Document:

2ND AMENDMENT TO SUBLEASE, DATED 6/30/03

 Exhibit 10.39 
  
 SECOND AMENDMENT TO SUBLEASE 
  
 THIS SECOND AMENDMENT TO SUBLEASE (this “Amendment”) is dated as of the 30 day of June, 2003, by and between Harvard Pilgrim Health Care,
Inc., a Massachusetts corporation (“Sublandlord”) and Coley Pharmaceutical Group, Inc., a Delaware corporation (“Subtenant”). 
  
 A. Pursuant to that certain sublease between Sublandlord and Subtenant, dated as of March 8, 2001, as amended by that certain First Amendment to Sublease,
dated as of February 21, 2003 (collectively, the “Original Sublease”) (together, the Original Sublease and this Amendment are referred to herein as the “Sublease”), Sublandlord agreed to sublease to Subtenant, and Subtenant
subleased from Sublandlord, certain premises located in the building known as 93 Worcester Street, Wellesley, Massachusetts, as further identified in the Original Sublease (the “Premises”) subject to the terms and conditions more
particularly set forth in the Original Sublease. 
  
 B.
Sublandlord and Subtenant now desire to extend the Sublease Term, to reduce the Base Rent of the Premises, to revise the Letter of Credit and to cause other changes to the Sublease in accordance with the terms and conditions set forth in this
Amendment. 
  
 NOW, THEREFORE, for good and valuable
consideration, the receipt and sufficiency of which are hereby acknowledged, and intending to be legally bound hereby, the parties hereto agree as follows: 
  
 1. From and after the date hereof, the Original Sublease is hereby amended to add the following new definitions to Section 1.1: 
  
 Second Amendment Effective Date: July 1, 2003. 
  
 2. From and after the Second Amendment Effective Date, the definitions of
“Base Rent” and “Renewal Term” set forth in Section 1.1 of the Original Sublease are hereby deleted and the following new definitions are added to the Sublease: 
  
 Base Rent: 
  

							
	 Time Period    

	  	Annual Rent

	  	Monthly Rent
Payable

	 July 1, 2003 - December 31, 2004
	  	$	611,226.00	  	$	50,935.50
			
	 January 1, 2005 - December 31, 2005
	  	$	629,748.00	  	$	52,479.00
			
	 January 1, 2006 - April 30, 2007
	  	$	648,270.00	  	$	54,022.50
			
	 May 1, 2007 - December 31, 2008
	  	$	666,792.00	  	$	55,566.00

  

			
	Sublease Term or Initial Term:	  	Approximately seven (7) years, nine (9) months and two (2) weeks commencing on the Commencement Date and expiring on December 31, 2008 (the “Fixed Expiration
Date”).
		
	Commencement Date:	  	March 15, 2001

  
 3. Term. The
Initial Term with regard to the Premises shall expire on December 31, 2008. All other terms and conditions of the Original Sublease with regard to the Initial Term shall remain in full force and effect. 
  
 4. Base Rent. From and after the Second Amendment Effective Date,
Subtenant shall pay Base Rent to Sublandlord in the amount set forth in Paragraph 2 of this Amendment. All Base Rent shall be paid by Subtenant at the times and in the manner set forth in the Original Sublease. From and after the Amendment Effective
Date, all references in the Sublease to “Base Rent” shall be deemed to mean the Base Rent set forth in Paragraph 2 of this Amendment. 
  
 5. Letter of Credit. From and after the Second Amendment Effective Date, Section 6.4.3 is hereby deleted and the following is inserted in its
place: “Provided that (a) Subtenant is not then in default of its obligations under the terms of this Sublease beyond applicable notice or grace periods, if any, and (b) there has not, within the twelve (12) calendar month period prior to any
Reduction Date (as hereinafter defined), existed an Event of Default by Subtenant (the foregoing subsections (a) and (b) are hereinafter referred to as the “Reduction Conditions”), Subtenant shall be entitled to reduce the Security Deposit
on the dates as listed below (the “Reduction Date”) to the amounts listed on the following schedule (or if the deposit is in the form of a letter of credit, Sublandlord shall exchange the letter of credit for a letter of credit delivered
by Subtenant which reduces the amount secured by the letter of credit to such amount): 
  

				
	 Reduction Date

	  	Security Deposit Amount

	 July 1, 2003
	  	$	366,736.00
		
	 January 1, 2005
	  	$	314,874.00
		
	 January 1, 2006
	  	$	269,162.00
		
	 January 1, 2007
	  	$	209,299.00

  
 In the event that Subtenant is not
entitled to reduce the Security Deposit (or exchange its letter of credit for one securing a reduced amount, as applicable) on any Reduction Date because it fails to comply with the Reduction Conditions, then Subtenant shall be entitled to such
reduction on the next following Reduction Date provided that upon such date Subtenant is in compliance with the Reduction Conditions (and the remainder of the reduction schedule would be delayed by such time period). 
  
 6. Broker. Each party represents and warrants to the other that
it has not dealt with any broker or person in connection with this Amendment. The execution and delivery of this Amendment by each party shall be conclusive evidence that such party has relied on the 

  

 
foregoing representation and warranty. Each party shall indemnify and hold the other party harmless from and against any and all claims for commission, fee
or other compensation by any person (other than the Broker) who shall claim to have dealt with such party in connection with this Amendment and for any and all costs incurred in connection with such claims, including, without limitation, reasonable
attorneys’ fees and disbursements. The indemnifying party shall have the right, at its sole cost and expense, to defend any such claim with counsel reasonably satisfactory to the indemnified party and to settle or compromise any such claim
provided that the indemnified party shall have no financial responsibility therefor or be otherwise prejudiced by any such compromise or settlement. The provisions of this Section shall survive the expiration of sooner termination of the Sublease or
this Amendment. 
  
 7. Prime Landlord Consent. This
Amendment is conditioned upon and subject to Prime Landlord’s consent and approval. 
  
 8. Miscellaneous. All other terms and conditions of the Original Sublease, as amended hereby, remain in full force and effect, as so amended. All capitalized terms used herein and not otherwise defined shall
have the meanings ascribed to them in the Sublease. The recitals set forth above are specifically incorporated into the body of this Amendment and shall be binding upon the parties hereto. Except as expressly amended hereby, all of the terms and
conditions of the Sublease remain unchanged and in full force and effect. This Amendment is deemed incorporated into the Sublease by reference as of the date hereof; provided, however, in the event of any conflict or inconsistency between the terms
and provisions of the Sublease and the terms and provisions of this Amendment, the terms and provisions of this Amendment shall govern and control. This Amendment may be executed in any number of counterparts with the same effect as if all of the
signatures on such counterparts appeared on one document, and each such counterpart shall be deemed to be an original. 
  
 [REMAINDER OF PAGE HAS BEEN INTENTIONALLY LEFT BLANK] 
  

 IN WITNESS WHEREOF, the parties hereto have caused this Amendment to be executed under seal as of the day
and year first above written. 
  

			
	SUBLANDLORD:
	
	Harvard Pilgrim Health Care, Inc.
		
	By:	 	/s/    HAROLD E. PUTNAM
JR.        
		
	 Name:
	 	Harold E. Putnam Jr.
		
	 Title:
	 	Vice President Finance and Treasurer

  

			
	
	SUBTENANT:
	
	Coley Pharmaceutical Group, Inc.
		
	By:	 	/s/    ROBERT FORRESTER        
		
	 Name:
	 	Robert Forrester
		
	 Title:
	 	SVPAMENDED AND RESTATED LANDLORD CONSENT TO SUB-LEASE DATED 02/21/03

 Exhibit 10.40 
  
 AMENDED AND RESTATED LANDLORD CONSENT 
 TO SUB-SUBLEASE 
  
 This
Amended and Restated Landlord Consent To Sub-Sublease (the “Consent Agreement”) is entered into as of this 21st day of February, 2003 by and among Wellesley Gateway LLC, a Massachusetts limited liability company (“Wellesley
Gateway”), Harvard Pilgrim Health Care, Inc., a Massachusetts corporation (“Sublessor”) and Coley Pharmaceutical Group, Inc., a Delaware corporation (“Sublessee”). 
  
 RECITALS: 
  

	A.	Wellesley Gateway, as tenant, and The Commonwealth of Massachusetts, Acting by and Through its Division of Capital Planning and Operations (“The Commonwealth”), as
landlord, are parties to that certain Ground Lease dated as July 23, 1998 (the “Ground Lease”), which Ground Lease demises a certain parcel of land commonly known as 93 Worcester Street, Wellesley, Massachusetts and the improvements
thereon (the “Premises”) to Wellesley Gateway. 

  
 Wellesley Gateway, as landlord, and Sublessor, as tenant, are parties to that certain Indenture of Lease dated as of March 31, 1998 and amended by that certain First Amendment to Indenture of Lease dated as of May 24, 2002 (as amended, the
“Prime Lease”), which Prime Lease demises the Premises to Sublessor. 
  

	B.	Sublessor and Sublessee have entered into (or are about to enter into) that certain First Amendment to Sublease agreement dated February 21, 2003 (the “First Amendment”)
which amends that certain sublease agreement dated March 8, 2001 (the “Original Sublease” and the Original Sublease as amended by the First Amendment is referred to herein as the “Sublease Agreement”). The First Amendment and the
Original Sublease arc attached hereto as Exhibit A. Pursuant to the Sublease Agreement, Sublessor has agreed to sub-sublease to Sublessee approximately 18,522 square feet of rentable area on the 1st floor (the “Sublet Premises”) of the corporate headquarters building (the “Building”) located on the Premises. The Sublet Premises are
substantially as shown by the diagonal marking on Exhibit A-l to the Sublease Agreement. 

  

	C.	Wellesley Gateway, Sublessor and Sublessee previously entered into a Landlord Consent to Sub-Sublease dated March 15, 2001 (the “Original Consent”) whereby Wellesley
Gateway consented to the Original Sublease upon the terms and conditions set forth in the Original Consent. 

  

	D.	Sublessor and Sublessee have requested the consent of Wellesley Gateway to the First Amendment to Sublease Agreement. 

  

	E.	Wellesley Gateway has agreed to give such consent upon the terms and conditions contained in this Consent Agreement. 

  

 NOW THEREFORE, in consideration of the foregoing preambles which by this reference are incorporated herein and other good
and valuable consideration, the receipt and sufficiency of which are hereby acknowledged, Wellesley Gateway hereby consents to the Sublease Agreement subject to the following terms and conditions, all of which are hereby acknowledged and agreed to
by Sublessor and Sublessee: 
  

	 	1.	Sublease Agreement. Sublessor and Sublessee hereby represent that a true and complete copy of the Sublease Agreement is attached hereto and made a part hereof as Exhibit
A. 

  

	 	2.	Representations. Sublessor hereby represents and warrants that Sublessor (i) has full power and authority to sublease the Sublet Premises to Sublessee, (ii) has not
transferred or conveyed its interest in the Prime Lease to any person or entity collaterally or otherwise, and (iii) has full power and authority to enter into the Sublease Agreement and this Consent Agreement. Sublessee hereby represents and
warrants that Sublessee has full power and authority to enter into the Sublease Agreement and this Consent Agreement. 

  

	 	3.	Indemnity and Insurance. Sublessee hereby assumes, with respect to Wellesley Gateway, the insurance and indemnity obligations of the Sublessor under the Prime Lease, provided
that the insurance carried by Sublessee may be in the amounts specified in the Sublease Agreement. The foregoing sentence shall not be construed as relieving or releasing Sublessor from any insurance or indemnity obligations under the Prime Lease.

  

	 	4.	No Release. Nothing contained in the Sublease Agreement or this Consent Agreement shall be construed as relieving or releasing Sublessor from any of its obligations under the
Prime Lease, it being expressly understood and agreed that Sublessor shall remain liable for such obligations notwithstanding anything contained in the Sublease Agreement, or in this Consent Agreement, or .any subsequent assignment(s), sublease(s)
or transfer(s) of the interest of the tenant under the Prime Lease. Sublessor shall be responsible for the collection of all rent due it from Sublessee, and for the performance of all the other terms and conditions of the Sublease Agreement, it
being understood that Wellesley Gateway is not a party to the Sublease Agreement and, notwithstanding anything to the contrary contained in the Sublease Agreement, Wellesley Gateway is not bound by any terms or provisions contained in the Sublease
Agreement or obligated to Sublessor or Sublessee for any of the duties and obligations contained therein. 

  

	 	5.	 Excess Rent. Notwithstanding anything to the contrary herein contained. Sublessor shall pay to Wellesley Gateway 50% of all “profit” which
Sublessor receives from Sublessee under the Sublease Agreement. For the purposes hereof, “profit” shall be defined as the excess of (i) all amounts paid by Sublessee to Sublessor pursuant to the Sublease Agreement, including, without

  

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limitation, rental payments and payments on account of other charges, over (ii) the rental due or becoming due from Sublessor to Wellesley Gateway pursuant
to the Prime Lease from and after the effective date of the Sublease Agreement (pro rated over the Sublet Premises) together with any expense incurred by Sublessor in making the space suitable for Sublessee. Sublessor shall pay Wellesley Gateway
such excess within 45 days after Sublessor’s receipt thereof, subject to adjustment at the time that the actual amount of operating costs and expenses for the calendar year in question is determined (the parties hereby acknowledging that the
rent in respect of the Sublet Premises includes estimated amounts on account of operating expenses due by Sublessor to Wellesley Gateway under the Prime Lease). 

  

	 	6.	No Transfer. Sublessee shall not further sublease the Sublet Premises, assign its interest as the Sublessee under the Sublease Agreement or otherwise transfer its interest in
the Sublet Premises or the Sublease Agreement to any person or entity without the written consent of Wellesley Gateway or The Commonwealth, if necessary, which consent the parties may withhold in their sole discretion. 

  

	 	7.	Prime Lease and Ground Lease. In no event shall the Sublease Agreement or this Consent Agreement be construed as granting or conferring upon the Sublessor or the Sublessee
any greater rights than those contained in the Prime Lease and the Ground Lease nor shall there be any diminution of the rights and privileges of Wellesley Gateway under the Prime Lease or The Commonwealth under the Ground Lease. Notwithstanding
anything to the contrary contained in the Sublease Agreement, the Sublease Agreement is and shall remain subject and subordinate in all respects to each and every term of the Ground Lease and the Prime Lease. Without limiting the scope of the
preceding sentence, any construction or alterations, including signage, performed in or to the Sublet Premises shall be performed with the prior written approval of Wellesley Gateway, which approval may be made or withheld in the sole discretion of
Wellesley Gateway, and shall be performed in accordance with the requirements of both the Prime Lease and the Ground Lease (including, without limitation, any requirement to obtain consent of The Commonwealth) and in accordance with the rules and
regulations set forth on Exhibit B hereto and such other reasonable rules and regulations that may be established by Wellesley Gateway from time to time. Nothing in this Consent Agreement shall be deemed to constitute Wellesley Gateway’s
approval of any alterations or signage set forth in the Sublease Agreement. 

  

	 	8.	 Attornment to Wellesley Gateway. If the Prime Lease or Sublessor’s right to possession thereunder terminates for any reason prior to expiration of the
Sublease Agreement, Sublessee agrees, at the election of Wellesley Gateway, to attorn to Wellesley Gateway upon the then executory terms and conditions of the Sublease Agreement for the remainder of the term of the Sublease Agreement. If Wellesley
Gateway does not so elect, the Sublease Agreement 

  

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and all rights of Sublessee in the Sublet Premises shall terminate upon the date of termination of the Prime Lease or Sublessor’s right to possession
thereunder, 

  

	 	9.	Attornment to The Commonwealth. If, for any reason prior to expiration of the Sublease Agreement: (i) the Prime Lease or Sublessor’s right to possession thereunder
terminates, and (ii) the Ground Lease or Wellesley Gateway’s right to possession thereunder has previously terminated, Sublessee agrees, at the election of The Commonwealth, to attorn to The Commonwealth upon the then executory terms and
conditions of the Sublease Agreement for the remainder of the term of the Sublease Agreement. If The Commonwealth does not so elect, the Sublease Agreement and all rights of Sublessee in the Sublet Premises shall terminate upon the date of
termination of the Prime Lease or Sublessor’s right to possession thereunder. 

  

	 	10.	Amendments. Sublessee and Sublessor shall not modify, supplement or amend the Sublease Agreement without the written consent of Wellesley Gateway. 

 

	 	11.	Prime Lease. As between Wellesley Gateway and Sublessor, (i) this Consent Agreement shall not release Sublessor from any existing or future duty, obligation or liability to
Wellesley Gateway pursuant to the Prime Lease; (ii) this Consent Agreement shall not change, modify or amend the Prime Lease in any manner; and (iii) the Prime Lease remains in full force and effect. Notwithstanding the generality of the foregoing,
this Consent Agreement expressly shall not absolve Sublessor from any requirement set forth in the Prime Lease that Sublessor obtain Wellesley Gateway’s prior written approval of any additional subleases, assignments or other dispositions of
its interest in the Prime Lease or the demised premises (as defined in the Prime Lease). 

  

	 	12.	Relationship of the Parties. Neither the Prime Lease, the Sublease Agreement nor this Consent Agreement shall be deemed, nor are such documents intended, to grant to
Sublessee any rights against Wellesley Gateway. Notwithstanding anything to the contrary contained in the Sublease Agreement, Sublessee hereby acknowledges and agrees that its sole remedy for any alleged or actual breach of Sublessee’s rights
in connection with the Sublease Agreement shall be solely against Sublessor. 

  

	 	13.	Broker’s Fee. Sublessor and Sublessee agree to indemnify and hold Wellesley Gateway harmless from and against any loss, cost, expense, damage or liability, including
reasonable attorneys’ fees, incurred as a result of a claim by any person or entity that it is entitled to a commission, finder’s fee or like payment in connection with the Sublease Agreement. 

  

	 	14.	 Counterparts. This Consent Agreement may be executed in counterparts and shall constitute an agreement binding on all parties notwithstanding that all
parties are not signatories to the original or the same counterpart provided that 

  

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all parties are furnished a copy or copies thereof reflecting the signature of all parties. 

  

	 	15.	Approval of Prime Landlord. To be binding upon Wellesley Gateway, any approval or consent of Prime Landlord (as defined in the Sublease Agreement) required pursuant to the
Sublease Agreement shall be in writing. 

  

	 	16.	Original Consent. The Original Consent is amended and restated in its entirety by this Consent Agreement. 

  

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 IN WITNESS WHEREOF, Wellesley Gateway, Sublessor and Sublessee have executed this Consent Agreement as of
this 21st day of February, 2003. 
  

											
	 Signed and acknowledged:
 in the presence of:
	 	 	 	 WELLESLEY GATEWAY:
 WELLESLEY
GATEWAY LLC,
a Massachusetts limited liability company

					
	 	 	 	 	 	 	By:	 	 TDC Holding Corp.,
 a Massachusetts
corporation, its Manager

						
	 	 	 	 	 	 	 	 	 By:
	 	/s/    RONALD M. DRUKER        
	 	 	 	 	 	 	 Name:
	 	Ronald M. Druker
	 	 	 	 	 	 	 	 	 Title:
	 	President
				
	 	 	 	 	 	 	SUBLESSOR:
				
	 	 	 	 	 	 	HARVARD PILGRIM HEALTH CARE, INC., a Massachusetts corporation
					
	 	 	 	 	 	 	 By:
	 	/s/    HAROLD
PUTNAM        
	Illegible	 	 	 	 	 	 Name:
	 	Harold Putnam
	 	 	 	 	 	 	 	 	 Title:
	 	V.P., Treasurer
	 	 	 	 	 	 	 
				
	 	 	 	 	 	 	SUBLESSEE:
				
	 	 	 	 	 	 	COLEY PHARMACEUTICAL GROUP, INC., a Delaware corporation
					
	 	 	 	 	 	 	 By:
	 	/s/    CHARLES E.
YON        
	/s/    ELLEN O.
WING        	 	 	 	 Name:
	 	Charles E. Yon
	 	 	 	 	 	 	 Title:
	 	VP, General Counsel

  

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