exv10w1



 




Exhibit 10.1





FIRST AMENDMENT TO LEASE




     This
First Amendment to Lease (this “Amendment”), made as of March 16, 2006, by and between
ARE-MA REGION NO. 28, LLC, a Delaware limited
liability company (“Landlord”) and ALNYLAM
PHARMACEUTICALS, INC., a Delaware corporation (“Tenant”).



W I T N E S S E T H:




     WHEREAS, Landlord is the owner of certain land and improvements located at 300 Third Street,
Cambridge, Massachusetts (the “Building”); and



     WHEREAS, Landlord has leased certain space within the Building including, but not limited to,
certain space on the third and fourth floors of the Building to Tenant pursuant to a certain Lease
dated as of September 26, 2003 (the “Original
Lease”) between Landlord’s predecessor in interest,
Three Hundred Third Street LLC, and Alnylam U.S., Inc., a
Delaware corporation that is a subsidiary of Tenant and was formerly known as Alnylam
Pharmaceuticals, Inc. (the “Original Tenant”), which Original Lease was assigned by the Original
Tenant to Tenant pursuant to an Assignment of Lease dated February 28, 2006, as more particularly
described in the Original Lease; and



     WHEREAS, Tenant desires to lease certain additional space on the fourth floor containing
approximately 17,823 square feet (the “Additional Premises”) and otherwise amend the Original
Lease in certain particulars; and



     WHEREAS, Landlord and Tenant have agreed to amend the Original Lease in certain particulars
to accomplish the foregoing and other matters set forth herein as more particularly provided
below.



     NOW, THEREFORE, in consideration of the foregoing premises and other good and valuable
consideration, the receipt and sufficiency of which are hereby acknowledged, the parties hereto
hereby covenant and agree as follows:



          1.    Defined Terms.



     All capitalized terms used and not otherwise defined herein shall have the respective
meanings ascribed to them in the Original Lease. In the event of any inconsistency between the
Original Lease and this Amendment, the provisions of this Amendment shall control, and all other
provisions of the Original Lease shall remain in full force and
effect. The Original Lease, as
amended by this Amendment, is hereinafter referred to as the “Lease”.



 









 





          2.    Additional Premises Commencement Date.



     The Effective Date and the Rent Commencement Date with respect to the Additional Premises
shall be July 1, 2006 (the “Additional Premises Commencement Date”).



          3.    Modifications to Original Lease. As of the Additional Premises Commencement
Date, the Original Lease is hereby modified as follows:




	 	(a)	 	Article 1D entitled “Premises” is hereby deleted in its entirety and
replaced with the following:






				
	 	D.    Premises:	 	Square feet (Rentable): A total of approximately 61,881 comprised of 32,537 square feet on Level 03
(the “Third Floor Premises”), 28,428 square feet on Level 04 (the “Fourth Floor Premises”), 366
square feet relating to the rooftop penthouse, 185 square feet relating to the acid neutralization
room and 365 square feet relating to the Level P-1 chemical storage room (the rooftop penthouse,
acid neutralization room and chemical storage room are hereinafter collectively referred to as the
“Peripheral Spaces”)






	 	(b)	 	Article 1F entitled “Landlord’s Address” is hereby deleted in its entirety and
replaced with the following:






				
	 	F.    Landlord’s Address:	 	c/o Cornerstone Real Estate Advisers LLC

Suite 401

180 Glastonbury Boulevard

Glastonbury, Connecticut 06033

Attention: Northeast Regional Director

 

And a copy to: Attention: David Romano,

           Vice President, Asset Manager






	 	(c)	 	Article 1K entitled “Monthly Rent” is hereby amended to add the following:






Monthly Rent for the Additional Premises:



	 	 	 	 	 	 
	 
	 	PERIOD	 	 	MONTHLY RENT	 
	 	July 1, 2006 — June 30, 2007
	 	 	$8,874.37	 
	 	July 1, 2007 — September 2011
	 	 	$17,748.74	 
	 





2









 







	 	(d)	 	Article 1R entitled “Parking Fee/Parking Spaces” is hereby amended to
delete the number “45” and substitute the number “55” in lieu thereof for
the period July 1, 2006 through June 30, 2007, and substitute the number
“65” in lieu thereof for the period from July 1, 2007 through the remainder
of the Term.
	 
	 	(e)	 	Article 4A is hereby amended to provide that, notwithstanding anything
contained herein to the contrary, Tenant shall have no obligation to pay
Tenant’s Pro Rata Share of Operating Expenses or Taxes attributable to fifty
percent (50%) of the Additional Premises during the period July 1, 2006
through and including June 30, 2007.
	 
	 	(f)	 	Article 30 is hereby amended to delete the following:
	 
	 	 	 	Joel R. Bloom, Esq.

Mintz Levin Cohn Ferris Glovsky and Popeo, PC

One Financial Center

Boston, MA 02111

	 
	 	 	 	and substitute the following in lieu thereof:
	 
	 	 	 	Joseph L. Faber

Faber Daeufer & Rosenberg PC

1050 Winter Street, Suite 1000

Waltham, MA 02451
	 
	 	(g)	 	Exhibit A of the Original Lease is hereby amended to add the Additional
Premises as more particularly shown on Exhibit A attached hereto.





          4.    Condition of Additional Premises. No promise of Landlord to alter, remodel,
repair or improve the Additional Premises and no representation, either expressed or implied,
respecting any matter or thing relating to the Additional Premises (including the condition of
the Additional Premises) has been made by Landlord to Tenant. Tenant shall perform the Tenant
Improvements to the Additional Premises in accordance with the terms and provisions contained
in Exhibit B hereto. The Additional Premises shall be taken “as is.” The taking of possession
of the Premises by Tenant shall conclusively establish that the Additional Premises were at such
time in satisfactory condition, subject to Landlord’s continuing obligations to provide
services pursuant to the terms of the Lease.



          5.    Ratification of Lease; Effect of Amendment. The Original Lease, as amended by
this Amendment, is hereby ratified and confirmed, and each and every provision, covenant,
condition, obligation, right and power contained in and under, or existing in connection with, the



3









 







Original Lease, as amended by this Amendment, shall continue in full force and effect
from and after the date hereof and throughout the Term. This Amendment is not intended to, and
shall not be construed to, effect a novation, and, except as expressly provided in this Amendment,
the Original Lease has not been modified, amended, canceled, terminated, surrendered, superseded
or otherwise rendered of no force and effect. Tenant acknowledges and agrees that the Original
Lease, as amended by this Amendment, is enforceable against Tenant in accordance with its terms.
The Original Lease and this Amendment shall be construed together as
a single instrument.



          6.    No Defaults, Counterclaims or Rights of Offset; Release of Landlord. Tenant
hereby warrants and represents that, to its knowledge, as of the date of the execution of this
Amendment by Tenant, there are no defaults under the Lease in respect of Landlord’s
performance thereunder and there exist no defenses, counterclaims or rights of offset with respect
thereto. Tenant, for itself, its officers, directors, members, shareholders and their respective legal
representatives, successors and assigns, does hereby absolutely and irrevocably waive, remise,
release and forever discharge Landlord, its successors, assigns, partners, employees,
affiliates, attorneys and agents, of and from, any and all manner of action and actions, cause and causes
of actions, suits, debts, dues, sums of money, accounts, reckoning, bonds, bills, specialties,
covenants, contracts, controversies, agreements, promises, variances, trespasses, damages, judgments,
extents, executions, claims and demands whatsoever, in law or in equity, for items or matters that
Tenant could have been aware of or known about, through and including the date of execution and
delivery of this Amendment in connection with or relating to the Lease or the transactions contemplated
hereby. Nothing contained in this paragraph shall be construed to release Tenant from its
obligations under the Lease throughout the Term of the Lease (including the Extended Term).



          7.    Brokers. Landlord and Tenant represent and warrant to each other that neither has
dealt with any broker, finder or agent in procuring this Amendment except for Meredith & Grew
(the “Broker”). Tenant and Landlord represent and warrant to each other that (except with
respect to the Broker, with whom Palm, Inc. has entered into a separate brokerage agreement and
Landlord shall have no liability or obligation to Broker whatsoever in connection therewith) no broker,
agent, commission salesperson, or other person has represented it in the negotiations for and
procurement of this Amendment and of the Additional Premises and that no commissions, fees, or
compensation of any kind are due and payable in connection herewith to any broker, agent, commission
salesperson, or other person. Tenant and Landlord agree to indemnify and hold harmless each
other, its agents, members, partners, representatives, officers, affiliates, shareholders,
employees, successors and assigns from and against any and all loss, liabilities, claims, suits, or
judgments (including, without limitation, reasonable attorneys’ fees and court costs incurred in
connection with any such claims, suits, or judgments, or in connection with the enforcement of this
indemnity) for any fees, commissions, or compensation of any kind which arise out of or are in any way
connected with any claimed agency relationship not referenced in this paragraph.



          8.    Successors and Assigns. This Amendment shall bind and inure to the benefit of the
parties hereto and their respective heirs, executors, administrators, legal representatives,
successors and assigns.



4









 





          9.    Counterparts. This Amendment may be executed in a number of identical
counterparts, each of which for all purposes shall be deemed to be an original, and all of
which shall collectively constitute but one agreement, fully binding upon, and enforceable against the
parties hereto.



          10.    Authority.



          (a)      Landlord represents and warrants that (i) the execution and delivery of this
Amendment by Landlord has been duly authorized; (ii) the individual executing this Amendment
on behalf of Landlord is duly authorized and empowered to do so and to bind Landlord
accordingly; (iii) the Landlord named herein is the holder of the interest of “Landlord” under
the Lease and has the full right, power and authority to enter into this Amendment; and (iv)
Landlord has obtained all consents, approvals or joinders of any third parties as are required in order
for Landlord to enter into, perform and give full force and effect to this Amendment



          (b)      Tenant represents and warrants that (i) the execution and delivery of this
Amendment by Tenant has been duly authorized; (ii) the individual executing this Amendment
on behalf of Tenant is duly authorized and empowered to do so and to bind Tenant accordingly;
(iii) the Tenant named herein is the holder of the interest of “Tenant” under the Lease and
has the full right, power and authority to enter into this Amendment; and (iv) Tenant has obtained all
consents, approvals or joinders of any third parties as are required in order for Tenant to
enter into, perform and give full force and effect to this Amendment.



REMAINDER OF PAGE INTENTIONALLY LEFT BLANK

SIGNATURES APPEAR THE FOLLOWING PAGE




5









 







     IN WITNESS WHEREOF, the parties hereto have executed this First Amendment as of the day
and year first written above.






	 	 	TENANT:
	 
	 	 	ALNYLAM PHARMACEUTICALS, INC.	 
	 
	 	   	By:	   	/s/
Patricia L. Allen
	 
	 	   	Name:	   	Patricia
L. Allen
	 
	 	  	Title:	  	VP,
Finance & Treasurer
	  
	 	  	Date as of:	  	3/16/06
	 







LANDLORD:



ARE-MA
REGION NO. 28, LLC,
a Delaware limited liability company




	 	 	By:  	Alexandria Real Estate Equities, L.P.,
a Delaware limited
liability company, its member






	 	 	By:  	ARE-QRS Corp., a Maryland corporation,

Its general partner






	 	 	 	 	 
	 	 	 
	 	By:  	/s/
Jennifer Pappas	 
	 	 	Name:  	Jennifer Pappas 	 
	 	 	Title:  	V.P. & Assistant Secretary	 
	 	 	Date:  3/16/06	 	 









6









 






	 	 	 	 	 



EXHIBIT
A


Additional Premises




[Graphical Depiction of Floor Plan of Additional Premises Appears Here]




 


 


 


 


 


 


 


 


 


 


 


A-1




 









 








EXHIBIT B




Tenant’s Work





     1.    (a)    Tenant shall, at such time as Tenant is prepared to so do (the “Plan Submission
Date”), at Tenant’s expense, submit to Landlord final and complete dimensioned and detailed
plans and drawings of partition layouts (including openings), ceiling and lighting layouts, colors,
mechanical and electrical circuitry plans and any and all other information as may be reasonably
necessary to complete the construction of the Additional Premises in accordance with this
Exhibit B (such plans are collectively referred to herein as “Tenant’s Plans”). The
partition layout, and ceiling and lighting layout plans shall be
1'0" = 1/8" scale. Tenant shall
submit Tenant’s Plans and any other plans required by this Exhibit B to Landlord in form,
quality and quantity acceptable for the purposes of filing for a building permit with the Building
Department of the City, and such plans shall be signed and sealed by an architect licensed in the
Commonwealth of Massachusetts;



          
 (b)    Landlord shall approve Tenant’s Plans as soon as reasonably possible or
designate by notice to Tenant the specific changes required to be made to Tenant’s Plans,
which Tenant shall make within three (3) business days of receipt. This procedure shall be repeated
until Tenant’s Plans are finally approved by Landlord.



          
 (c)    Any architect or designer acting for or on behalf of Tenant shall be
deemed an agent of and authorized to bind Tenant in all respects.



          
 (d)    All plans, drawings and specifications with respect to the Additional
Premises required to be submitted by Tenant to Landlord shall comply with and conform to the
Building plans filed with the Department of Buildings, Building standard specifications (the
receipt of which Tenant hereby acknowledges) and with all the rules, regulations and/or other
requirements of any governmental department having jurisdiction over the construction of the
Building and/or Additional Premises. Tenant shall prepare drawings in accordance with pre-existing conditions and field measurements.



          
 (e)    Landlord’s review of Tenant’s Plans is solely to protect the interests of
Landlord in the Building and the Additional Premises, and Landlord shall be neither the
guarantor of, nor responsible for, the correctness or accuracy of Tenant’s Plans, or the
compliance of Tenant’s Plans with applicable requirements of any governmental authority.
Landlord’s review and approval of any submissions shall not be deemed to be an approval of the
adequacy for any particular purpose or system capacity or the cost of the Tenant Improvements.



          
 (f)    Tenant shall reimburse Landlord for actual costs incurred by Landlord to
approve all submissions submitted pursuant to this Exhibit B.



     2.    (a)    Tenant shall, at its expense (except for the Allowance), in accordance with the terms
and conditions of this Exhibit B. be responsible for the construction of all improvements
and alterations necessary to prepare the Additional Premises to conform with Tenant’s Plans (the
“Tenant Improvements”). After completion of Tenant’s Plans, Tenant shall submit Tenant’s
Plans to the appropriate governmental body for plan checking and a building permit. Tenant
shall deliver a copy of the building permit to Landlord prior to the



 









 








commencement of construction of the Tenant Improvements. Tenant shall not make any changes
to Tenant’s Plans once finally approved by Landlord without Landlord’s consent.



          
 (b)    Tenant shall select a contractor (the “Contractor”), subject to the
approval of Landlord, which approval will not be unreasonably withheld and shall be granted or
denied within 15 calendar days of request for such approval. With its request for approval of
the Contractor, Tenant shall furnish to Landlord such information concerning the proposed
Contractor’s background and experience as Landlord may reasonably require. A price for a
construction contract based on Tenant’s Plans shall be mutually agreed upon by Tenant and the
Contractor. Tenant shall enter into an agreement with the Contractor to build the Tenant
Improvements, at Tenant’s sole cost, except for the Allowance. Notwithstanding anything
contained herein to the contrary, Tenant shall be required to use AHA Consultants for any
engineering of Tenant Improvements related to mechanical, electrical or plumbing work.



          The construction contract will provide for progress payments, no more frequently than once per
calendar month, in minimum increments of $25,000.00, and each progress payment will be funded as
follows: Landlord will fund the percentage of each progress payment equal to a fraction expressed
as a percentage, the numerator of which is the Allowance and the denominator of which is the total
cost of the Tenant Improvements; and Tenant will fund the remainder. Ten percent (10%) of each
progress payment shall be retained by Landlord until Tenant delivers, or causes to be delivered, to
Landlord a certificate of occupancy or certificate of completion, in form and substance reasonably
satisfactory to Landlord, with respect to the Additional Premises together with final and
unconditional waivers of mechanic’s liens concerning the work for all labor and services performed
and all material furnished in connection with the work, signed by the Contractor and all
subcontractors, suppliers, and laborers involved in the work. Notwithstanding anything contained
herein or in the Lease to the contrary, Landlord shall have no obligation to disburse any portion
of the Allowance during any period of time that Tenant is in default of its obligations under the
Lease or upon or following termination of the Lease.



          
 (c)    If the cost of the design and construction of the Tenant Improvements is
less than the Allowance, the difference shall be retained by Landlord. In the event that
Tenant requests any changes to Tenant’s Plans, Landlord shall not unreasonably withhold its consent
to any such changes, provided the changes do not adversely affect the Building’s structure,
systems, equipment or appearance, but if such changes increase the cost of constructing the Tenant
Improvements shown on Tenant’s Plans, Tenant shall pay such increased costs to the Contractor
when the request is approved by Landlord.



          
 (d)    The Allowance will be applied to the construction of the Tenant
Improvements, related design and engineering costs and for no other purpose. The Allowance
shall be an amount equal to $445,575.00 (the “Allowance”). All costs attributable to
the Tenant Improvements in excess of the Allowance shall be paid for by Tenant.



     3.    (a)    Before beginning the Tenant Improvements, Tenant shall pay for and deliver to Landlord
policies and certificates of insurance in amounts and with such companies as shall be reasonably
satisfactory to Landlord, such as, but not limited to Public Liability, Property Damage and
Workmen’s Compensation, to protect Landlord and Tenant during the period of performing the Tenant
Improvements. Landlord and the Contractor shall be named as insured parties in such policies or
certificates of insurance and the same shall remain in effect during the period of the performance
of the Tenant Improvements.



B-2




 









 








          
 (b)    All the Tenant Improvements shall be in accordance with the rules and
regulations of any governmental department or bureau having jurisdiction thereover and shall
not conflict with, or be in violation or cause any violation of, Landlord’s basic Building plans
and/or the construction of the Building, and all the Tenant Improvements shall be completed free of
all liens and encumbrances. All permits which may be required by Tenant for the Tenant
Improvements shall be procured and paid for by Tenant or, if Landlord shall deem the same
advisable, Landlord may procure such permits and Tenant shall pay for the same. No plans
and/or specifications required to be filed by Tenant pursuant to any work contemplated to be
performed by it within the Additional Premises shall be filed or submitted to any governmental
authority having jurisdiction thereover without first having obtained Landlord’s approval of
same.



          
 (c)    Upon completion of the Tenant Improvements, Tenant will remove all
debris and excess materials from the Building and the Additional Premises.



          
 (d)    The labor employed by Tenant or the Contractor shall always be
harmonious and compatible with the labor employed by Landlord or any
contractors or sub-contractors of Landlord. Should such labor be incompatible with such Landlord’s labor as shall
be determined by the sole judgment of Landlord, to be exercised in good faith, Landlord may
require Tenant to withdraw from the Additional Premises until the completion of work by
Landlord.



          
 (e)    In the event Tenant or the Contractor shall enter upon the Additional
Premises or any other part of the Building, as may be permitted by Landlord, Tenant shall
indemnify and save Landlord free and harmless from and against any and all claims arising from
or out of any entry thereon or the performance of the Tenant Improvements and from and against
any and all claims arising from or claimed to arise from any act or neglect of Tenant or
Tenant’s representatives or from any failure to act, or for any other reason whatsoever arising out of
said entry or such work.



          
 (f)    Tenant Improvements which Landlord reasonably determines are specialized to Tenant’s use
and occupancy of the Additional Premises including, without limitation, wiring and cabling shall,
at the election of Landlord, either (1) be removed by Tenant at its expense before the expiration
or earlier termination of the term of the Lease or (2) remain upon the Additional Premises and be
surrendered therewith without disturbance, molestation or injury upon the expiration or earlier
termination of the Lease. If Landlord requires the removal of all or part of the specialized
Tenant Improvements, Tenant, at its expense, shall repair any damage to the Additional Premises or
the Building caused by such removal. If Tenant fails to remove any specialized Tenant Improvements
upon Landlord’s request, then Landlord may (but shall not be obligated to) remove the same and the
cost of such removal and repair of any damage caused by the same, together with any and all
damages which Landlord may suffer and sustain by reason of the failure of Tenant to remove the
same, shall be charged to Tenant and paid upon demand.



     4.    Tenant accepts the Additional Premises in its “as is” condition and acknowledges that it
has had an opportunity to inspect the Additional Premises. In no event shall Tenant be eligible to
receive or entitled to any credit for any portion of the Allowance not used by Tenant by July 31,
2008. Tenant shall be responsible for the maintenance, repair and



B-3




 









 








replacement of all Tenant Improvements unless the same is necessitated by the negligent acts
of Landlord.



     5. Tenant hereby authorizes David M. Konys as Tenant’s representative to
act on its behalf and represent its interests with respect to all matters which pertain to the
construction of Tenant Improvements, and to make decisions binding upon Tenant with respect
to such matters. Landlord hereby authorizes William Byrne to be Landlord’s representative in
connection with construction of the Tenant Improvements. Tenant hereby expressly recognizes
and agrees that no other person claiming to act on behalf of the Landlord is authorized to do
so, and any costs, expenses liabilities or obligations incurred or paid by Tenant in reliance on
the discretion of any such other person shall be Tenant’s sole responsibility.



     6.    In the event of a conflict between the terms and provisions of the Lease
and the terms and provisions of this Exhibit, the terms and provisions of this Exhibit shall
control.



B-4




 









 








ASSIGNMENT OF LEASE




     FOR VALUE RECEIVED, the receipt and sufficiency of which are hereby acknowledged, Alnylam
U.S., Inc. f/k/a Alnylam Pharmaceuticals, Inc., having a principal address of 300 Third Street,
Cambridge, Massachusetts (“Assignor”), hereby assigns to the Alnylam Pharmaceuticals, Inc., its
parent, having a principal address of 300 Third Street, Cambridge, Massachusetts (“Assignee”), that
certain Lease (the “Lease”) dated as of September 26, 2003, by and between Three Hundred Third
Street, LLC, as Lessor, and the Assignor, as Lessee, relating to premises located in 300 Third
Street, Cambridge, Massachusetts, as described in the Lease, a Notice of which is filed and
recorded with the Middlesex South Registry of Deeds recorded in Book 41095, Page 076.



     Further, Assignee hereby accepts such assignment and assumes all of Lessee’s obligations under
the Lease.



     This Assignment of Lease shall inure to the benefit of and be binding upon Assignor and
Assignee and their respective successors and assigns.



     EXECUTED as an instrument under seal as of the 28th day of February, 2006.



 









 





	 	 	 	 	 
	ASSIGNEE:

	 	ASSIGNOR:
	 	 
	 
	 	 	 	 
	ALNYLAM PHARMACEUTICALS, INC.

	 	ALNYLAM U.S., INC.

f/k/a Alnylam Pharmaceuticals, Inc.	 	 
	 
	 	 	 	 
	By: /s/ Patricia L. Allen


	 	By: /s/ Patricia L. Allen
	 	 
	 

	 	 	 	 
	Name: Patricia L. Allen

Title VP, Finance & Treasurer

	 	Name: Patricia L. Allen

Title: Treasurer	 	 






COMMONWEALTH OF MASSACHUSETTS




			
	Middlesex, ss
	 	March 1, 2006               






     Before me, the undersigned notary public, personally appeared Patricia Allen, VP Finance &
Treasurer, whose name is signed on the preceding document, and such person acknowledged to me that
he signed such document voluntarily for its stated purpose. The identity of such person was proved
to me through satisfactory evidence of identification, which was [_] photographic identification
with signature issued by a federal or state governmental agency, [_] oath or affirmation of a
credible witness, or [x] personal knowledge of the undersigned,



/s/ Ann M. Saitta                         

Notary Public

My Commission Expires: March 7, 2008




COMMONWEALTH OF MASSACHUSETTS




			
	Middlesex, ss
	 	March 1, 2006               






     Before me, the undersigned notary public, personally appeared Patricia Allen, Treasurer, whose
name is signed on the preceding document, and such person acknowledged to me that he signed such
document voluntarily for its stated purpose. The identity of such person was proved to me through
satisfactory evidence of identification, which was [_] photographic identification with signature
issued by a federal or state governmental agency, [_] oath or affirmation of a credible witness, or
[x] personal knowledge of the undersigned,



/s/ Ann M. Saitta                

Notary Public

My Commission Expires: March 7, 2008