Document:

Second Amendment Lease by and between the Irvine Company and the Company

 EXHIBIT 10.1 
  
 SECOND AMENDMENT TO LEASE 
  

	I.	PARTIES AND DATE. 

  
 This Second Amendment to Lease (“Amendment”) dated October 21, 2003, is by and between THE IRVINE COMPANY (“Landlord”), and NUVELO,
INC., a Nevada corporation formerly known as HYSEQ, INC., a Nevada corporation (“Tenant”). 
  

	II.	RECITALS. 

  
 On April 30, 2001, Landlord and Tenant (then known as Hyseq, Inc., a Nevada corporation), entered into a lease (“Original Lease”) for space in a
building located at 985 Almanor Avenue, Sunnyvale, California (“Premises”), which lease was amended by a First Amendment to Lease (“First Amendment”) dated August 1, 2002 (as amended, inclusive of this Amendment, the
“Lease”). On or about January 31, 2003, Tenant changed its name to Nuvelo, Inc., a Nevada corporation. 
  
 Landlord and Tenant each desire to modify the Lease to adjust the Basic Rent and make such other modifications as are set forth in “III.
MODIFICATIONS” next below. 
  

	III.	MODIFICATIONS. 

  
 A. Basic Lease Provisions. The Basic Lease Provisions are hereby amended as follows: 
  
 1. Effective as of October 1, 2003, Item 6 shall be deleted in its entirety and the following shall be
substituted in lieu thereof: 
  
 “Basic Rent: Three Hundred
Five Thousand One Hundred Thirty-Six Dollars ($305,136.00) per month. 
  
 Basic Rent is subject to adjustment as follows: 
  
 Commencing July 1, 2004, the Basic Rent shall be Zero Dollars ($0.00) per month. 
  
 Commencing April 1, 2005, the Basic Rent shall be Three Hundred Sixty Thousand Six Hundred Fifteen Dollars ($360,615.00) per month. 
  
 Commencing June 1, 2005, the Basic Rent shall be Four Hundred Forty-Six Thousand Two Hundred Seven Dollars ($446,207.00) per
month. 
  
 Commencing June 1, 2006, the Basic Rent shall be Four
Hundred Sixty-Four Thousand Fifty-Five Dollars ($464,055.00) per month. 
  
 Commencing June 1, 2007, the Basic Rent shall be Four Hundred Eighty-Two Thousand Six Hundred Seventeen Dollars ($482,617.00) per month. 
  
 Commencing June 1, 2008, the Basic Rent shall be Five Hundred One Thousand Nine Hundred Twenty-Two Dollars ($501,922.00) per
month. 
  
 Commencing June 1, 2009, the Basic Rent shall be Five
Hundred Twenty-One Thousand Nine Hundred Ninety-Nine Dollars ($521,999.00) per month. 
  
 Commencing June 1, 2010, the Basic Rent shall be Five Hundred Forty-Two Thousand Eight Hundred Seventy-Nine Dollars ($542,879.00) per month.” 
  
 B. Current Payment. Concurrently with Tenant’s execution and delivery of this Amendment to Landlord, Tenant
shall pay the sum of Two Million Seven Hundred Forty-Six Thousand Two Hundred Twenty-Four Dollars ($2,746,224.00) to Landlord as and for prepaid Basic Rent for the period of October 1, 2003 through June 30, 2004. 
  
  

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 C. Additional Deferred Base Rent Obligation. Tenant acknowledges that by virtue of the revised
rental schedule set forth above, Landlord shall receive less Basic Rent than would previously have been payable by Tenant for the time period of October 1, 2003 through May 31, 2005. The total amount deferred pursuant to this Amendment is Three
Million Seventy-Nine Thousand Ninety-Eight Dollars ($3,079,098.00) (the “Additional Deferred Base Rent”). In consideration of the foregoing rent deferral, Tenant agrees to pay Landlord, in addition to the Basic Rent listed above, the
Additional Rent payable pursuant to the First Amendment, and all other sums payable pursuant to the Lease, the sum of Two Million Eight Hundred Seventy-Nine Thousand Ninety-Eight Dollars ($2,879,098.00) (the “Additional Deferred Base Rent
Payment”) on May 30, 2011. If Tenant extends the Term of the Lease pursuant to Section 3.3 or if Landlord and Tenant hereafter agree to renew or extend the Lease Term for at lease three (3) years, then Tenant may elect to pay the Additional
Deferred Base Rent Payment in thirty-six (36) monthly installments of Seventy-Nine Thousand Nine Hundred Seventy-Five Dollars ($79,975.00) per month commencing June 1, 2011 and continuing through May 1, 2015. Any such election to pay the Additional
Deferred Base Rent Payment in installments shall be delivered in writing to Landlord concurrently with the Commitment Notice or execution of an amendment to the Lease renewing or extending the Term, as applicable. If Tenant makes any such election,
the parties shall promptly memorialize the election on an amendment to the Lease. 
  
 D. Effect of Default. In the event of any default under the Lease by Tenant, Landlord may elect to declare the full amount of any accrued Deferred Base Rent and Additional Deferred Base Rent to be immediately
due and payable, in which case the Basic Rent shall immediately be increased to the rates set forth in the Original Lease. 
  
 E. Prepayment. Paragraph C of the First Amendment is hereby deleted in its entirety and the following is substituted in lieu thereof: 

 
 “Prepayment. Tenant may, at any time, elect to pay to Landlord
the full amount of any accrued Deferred Base Rent and Additional Deferred Base Rent, in which event the rent schedule set forth in the Original Lease shall again become effective. In such event, the parties shall promptly memorialize the change on
an amendment to the Lease.” 
  
 F. Early Reinstatement of
Rent. Paragraph D of the First Amendment is hereby deleted in its entirety and the following is substituted in lieu thereof: 
  
 “Early Reinstatement of Rent. In the event that Tenant shall successfully raise Seventy-Five Million Dollars ($75,000,000.00) in cash as a
result of a single public or private offering, the full amount of any accrued Deferred Base Rent and Additional Deferred Base Rent shall become immediately due and the rent schedule set forth in the Original Lease shall again become effective.
Tenant agrees that it shall give prompt written notice to Landlord of any such offering.” 
  
 G. Effect of Sublease. In the event that Tenant shall sublease all or any portion of the Premises, the rent schedule set forth in the Original Lease shall again become effective as to such subleased portion of
the Premises. In such event, the parties shall promptly memorialize the change on an amendment to the Lease, which amendment shall include an adjustment to the calculations of Deferred Base Rent and/or Additional Deferred Base Rent to reflect any
change in the amounts thereof caused by the return of the subleased portion of the Premises to the rent schedule set forth in the Original Lease. Nothing in this paragraph shall be deemed to modify or amend any restrictions or requirements set forth
in Article IX or otherwise applicable to the subleasing of the Premises by Tenant. 
  
 F. Security. Tenant and Guarantor understand that all terms and conditions of the Guarantee of Lease dated April 30, 2001 and executed by Dr. George B. Rathmann will remain in full force and effect, and the
terms and conditions of Paragraph F of the First Amendment will also remain in full force and effect notwithstanding the modifications set forth in this Amendment. 
  
 G. Broker’s Commission. Landlord shall not be responsible for the payment of any brokerage commissions or offer
any tenant improvement allowances in connection with this Amendment. 
  
 H. Lender Consent. Landlord hereby represents that no lender consent is required for this Amendment. 
  

	IV.	GENERAL. 

  
 A. Effect of Amendments. The Lease shall remain in full force and effect except to the extent that it is modified by this Amendment. 
  

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 B. Entire Agreement. This Amendment embodies the entire understanding between Landlord and Tenant
with respect to the modifications set forth in “III. MODIFICATIONS” above and can be changed only by a writing signed by Landlord and Tenant. 
  
 C. Authorization/Reasonably Equivalent Value: Tenant represents and warrants that in the execution of this Amendment, Tenant was not acting under
any misapprehension as to the effect hereof, and acted freely and voluntarily and was not acting under coercion or duress; that the execution of this Amendment was duly authorized by Tenant; and that Tenant believed and now believes that the
consideration given by each party for this Amendment represents reasonably equivalent value. 
  
 D. Solvency of Tenant: Tenant represents and warrants that it is not currently insolvent as that term is defined in section 101(32) of Title 11 of the United States Code, 11 U.S.C. §§ 101-1330,
nor will Tenant become insolvent as a result of this Amendment. 
  
 E. Amendment Improves Tenant’s Financial Position: Tenant represents and warrants that the completion of this Amendment will enhance Tenant’s overall financial position and that Tenant has proffered and requested this
Amendment to improve its financial position. 
  
 F.
Counterparts. If this Amendment is executed in counterparts, each is hereby declared to be an original; all, however, shall constitute but one and the same amendment. In any action or proceeding, any photographic, photostatic, or other copy
of this Amendment may be introduced into evidence without foundation. 
  
 G. Defined Terms. All words commencing with initial capital letters in this Amendment and defined in the Lease shall have the same meaning in this Amendment as in the Lease, unless they are otherwise defined in this Amendment.

  
 H. Authority. If Tenant is a corporation, limited
liability company or partnership, or is comprised of any of them, each individual executing this Amendment for the corporation, limited liability company or partnership represents that he or she is duly authorized to execute and deliver this
Amendment on behalf of such entity and that this Amendment is binding upon such entity in accordance with its terms. 
  
 I. Attorneys’ Fees. The provisions of the Lease respecting payment of attorneys’ fees shall also apply to this Amendment. 
  

	V.	EXECUTION. 

  
 Landlord and Tenant executed this Amendment on the date as set forth in “I. PARTIES AND DATE.” above. 
  
 [LEGAL APPROVAL STAMP] 
  

	 LANDLORD:
  
 THE IRVINE COMPANY
	 	 	 	 TENANT
  
 NUVELO, INC.

					
	By	 	/s/    William R. Halford        	 	 	 	By	 	/s/    Ted W. Love        
	 	
	 	 	 	 	

	 Name
	 	 William R. Halford
	 	 	 	 Name
	 	 Ted W. Love

	 Title
	 	 President
	 	 	 	 Title
	 	 President & CEO

	 	 	 Office Properties
	 	 	 	 	 	 
	 	 	 	 	 
					
	By	 	/s/    Donald S. McNutt        	 	 	 	By	 	/s/    Peter S. Garcia        
	 	
	 	 	 	 	

	 Name
	 	 Donald S. McNutt
	 	 	 	 Name
	 	 Peter S. Garcia

	 Title
	 	 Senior Vice President
	 	 	 	 Title
	 	 Sr. VP & CFO

	 	 	 Office Properties
	 	 	 	 	 	 

  

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 ACKNOWLEDGMENT OF GUARANTOR 
  
 The undersigned, as Guarantor under that certain Guarantee of Lease dated April 30, 2001, does hereby acknowledge and agree
that the provisions of said Guarantee shall remain in full force and effect as to the obligations of Tenant under the Lease, as amended herein. The undersigned Guarantor acknowledges that Landlord would not have executed this Amendment without this
acknowledgment and agreement on the part of the undersigned Guarantor. 
  
 GUARANTOR: 
  

	
	/s/    George B. Rathmann        
	

	 Dr. George B. Rathmann

  

 4Assignment and Assumption of Lease by and between the Company and Identix, Inc.

 EXHIBIT 10.2 
  
 ASSIGNMENT AND ASSUMPTION OF LEASE 
  
 THIS ASSIGNMENT AND ASSUMPTION OF LEASE (this “Assignment”) is entered into as of the 28 day of October,
2003 (the “Effective Date”), by NUVELO, INC., a Nevada corporation, successor by merger to Variagenics, Inc., a Delaware corporation (“Assignor”), and IDENIX PHARMACEUTICALS, INC., a Delaware corporation
(“Assignee”). 
  
 Recitals 
  
 A. BHX, LLC, a Massachusetts limited liability company, as Trustee of 205
Broadway Realty Trust (“Landlord”), and Assignor are parties to a Lease dated May 15, 1998 (the “Lease”), pursuant to which Landlord leased to Assignor, and Assignor leased from Landlord, the entire Building owned
by Landlord located at and known as 205 Broadway, Cambridge, Massachusetts, now known as 60 Hampshire Street, Cambridge, Massachusetts. All capitalized terms used in this Assignment which are defined in the Lease and not otherwise defined in this
Assignment shall have the meanings given in the Lease. 
  
 B.
Assignor desires to assign its right, title and interest in and to the Lease to Assignee, and Assignee desires to accept such assignment and to assume the obligations of Assignor under the Lease on and subject to the terms and conditions set forth
herein. 
  
 Statement of Assignment and Assumption

  
 In consideration of the mutual covenants and agreements set
forth herein, Assignor and Assignee hereby agree as follows: 
  
 l. Assignment and Assumption. Assignor assigns all of Assignor’s right, title and interest in and to the Lease to Assignee, on and subject to the terms and conditions set forth herein. Assignee accepts such assignment and
assumes the obligations of Assignor under the Lease, on and subject to the terms and conditions set forth herein. 
  
 2. Delivery of Premises and FF&E. Assignor shall deliver possession of the Premises to Assignee on the Effective Date, decommissioned in
accordance with the decommissioning requirements set forth in Exhibit A hereto, and with the furniture, fixtures and equipment identified in Exhibit B hereto located in the Premises. Subject to satisfaction with the decommissioning
requirements set forth in Exhibit A hereto. Assignee accepts the Premises from Assignor in its “as is” condition, without any representation or warranty from Assignor. Contemporaneously with the execution of this Assignment,
Assignor shall execute and deliver to Assignee a bill of sale for the FF&E, thereby transferring the FF&E to Assignee, as is, without any warranty other than a warranty as to title. 
  
 3. Tenant Improvements; Allowance. It is understood that the Premises
are not presently suitable for Assignee’s intended use, and that substantial alterations need to be made to prepare the Premises for Assignee’s use. Assignor shall provide the sum of $1,500,000 (the “Allowance”) to pay or
reimburse Assignee for costs of such alterations and improvements. Assignor shall pay the Allowance to LandAmerica Financial Group, Inc. (“LandAmerica”), to be held in escrow by LandAmerica and disbursed by LandAmerica in accordance
with the terms and conditions of an Escrow Agreement entered into contemporaneously herewith by Assignor, Assignee and LandAmerica. The Allowance shall be paid to LandAmerica through an assignment by Landlord to LandAmerica of the letter of credit
(the “Letter of Credit”) posted by Assignor with Landlord as the security deposit under the Lease and by LandAmerica drawing on the Letter of Credit in accordance with the Escrow Agreement. Assignor and Assignee shall authorize and
direct LandAmerica to draw on the Letter of Credit for the purpose of funding the Allowance, even though an Event of Default does not presently exist under the Lease. The process for payment of the Allowance to LandAmerica shall commence on the
Effective Date, by Landlord forwarding the Letter of Credit to the issuing bank for endorsement with written instructions to assign the Letter of Credit to LandAmerica, and shall be completed as soon as practical after the Effective 

  

 
Date. If Assignee does not use the entire Allowance to pay costs of alterations and improvements to the Premises (that is, the cost of the alterations and
improvements is less than $1,500,000), the unused portion of the Allowance shall be returned by LandAmerica to Assignor after completion of the alterations and improvements and payment of all costs thereof. 
  
 4. Landlord Consent. As a condition of this Assignment, Landlord shall
execute the Consent and Release by Landlord which appears at the end of this Assignment (the “Consent and Release”), thereby (a) consenting to this Assignment, (b) releasing Assignor from any obligations under the Lease or
the Amended Lease (as defined in Section 5) accruing on or after the Effective Date (subject, however, to Assignor’s obligations under this Assignment), (c) acknowledging that Assignee shall not be responsible for any obligations under the
Lease accruing prior to the Effective Date, (d) agreeing to assign the Letter of Credit to LandAmerica, provided that Assignor has delivered the Premises and the FF&E to Assignee in accordance with Section 2, and to execute such documents
reasonably required by the issuing bank to effect the assignment of the Letter of Credit, and (e) representing that Landlord has obtained such consent to this Assignment as is required from Landlord’s lender. In order to induce Landlord to
execute the Consent and Release, Assignee agrees to pay to Landlord the sum of $114,992.55 on each of October 1, 2003 and November 1, 2003. 
  
 5. Amendment and Restatement of Lease. As a condition of this Assignment, Landlord and Assignee shall, contemporaneously with the execution of this
Assignment, enter into an Amended and Restated Lease (the “Amended Lease”), pursuant to which the Lease is amended and restated in its entirety as of the Effective Date. 
  
 6. Performance of Obligations Under Lease. Assignor shall be responsible for the payment and performance of all of
the obligations of the tenant under the Lease accruing prior to the Effective Date, and shall indemnify and hold Assignee harmless from and against any and all liabilities, losses, damages and claims with respect to such obligations. Assignee shall
be responsible for the payment and performance of all of the obligations of the tenant under the Amended Lease accruing on or after the Effective Date, and shall indemnify and hold Assignor harmless from and against any and all liabilities, losses,
damages and claims with respect to such obligations. 
  
 7.
Brokers. Each of Assignor and Assignee represents to the other that it has not dealt with any broker or other commissionable agent in connection with this Assignment, other than Grubb & Ellis. Assignor shall pay and be responsible for any
commission owing to Grubb & Ellis in connection with this Assignment. 
  
 8. Third Party Beneficiary. In consideration for Landlord executing the Consent and Release, Landlord shall be a third party beneficiary of the obligations of Assignor and Assignee under this Assignment.

  
 9. Multiple Counterparts. This Assignment may be
executed in multiple counterparts, each of which will be an original, but all of which, taken together, will constitute one and the same Assignment. 
  
 IN WITNESS WHEREOF, Assignor and Assignee have executed this Assignment as of the Effective Date. 
  

	NUVELO, INC.
		
	By:	 	 /s/ Peter S. Garcia

	 	

	 Name:
	 	 Peter S. Garcia

	 Title:
	 	 Sr. VP & CFO

  

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	 IDENIX PHARMACEUTICALS, INC.

		
	By:	 	 
	 	

	 Name:
	 	  

	 Title:
	 	  

  
 CONSENT AND
RELEASE BY LANDLORD 
  
 In satisfaction of the condition set
forth in Section 4 of the above Assignment and Assumption of Lease (the “Assignment”), and in consideration of the covenants and agreements of Assignor and Assignee set forth in the Assignment, Landlord hereby (a) consents to the
Assignment, (b) releases Assignor from any obligations under the Lease or the Amended Lease accruing on or after the Effective Date (subject, however, to Assignor’s obligations under the Assignment), (c) acknowledge that Assignee shall not be
responsible for any obligations under the Lease accruing prior to the Effective Date, (d) agrees to assign the Letter of Credit to LandAmerica, provided that Assignor has delivered the Premises and the FF&E to Assignee in accordance with Section
2 of the Assignment, and to execute such documents reasonably required by the issuing bank to effect the assignment of the Letter of Credit, and (e) represents that Landlord has obtained such consent to the Assignment as is required from
Landlord’s lender. All capitalized terms used in this Consent and Release which are defined in the Assignment and not otherwise defined in this Consent and Release shall have the meanings given in the Assignment. 
  
 IN WITNESS WHEREOF, Landlord has executed this Consent and Release as of the
28 day of October, 2003. 
  

	BHX, LLC, as Trustee of 205 Broadway Realty Trust
		
	By:	 	 /s/ Robert A. Schlager

	 	

	 Name:
	 	 Robert A. Schlager

	 Title:
	 	 Member

  

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