the Series E Preferred Stock or Series Warrants or any affiliate thereof. 

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. 

  
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 (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 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). 

(e) This Warrant and the Warrant Shares shall be subject to the restrictions on transfer set forth in Article 6 of the Purchase Agreement.

 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 ten (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. 

  
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 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 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 (2) 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 (1) 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 

  
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 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 
 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 Company and the holders of Series Warrants exercisable for a number of shares of Common Stock equal to more than 50% of the total number of
shares of Common Stock issuable upon exercise of all Series Warrants. 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 State of Delaware (without reference to the conflicts of law provisions thereof). 

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

  
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 EXECUTED as of the Date of Issuance indicated above. 

 

			
	Idera Pharmaceuticals, Inc.
		
	By:	 	 
		
	Title:	 	 

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

 ̈   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): 
  

	 	 ̈	$                     in lawful money of the United States;
and/or 

  

	 	 ̈	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 

  

	 	 ̈	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:
	 	 	 	
			
		 	 	 	

  
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 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:	 		 		  	
					
	Dated:	 	 	 		 		  	

  
 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. 

  
 - 13 -EX-10.4

 Exhibit 10.4 

IDERA PHARMACEUTICALS, INC. 
 AMENDMENT NO. 1 TO CONVERTIBLE PREFERRED STOCK AND WARRANT PURCHASE AGREEMENT 
 This Amendment No. 1 to Convertible Preferred Stock and Warrant Purchase Agreement (this “Agreement”) is made as of November 9, 2012, by and between Idera
Pharmaceuticals, Inc., a Delaware corporation (the “Company”), and Pillar Pharmaceuticals I, L.P. (the “Purchaser”). 
 WHEREAS, the Company and Purchaser entered into that certain Convertible Preferred Stock and Warrant Purchase Agreement, dated as of November 4, 2011 (the “Purchase
Agreement”), by and between the Company and Purchaser; 
 WHEREAS, the Company and the Purchaser desire to amend
certain sections of the Purchase Agreement, as set forth below; 
 WHEREAS, pursuant to Section 7.4 of the Purchase
Agreement, any amendment of the Purchase Agreement requires the written consent of the Company and the Purchasers holding a majority of the shares of Series D Preferred Stock (as defined in the Purchase Agreement) then outstanding; 

NOW, THEREFORE, in consideration of the foregoing, and for other valuable consideration, the receipt and sufficiency of which are hereby
acknowledged, the Company and the Purchaser hereby agree as follows: 
 1. Section 5.2 of the Purchase Agreement is hereby
terminated and of no further force and effect. 
 2. The Company hereby agrees that the purchase by certain affiliates of the
Purchaser of securities of the Company pursuant to that certain Convertible Preferred Stock and Warrant Purchase Agreement, dated November 9, 2012, among the Company and the Purchasers named therein shall not be in violation of Section 5.7
of the Purchase Agreement. 
 3. Section 5.8 of the Purchase Agreement is hereby amended by deleting such Section in its
entirety from the Purchase Agreement and inserting the following in lieu thereof: 
 “5.8 Voting Rights. 

(A) Each Purchaser hereby agrees that, to the extent that and for so long as the total number of shares of Common Stock
beneficially owned by the Purchaser and its affiliates and any other persons whose beneficial ownership of Common Stock would be aggregated with the Purchaser for purposes of Section 13(d) of the Exchange Act exceeds 19.99% (prior to the date
that the stockholders of the Company approve the Nasdaq Proposal (as defined by and in accordance with Section 5.11(B) of that certain Convertible Preferred Stock and Warrant Purchase Agreement, dated November 9, 2012, among the Company
and the Purchasers named therein (the “SERIES E PURCHASE AGREEMENT”)) or 25% 

 
(effective upon the date that the stockholders of the Company approve the Nasdaq Proposal), in any election of directors and in any other vote to be taken by the stockholders of the Company
(whether taken at an annual or special meeting of stockholders or by written action), it and its affiliates will vote any Excess Shares (as defined below) held in the same manner as and in the same proportion to the votes cast by the other holders
of the Company’s Common Stock or other voting securities. 
 (B) Each Purchaser hereby constitutes and
appoints as the proxies of the party and hereby grants a power of attorney to the officers of the Company, and each of them, with full power of substitution, with respect to clause (A) above, and hereby authorizes each of them to represent and
to vote, if and only if the Purchaser (i) fails to vote or (ii) attempts to vote (whether by proxy, in person or by written consent), in a manner which is inconsistent with the terms of clause (A), all of such Purchaser’s Excess
Shares in accordance with the terms of clause (A). Each of the proxy and power of attorney granted pursuant to the immediately preceding sentence is given in consideration of the agreements and covenants of the Company and the parties in connection
with the transactions contemplated by this Agreement and, as such, each is coupled with an interest and shall be irrevocable unless and until this Agreement terminates or expires. Each Purchaser hereby revokes any and all previous proxies or powers
of attorney with respect to the Excess Shares and shall not hereafter, unless and until this Agreement terminates or expires, purport to grant any other proxy or power of attorney with respect to any of such Excess Shares, deposit any of such Excess
Shares into a voting trust or enter into any agreement (other than this Agreement), arrangement or understanding with any person, directly or indirectly, to vote, grant any proxy or give instructions with respect to the voting of any of such Excess
Shares, in each case, with respect to clause (A) above. 
 (C) Each Purchaser agrees to refrain from
exercising (and hereby affirmatively waives) any dissenters’ rights or rights of appraisal under applicable law at any time with respect to any Sale of the Corporation (as defined in the Corporation’s Certificate of Designations,
Preferences and Rights of Series E Preferred Stock) to the extent such Sale of the Corporation has been approved by the Company’s Board of Directors. 
 (D) For purposes of this Section 5.8, “Excess Shares” means for any Purchaser the number of shares of voting stock held by the Purchaser and its affiliates equal to (i) the total
number of shares of Common Stock held by the Purchaser and its affiliates (including Conversion Shares and shares of Common Stock issuable upon conversion of other series of Preferred Stock held by the Purchaser and its affiliates), less
(ii) 19.99% (prior to the date that the stockholders of the Company approve the Nasdaq Proposal) or 25% (effective upon the date that the stockholders of the Company approve the Nasdaq Proposal) of the total number of shares of Common Stock
then outstanding (including all Conversion Shares and all other shares of Common Stock then issuable upon conversion of other series of Preferred Stock then outstanding).” 

  
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 4. Section 6.1 of the Purchase Agreement is hereby amended by deleting such Section in
its entirety from the Purchase Agreement and inserting the following in lieu thereof: 
 “6.1 Restrictions on
Transferability. 
 (A) Subject to Section 6.1(B), the Securities shall not be sold, transferred,
assigned or hypothecated unless (i) there is an effective registration statement under the Securities Act covering such Securities, (ii) the sale is made in accordance with Rule 144 under the Securities Act, or (iii) the Company
receives an opinion of counsel for the holder of the Securities reasonably satisfactory to the Company stating that such sale, transfer, assignment or hypothecation is exempt from the registration requirements of the Securities Act, and each such
case upon all other conditions specified in this Section 6.1. Notwithstanding the provisions of the preceding sentence, no such registration statement or opinion of counsel shall be required for any transfer of any Securities by a Purchaser
that is a partnership, a limited liability company or a corporation to (a) a partner of such partnership, a member of such limited liability company or a stockholder of such corporation, (b) an entity that controls, or is controlled by, or
is under common control with such partnership, limited liability company or corporation, or (c) the estate of any such partner, member or stockholder (collectively, clauses (a) through (c) the “PERMITTED TRANSFEREES”);
provided, that in each of the foregoing cases the proposed transferee of the Securities held by the Purchaser agrees in writing to take and hold such Securities subject to the provisions and upon the conditions specified in this Section 6.

 (B) Notwithstanding anything to the contrary set forth in this Agreement, without the prior written consent of
the Company, the Purchaser may not sell or transfer any Securities to a person, entity or group (within the meaning of Section 13(d) of the Exchange Act) in one or more transactions if such sale or transfer would, in the aggregate, result in
the transfer to such person, entity or group Securities representing, or exercisable for stock of the Company representing, more than 5% of the then outstanding combined voting power of the outstanding securities of the Company (other than a sale or
transfer to a Permitted Transferee who agrees in writing to be bound by such restrictions or in connection with a resale of such Securities in connection with an underwritten public offering that has been approved by the Board). 

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

  
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 5. Section 7.6 of the Purchase Agreement is hereby amended by deleting the phrase
“Commonwealth of Massachusetts” and inserting the phrase “State of Delaware” in lieu thereof. 
 6. The
Purchase Agreement, as amended by this Agreement, together with any other writings referred to in the Purchase Agreement or delivered pursuant thereto which form a part thereof, contain the entire agreement among the parties with respect to the
subject matter thereof and amend, restate and supersede all prior and contemporaneous arrangements or understandings with respect thereto. 
 7. Upon the effectiveness of this Agreement, on and after the date hereof, each reference in the Purchase Agreement to “this Agreement,” “hereunder,” “hereof,”
“herein” or words of like import shall mean and be a reference to the Purchase Agreement, as amended hereby. Except as specifically amended above, the Purchase Agreement shall remain in full force and effect and are hereby ratified and
confirmed. 
 8. This Agreement shall be governed by and construed in accordance with the General Corporation Law of the State of
Delaware as to matters within the scope thereof, and as to all other matters shall be governed by and construed in accordance with the internal laws of the State of Delaware, without regard to conflict of laws principles that would result in the
application of any law other than the law of the State of Delaware. 
 9. This Agreement may be executed in any number of
counterparts, and each such counterpart shall be deemed to be an original instrument, but all such counterparts together shall constitute but one agreement. 
 [Remainder of Page Intentionally Left Blank] 

  
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 IN WITNESS WHEREOF, this Amendment No. 1 to Convertible Preferred Stock and
Warrant Purchase Agreement has been executed by the parties hereto as of the day and year first above written. 
  

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

 Amendment No. 1 to Convertible Preferred Stock and Warrant Purchase Agreement 

 IN WITNESS WHEREOF, this Amendment No. 1 to Convertible Preferred Stock and
Warrant Purchase Agreement has been executed by the parties hereto as of the day and year first above written. 
  

			
	PURCHASER:
	
	PILLAR PHARMACEUTICALS I, L.P.
		
	By:	 	/s/ Youssef El Zein
	 Name:
	 	Youssef El Zein
	 Title:
	 	Director

 Amendment No. 1 to Convertible Preferred Stock and Warrant Purchase Agreement

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