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Exhibit 10.3    
    

 
 

MASTER SECURITY AGREEMENT
  dated as of June 9, 2006 ("Agreement")    
    

        THIS AGREEMENT is between General Electric Capital Corporation (together with its successors and assigns, if any,
"Secured Party") and Helicos BioSciences Corporation ("Debtor"). Secured Party has an office at 83 Wooster Heights Road, Danbury, CT 06810. Debtor is a corporation organized and existing under the
laws of the state of Delaware ("the State"). Debtor's mailing address and chief place of business is One Kendall Square, Building 200, Cambridge, MA 02139. 

1.     CREATION OF SECURITY INTEREST.  

        Debtor grants to Secured Party, its successors and assigns, a security interest in and against all property listed on any collateral schedule now or in the future
annexed to or made a part of this Agreement ("Collateral Schedule"), and in and against all additions, attachments, accessories and accessions to such property, all substitutions, replacements or
exchanges therefor, and all insurance and/or other proceeds thereof (all such property is individually and collectively called the "Collateral"). This security interest is given to secure the payment
and performance of all debts, obligations and liabilities of any kind whatsoever of Debtor to Secured Party, now existing or arising in the future, including but not limited to the payment and
performance of certain Promissory Notes from time to time identified on any Collateral Schedule (collectively "Notes" and each a "Note"), and any renewals, extensions and modifications of such debts,
obligations and liabilities (such Notes, debts, obligations and liabilities are called the "Indebtedness"). 

2.     REPRESENTATIONS, WARRANTIES AND COVENANTS OF DEBTOR.  

        Debtor represents, warrants and covenants as of the date of this Agreement and as of the date of each Collateral Schedule that: 

        (a)   Debtor's
exact legal name is as set forth in the preamble of this Agreement and Debtor is, and will remain, duly organized, existing and in good standing under the laws
of the State set forth in the preamble of this Agreement, has its chief executive offices at the location specified in the preamble, and is, and will remain, duly qualified and licensed in every
jurisdiction wherever necessary to carry on its business and operations, except where the failure to be so qualified would not have a Material Adverse Effect (as hereinafter defined); 

        (b)   Debtor
has adequate power and capacity to enter into, and to perform its obligations under this Agreement, each Note and any other documents evidencing, or given in
connection with, any of the Indebtedness (all of the foregoing are called the "Debt Documents"); 

        (c)   This
Agreement and the other Debt Documents have been duly authorized, executed and delivered by Debtor and constitute legal, valid and binding agreements enforceable in
accordance with their terms, except to the extent that the enforcement of remedies may be limited under applicable bankruptcy and insolvency laws or general equitable principles; 

        (d)   No
approval, consent or withholding of objections is required from any governmental authority or instrumentality with respect to the entry into, or performance by Debtor
of any of the Debt Documents, except any already obtained; 

        (e)   The
entry into, and performance by, Debtor of the Debt Documents will not (i) violate any of the organizational documents of Debtor or any judgment, order, law or
regulation applicable to Debtor, or (ii) result in any breach of or constitute a default in any material respect under any contract to which Debtor is a parry, or result in the creation of any
lien, claim or encumbrance on any of 

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Debtor's
property (except for liens in favor of Secured Party) pursuant to any indenture, mortgage, deed of trust, bank loan, credit agreement, or other agreement or instrument to which Debtor is a
party; 

        (f)    There
are no suits or proceedings pending in court or before any commission, board or other administrative agency against or affecting Debtor which could, in the
aggregate, have a material adverse effect on Debtor, its business or operations, or its ability to perform its obligations under the Debt Documents (a "Material Adverse Effect"), nor does Debtor have
reason to believe that any such suits or proceedings are threatened; 

        (g)   All
financial statements delivered to Secured Party in connection with the indebtedness have been prepared in accordance with generally accepted accounting principles,
and since the date of the most recent financial statement, there has been no material adverse change in Debtors financial condition; 

        (h)   The
Collateral is not, and will not be, used by Debtor for personal, family or household purposes; 

        (i)    The
Collateral is, and will remain, in good condition and repair, normal wear and tear excepted, and Debtor will not be negligent in its care and use; 

        (j)    Debtor
is, and will remain, the sole and lawful owner, and in possession of, the Collateral, and has the sole right and lawful authority to grant the security interest
described in this Agreement; 

        (k)   The
Collateral is, and will remain, free and clear of all liens, claims and encumbrances of any kind whatsoever, except for (i) liens in favor of Secured Party,
(ii) liens for taxes not yet due or for taxes being contested in good faith and which do not involve, in the judgment of Secured Party, any risk of the sale, forfeiture or loss of any of the
Collateral, and (iii) inchoate materialmen's, mechanic's, repairmen's and similar liens arising by operation of law in the normal course of business for amounts which are not delinquent (all of
such liens are called "Permitted Liens"); 

        (l)    Debtor
is and will remain in compliance in all material respects with all laws and regulations applicable to it including, without limitation, (i) ensuring that
no person who owns a controlling interest in or otherwise controls Debtor is or shall be (Y) listed on the Specially Designated Nationals and Blocked Person List maintained by the Office of
Foreign Assets Control ("OFAC"), Department of the Treasury, and/or any other similar lists maintained by OFAC pursuant to any authorizing statute, Executive Order or regulation or (Z) a person
designated under Section 1(b), (c) or (d) of Executive Order No. 13224 (September 23, 2001), any related enabling legislation or any other similar Executive Orders,
and (ii) compliance with all applicable Bank Secrecy Act ("BSA") laws, regulations and government guidance on BSA compliance and on the prevention and detection of money laundering violations;
and 

3.     COLLATERAL.  

        (a)   Until
the declaration of any default hereunder, Debtor shall remain in possession of the Collateral; except that Secured Party shall have the right to possess
(i) any chattel paper or instrument that constitutes a part of the Collateral, and (ii) any other Collateral in which Secured Party's security interest may be perfected only by
possession. Secured Party may inspect any of the Collateral during normal business hours after giving Debtor reasonable prior notice. If Secured Party asks, Debtor will promptly notify Secured Party
in writing of the location of any Collateral. 

        (b)   Debtor
shall (i) use the Collateral only in its trade or business, (ii) maintain all of the Collateral in good operating order and repair, normal wear and
tear excepted, (iii) use and maintain the Collateral only in compliance with manufacturers recommendations and all applicable laws, and 

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(iv) keep
all of the Collateral free and clear of all liens, claims and encumbrances (except for Permitted Liens). 

        (c)   Secured
Party does not authorize and Debtor agrees it shall not (i) part with possession of any of the Collateral (except to Secured Party or for maintenance and
repair), (ii) remove any of the Collateral from the continental United States, or (iii) sell, rent, lease, mortgage, license, grant a security interest in or otherwise transfer or
encumber (except for Permitted Liens) any of the Collateral, other than the disposition by Debtor in the ordinary course of its business of obsolete or worn-out equipment, to be limited to
a maximum $100,000 annually. 

        (d)   Debtor
shall pay promptly when due all taxes, license fees, assessments and public and private charges levied or assessed on any of the Collateral, on its use, or on
this Agreement or any of the other Debt Documents. At its option, Secured Party may discharge taxes, liens, security interests or other encumbrances at any time levied or placed on the Collateral and
may pay for the maintenance, insurance and preservation of the Collateral and effect compliance with the terms of this Agreement or any of the other Debt Documents. Debtor agrees to reimburse Secured
Party, on demand, all costs and expenses incurred by Secured Party in connection with such payment or performance and agrees that such reimbursement obligation shall constitute Indebtedness. 

        (e)   Debtor
shall, at all times, keep accurate and complete records of the Collateral, and Secured Party shall have the right to inspect and make copies of all of Debtor's
books and records relating to the Collateral during normal business hours, after giving Debtor reasonable prior notice. 

        (f)    Debtor
agrees and acknowledges that any third person who may at any time possess all or any portion of the Collateral shall be deemed to hold, and shall hold, the
Collateral as the agent of, and as pledge holder for, Secured Party. Secured Party may at any time give notice to any third person described in the preceding sentence that such third person is holding
the Collateral as the agent of, and as pledge holder for, the Secured Party. 

4.     INSURANCE.  

        (a)   Debtor
shall at all times hear the entire risk of any loss, theft, damage to, or destruction of, any of the Collateral (other than Collateral in Secured Party's
possession) from any cause whatsoever. 

        (b)   Debtor
agrees to keep the Collateral insured against loss or damage by fire and extended coverage perils, theft, burglary, and for any or all Collateral which are
vehicles, for risk of loss by collision, and if requested by Secured Party, against such other risks as Secured Party may reasonably require. The insurance coverage shall be in an amount no less than
the full replacement value of the Collateral, and deductible amounts, insurers and policies shall be acceptable to Secured Party. Debtor shall deliver to Secured Party upon request policies or
certificates of insurance evidencing such coverage. Each policy shall name Secured Party as a loss payee, shall provide for coverage to Secured Party regardless of the breach by Debtor of any warranty
or representation made therein, shall not be subject to co-insurance, and shall provide that coverage may not be canceled or altered by the insurer except upon thirty (30) days
prior written notice to Secured Party. Debtor appoints Secured Party as its attorney-in-fact to make proof of loss, claim for insurance and adjustments with insurers, and to
receive payment of and execute or endorse all documents, checks or drafts in connection with insurance payments. Secured Party shall not act as Debtor's attorney-in-fact unless
Debtor is in default hereunder. Proceeds of insurance shall be applied, at the option of Secured Party, to repair or replace the Collateral or to reduce any of the Indebtedness. 

5.     REPORTS.  

        (a)   Debtor
shall promptly notify Secured Party of (i) any change in the name of Debtor, (ii) any change in the state of its incorporation, organization or
registration, (iii) any relocation of its chief 

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executive
offices, (iv) any relocation of any of the Collateral, (v) any of the Collateral being lost, stolen, missing, destroyed, materially damaged or worn out, or (vi) any
lien, claim or encumbrance other than Permitted Liens attaching to or being made against any of the Collateral. 

        (b)   Debtor
will deliver to Secured Party financial statements as follows. If Debtor is a privately held company, then Debtor agrees to provide monthly financial statements,
certified by Debtor's president or chief financial officer including a balance sheet, statement of operations and cash flow statement within 30 days of each month end and its complete audited
annual financial statements, certified by a recognized firm of certified public accountants, within 120 days of fiscal year end or at such time as Debtor's Board of Directors receives the
audit. If Debtor is a publicly held company, then Debtor agrees to provide quarterly unaudited statements and annual audited statements, certified by a recognized firm of certified public accountants,
within 10 days after the statements are provided to the Securities and Exchange Commission ("SEC"). All such statements are to be prepared using generally accepted accounting principles
("GAAP") and, if Debtor is a publicly held company, are to he in compliance with SEC requirements. 

6.     FURTHER ASSURANCES.  

        (a)   Debtor
shall, upon request of Secured Party, furnish to Secured Party such further information, execute and deliver to Secured Party such documents and instruments
(including, without limitation, Uniform Commercial Code financing statements) and shall do such other acts and things as Secured Party may at any time reasonably request relating to the perfection or
protection of the security interest created by this Agreement or for the purpose of carrying out the intent of this Agreement. Without limiting the foregoing, Debtor shall cooperate and do all acts
deemed necessary or advisable by Secured Party to continue in Secured Party a perfected first security interest in the Collateral, and shall obtain and furnish to Secured Party any subordinations,
releases, landlord waivers, lessor waivers, mortgagee waivers, or control agreements, and similar documents as may be from time to time reasonably requested by, and in form and substance reasonably
satisfactory to, Secured Party. 

        (b)   Debtor
authorizes Secured Party to file a financing statement and amendments thereto describing the Collateral and containing any other information required by
the applicable Uniform Commercial Code. Debtor irrevocably grants to Secured Party the power to sign Debtor's name and generally to act on behalf of Debtor to execute and file applications for title,
transfers of title, financing statements, notices of lien and other documents pertaining to any or all of the Collateral; this power is coupled with Secured Party's interest in the Collateral. Debtor
shall, if any certificate of title be required or permitted by law for any of the Collateral, obtain and promptly deliver to Secured Party such certificate showing the lien of this Agreement with
respect to the Collateral. Debtor ratifies its prior authorization for Secured Party to file financing statements and amendments thereto describing the Collateral and containing any other information
required by the Uniform Commercial Code if filed prior to the date hereof. 

        (c)   Debtor
shall indemnify and defend the Secured Party, its successors and assigns, and their respective directors, officers and employees, from and against all claims,
actions and suits (including, without limitation, related attorneys fees) of any kind whatsoever arising, directly or indirectly, in connection with any of the Collateral. 

7.     DEFAULT AND REMEDIES.  

        (a)   Debtor
shall he in default under this Agreement and each of the other Debt Documents if: 

        (i)    Debtor
breaches its obligation to pay when due any installment or other amount due or coming due under any of the Debt Documents and fails to cure the breach within ten
(10) days; 

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        (ii)   Debtor,
without the prior written consent of Secured Party, attempts to or does sell, rent, lease, license, mortgage, grant a security interest in, or otherwise
transfer or encumber (except for Permitted Liens or as permitted in accordance with Section 3(c) hereof) any of the Collateral; 

        (iii)  Debtor
breaches any of its insurance obligations under Section 4; 

        (iv)  Debtor
breaches any of its other obligations under any of the Debt Documents and fails to cure that breach within thirty (30) days after written notice from
Secured Party: 

        (v)   Any
warranty, representation or statement made by Debtor in any of the Debt Documents or otherwise in connection with any of the Indebtedness shall be false or
misleading in any material respect when made; 

        (vi)  Any
of the Collateral is subjected to attachment, execution, levy, seizure or confiscation in any legal proceeding or otherwise, or if any legal or administrative
proceeding is commenced against Debtor or any of the Collateral, which in the good faith judgment of Secured Party subjects any of the Collateral to a material risk of attachment, execution, levy,
seizure or confiscation and no bond is posted or protective order obtained to negate such risk; 

        (vii) Debtor
breaches or is in default under any other agreement between Debtor and Secured Party; 

        (viii) Debtor
or any guarantor or other obligor for any of the Indebtedness (collectively "Guarantor") dissolves, terminates its existence, becomes insolvent or ceases to do
business as a going concern; 

        (ix)  If
Debtor or any Guarantor is a natural person, Debtor or any such Guarantor dies or becomes incompetent; 

        (x)   A
receiver is appointed for all or of any part of the property of Debtor or any Guarantor, or Debtor or any Guarantor makes any assignment for the benefit of creditors; 

        (xi)  Debtor
or any Guarantor tiles a petition under any bankruptcy, insolvency or similar law, or any such petition is filed against Debtor or any Guarantor and is not
dismissed within forty-five (45) days; 

        (xii) Debtor's
improper filing of an amendment or termination statement relating to a filed financing statement describing the Collateral; 

        (xiii) There
is a material adverse change in the Debtor's financial condition as determined solely by Secured Party in its reasonable business judgment; 

        (xiv) Any
Guarantor revokes or attempts to revoke its guaranty of any of the Indebtedness or fails to observe or perform any covenant, condition or agreement to be performed
under any guaranty or other related document to which it is a party; 

        (xv) Debtor
defaults under any other material obligation for (A) borrowed money, (B) the deferred purchase price of property or (C) payments due under
any lease agreement, or 

        (xvi) At
any time during the term of this Agreement Debtor experiences a change of control such that any person or entity that is not a stockholder of Debtor (or an
affiliate thereof) as of the date hereof acquires either more than 50% or the voting stock of Debtor or all or substantially all of Debtor's assets, in either case, without Secured Party's prior
written consent. 

        (b)   If
Debtor is in default, the Secured Party, at its option, may declare any or all of the Indebtedness to be immediately due and payable, without demand or notice to
Debtor or any Guarantor. The accelerated obligations and liabilities shall bear interest (both before and after any 

5

 

judgment)
until paid in full at the lower of eighteen percent (18%) per annum or the maximum rate not prohibited by applicable law. 

        (c)   After
default, Secured Party shall have all of the rights and remedies of a Secured Party under the Uniform Commercial Code, and under any other applicable law. Without
limiting the foregoing, Secured Party shall have the right in accordance with applicable law to (i) notify any account debtor of Debtor or any obligor on any instrument which constitutes part
of the Collateral to make payment to the Secured Party, (ii) with or without legal process, enter any premises where the Collateral may be and take possession of and remove the Collateral from
the premises or store it on the premises, (iii) sell the Collateral at public or private sale, in whole or in part, and have the right to bid and purchase at said sale, or (iv) lease or
otherwise dispose of all or part of the Collateral, applying proceeds from such disposition to the obligations then in default. If requested by Secured Party, Debtor shall promptly assemble the
Collateral and make it available to Secured Party at a place to be designated by Secured Party which is reasonably convenient to both parties. Secured Party may also render any or all of the
Collateral unusable at the Debtor's premises and may dispose of such Collateral on such premises without liability to Debtor for rent or costs. Any notice that Secured Party is required to give to
Debtor under the Uniform Commercial Code of the time and place of any public sale or the time after which any private sale or other intended disposition of the Collateral is to be made shall be deemed
to constitute reasonable notice if such notice is given to the last known address of Debtor at least ten (10) days prior to such action. 

        (d)   Proceeds
from any sale or lease or other disposition shall be applied: first, to all costs of repossession, storage, and disposition including without limitation
attorneys', appraisers', and auctioneers' fees; second, to discharge the obligations then in default; third, to discharge any other indebtedness of Debtor to Secured Party, whether as obligor,
endorser, guarantor, surety or indemnitor; fourth, to expenses incurred in paying or settling liens and claims against the Collateral; and lastly, to Debtor, if there exists any surplus. Debtor shall
remain fully liable for any deficiency. 

        (e)   Debtor
agrees to pay all reasonable attorneys' fees and other costs incurred by Secured Party in connection with the enforcement, assertion, defense or preservation of
Secured Party's rights and remedies under this Agreement, or if prohibited by law, such lesser sum as may be permitted. Debtor further agrees that such fees and costs shall constitute Indebtedness. 

        (f)    Secured
Party's rights and remedies under this Agreement or otherwise arising are cumulative and may be exercised singularly or concurrently. Neither the failure nor any
delay on the part of the Secured Party to exercise any right, power or privilege under this Agreement shall operate as a waiver, nor shall any single or partial exercise of any right, power or
privilege preclude any other or further exercise of that or any other right, power or privilege. SECURED PARTY SHALL NOT BE DEEMED TO HAVE WAIVED ANY OF ITS RIGHTS UNDER THIS AGREEMENT OR UNDER ANY
OTHER AGREEMENT, INSTRUMENT OR PAPER SIGNED BY DEBTOR UNLESS SUCH WAIVER IS EXPRESSED IN WRITING AND SIGNED BY SECURED PARTY. A waiver on any one occasion shall not be construed as a bar to or waiver
of any right or remedy on any future occasion. 

        (g)   DEBTOR
AND SECURED PARTY UNCONDITIONALLY WAIVE THEIR RIGHTS TO A JURY TRIAL OF ANY CLAIM OR CAUSE OF ACTION BASED UPON OR ARISING OUT OF THIS AGREEMENT, ANY OF THE OTHER
DEBT DOCUMENTS, ANY OF THE INDEBTEDNESS SECURED HEREBY, ANY DEALINGS BETWEEN DEBTOR AND SECURED PARTY RELATING TO THE SUBJECT MATTER OF THIS TRANSACTION OR ANY RELATED TRANSACTIONS, AND/OR THE
RELATIONSHIP THAT IS BEING ESTABLISHED BETWEEN DEBTOR AND SECURED PARTY. THE SCOPE OF THIS WAIVER IS INTENDED TO BE ALL ENCOMPASSING OF ANY AND ALL DISPUTES THAT MAY BE FILED IN ANY COURT. THIS WAIVER
IS IRREVOCABLE. THIS WAIVER MAY NOT BE MODIFIED EITHER ORALLY OR 

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IN
WRITING. THE WAIVER ALSO SHALL APPLY TO ANY SUBSEQUENT AMENDMENTS, RENEWALS, SUPPLEMENTS OR MODIFICATIONS TO THIS AGREEMENT, ANY OTHER DEBT DOCUMENTS, OR TO ANY OTHER DOCUMENTS OR AGREEMENTS
RELATING TO THIS TRANSACTION OR ANY RELATED TRANSACTION. THIS AGREEMENT MAY BE FILED AS A WRITTEN CONSENT TO A TRIAL BY THE COURT. 

8.     MISCELLANEOUS.  

        (a)   This
Agreement, any Note and/or any of the other Debt Documents may be assigned, in whole or in part, by Secured Party without prior notice to Debtor, and Debtor agrees
not to assert against any such assignee, or assignee's assigns, any defense, set-off, recoupment claim or counterclaim which Debtor has or may at any time have against Secured Party for
any reason whatsoever. Debtor agrees that if Debtor receives written notice of an assignment from Secured Party, Debtor will pay all amounts payable under any assigned Debt Documents to such assignee
or as instructed by Secured Party. Debtor also agrees to confirm in writing receipt of the notice of assignment as may be reasonably requested by Secured Party or assignee. 

        (b)   All
notices to be given in connection with this Agreement shall be in writing, shall be addressed to the parties at their respective addresses set forth in this
Agreement (unless and until a different address may be specified in a written notice to the other party), and shall be deemed given (i) on the date of receipt if delivered in hand or by
facsimile transmission, (ii) on the next business day atter being sent by express mail or overnight delivery service, and (iii) on the fourth business day after being sent by regular,
registered or certified mail. As used herein, the term "business day" shall mean and include any day other than Saturdays, Sundays, or other days on which commercial banks in New York, New York are
required or authorized to be closed. 

        (c)   Secured
Party may correct patent errors and fill in all blanks in this Agreement or in any Collateral Schedule consistent with the agreement of the parties. 

        (d)   Time
is of the essence of this Agreement. This Agreement shall be binding, jointly and severally, upon all parties described as the "Debtor" and their respective heirs,
executors, representatives, successors and assigns, and shall inure to the benefit of Secured Party, its successors and assigns. 

        (e)   This
Agreement and its Collateral Schedules constitute the entire agreement between the parties with respect to the subject matter of this Agreement and supersede all
prior understandings (whether written, verbal or implied) with respect to such subject matter. THIS AGREEMENT AND ITS COLLATERAL SCHEDULES SHALL NOT BE CHANGED OR TERMINATED ORALLY OR BY COURSE OF
CONDUCT, BUT ONLY BY A WRITING SIGNED BY BOTH PARTIES. Section headings contained in this Agreement have been included for convenience only, and shall not affect the construction or interpretation of
this Agreement. 

        (f)    This
Agreement shall continue in full force and effect until all of the Indebtedness has been indefeasibly paid in full to Secured Party or its assignee. The surrender,
upon payment or otherwise, of any Note or any of the other documents evidencing any of the Indebtedness shall not affect the right of Secured Party to retain the Collateral for such other Indebtedness
as may then exist or as it may be reasonably contemplated will exist in the future. This Agreement shall automatically be reinstated if Secured Party is ever required to return or restore the payment
of all or any portion of the Indebtedness (all as though such payment had never been made). 

        (g)   Debtor
authorizes Secured Party to use its name, logo and/or trademark without notice to or consent by Debtor, in connection with certain promotional materials that
Secured Party may disseminate to the public. The promotional materials may include, but are not limited to, brochures, video tape, internet website, press releases, advertising in newspaper and/or
other periodicals, lucites, 

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and
any other materials relating the fact that Secured Party has a financing relationship with Debtor and such materials may be developed, disseminated and used without Debtor's review. Nothing herein
obligates Secured Party to use Debtor's name, logo and/or trademark, in any promotional materials of Secured Party. 

        (h)   THIS
AGREEMENT AND THE RIGHTS AND OBLIGATIONS OF THE PARTIES HEREUNDER SHALL IN ALL RESPECTS BE GOVERNED BY AND CONSTRUED IN ACCORDANCE WITH, THE INTERNAL LAWS OF THE
STATE OF DELAWARE (WITHOUT REGARD TO THE CONFLICT OF LAWS PRINCIPLES OF SUCH STATE), INCLUDING ALL MATTERS OF CONSTRUCTION, VALIDITY AND PERFORMANCE, REGARDLESS OF THE LOCATION OF THE COLLATERAL. 

        IN WITNESS WHEREOF, Debtor and Secured Party, intending to be legally bound hereby, have duly executed this Agreement in one or more
counterparts, each of which shall be deemed to be an original, as of the day and year first aforesaid. 

	SECURED PARTY:	 	DEBTOR:
	

General Electric Capital Corporation	
 	

Helicos BioSciences, Inc.
	

By:	
 	

    
	
 	

By:	
 	

/s/ Stanley N. Lapidus

	Name:	 	    
	 	Name:	 	Stanley N. Lapidus

	Title:	 	    
	 	Title:	 	President

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QuickLinks

Exhibit 10.3

MASTER SECURITY AGREEMENT dated as of June 9, 2006 ("Agreement")QuickLinks
 -- Click here to rapidly navigate through this document

 
 

Exhibit 10.5    
    

 
 

CUMMINGS PROPERTIES, LLC
  STANDARD FORM
  COMMERCIAL LEASE    
    

12050800-DJC

        In
consideration of the covenants herein, Cummings Properties, LLC ("LESSOR") hereby leases to Helicos Biosciences Corporation (a DE corp.), one Kendall Square, Building 200, Cambridge,
MA 02139 ("LESSEE") the following premises, approximately 6,230 square feet at 6-C Gill Street, Woburn, MA 01801 ("the leased premises"), for a term of one (1) year commencing at
noon on February 1, 2006 and ending at noon on January 30, 2007 unless sooner terminated as herein provided. LESSOR and LESSEE now covenant and agree that the following terms and
conditions shall govern this lease. 

        1.     RENT. LESSEE shall pay to LESSOR base rent at the rate of one hundred nine thousand two hundred twenty six (109,226) U.S.
dollars per year, drawn on a U.S. bank, payable in advance in monthly installments of $9,102.16 on the first day of each calendar month, without offset or deduction. The first monthly payment, plus an
appropriate fraction of a monthly payment for any portion of a month at the commencement of the lease term, shall be made up on LESSEE's execution of this lease. All payments shall be made to LESSOR
at 200 West Cummings Park, Woburn, Massachusetts 01801, or at such other place as designated in writing by LESSOR. If the "Cost of Living" has increased as shown by the Consumer Price Index (Boston,
Massachusetts, all items, all urban consumers), U.S. Bureau of Labor Statistics, then base rent due during each calendar year of this lease and any extensions thereof shall be annually adjusted in
proportion to any increase in the Index. All such adjustments shall take place with the rent due each January 1. The base month from which to determine the amount of each increase in the index
shall be January 2006, which figure shall be compared with the figure for November 2006, and each November thereafter to determine the increase (if any) in the base rent to be paid
during the following calendar year. If the Consumer Price Index referenced above is discontinued as a measure of "Cost of Living" changes, LESSOR shall substitute a comparable index then in general
use. 

        2.     SECURITY DEPOSIT. LESSEE shall pay to LESSOR a security deposit of twenty seven thousand three hundred (27,300) U.S.
dollars, drawn on a U.S. bank, upon LESSEE's execution of this lease, which shall be held as security for LESSEE's performance hereunder and refunded to LESSEE without interest at the end of this
lease, subject to LESSEE's satisfactory compliance with the conditions hereof. LESSEE may not apply the security deposit to any payment due under the lease. In the event of any default or breach of
this lease by LESSEE, however, LESSOR may elect to apply the security deposit first to any unamortized improvements completed for LESSEE's occupancy, then to offset any outstanding invoice or other
payment due to LESSOR, and then to outstanding rent. If all or any portion of the security deposit is applied to cure a default or breach during the term of this lease, LESSEE shall restore said
deposit forthwith. LESSEE'S failure to remit the full security deposit or any portion thereof or to restore said deposit when due shall constitute a substantial lease default. If LESSEE fails to pay
the security deposit and first month's rent on a timely basis, LESSOR may retake possession and relet the leased premises for LESSEE's account, or declare this lease null and void for failure of
consideration. 

        3.     USE OF PREMISES. LESSEE shall use the leased premises only for executive and administrative offices and laboratory. 

        4.     REAL ESTATE TAX INCREASES. LESSEE shall pay to LESSOR as additional rent a proportionate share (based on square footage
leased by LESSEE as compared with the total leaseable square footage of the building or buildings of which the leased premises are a part (hereinafter called the building)) of any increase in the real
estate taxes levied against the land and building, whether such increase is caused by an increase in the tax rate or the assessment on the property, or a change in the method of determining real
estate taxes. Any additional rent shall be prorated should the lease 

terminate
before the end of any tax year. The base from which to determine the amount of any increase in taxes shall be the rate and the assessment in effect as of July 1, 2005, net of
abatements, if any. 

        5.     UTILITIES. LESSOR shall provide equipment per LESSOR's building standards to heat the leased premises in season and to
cool all office areas between May 1 and November 1. LESSEE shall pay all charges for utilities used on the leased premises, including electricity, gas, oil, water and sewer, and shall
use whichever utility service provider LESSOR shall designate at any time. LESSEE shall pay the utility provider or LESSOR, as applicable, for all such utility charges as determined by separate meters
serving the leased premises and/or as a proportionate share of the utility charges for the building if not separately metered. LESSEE shall also pay LESSOR a proportionate share of any other fees and
charges relating in any way to utility use at the building, including charges for routine maintenance of any on-site septic system. 

        6.     COMPLIANCE WITH LAWS. LESSEE agrees not to use the leased premises in any way that may be unlawful, improper, noisy,
offensive or contrary to any applicable statute, regulation, ordinance or bylaw. LESSEE shall keep all employees working in the leased premises covered by Worker's Compensation Insurance and shall
obtain any licenses and permits necessary for LESSEE's use and occupancy. LESSEE shall be responsible for causing the leased premises and any alterations by LESSEE allowed hereunder to be in full
compliance with any applicable statute, regulation, ordinance or bylaw. 

        7.     FIRE, CASUALTY, EMINENT DOMAIN. Should a substantial portion of the leased premises, or of the property of which they are
a part, be substantially damaged by fire or other casualty, or be taken by eminent domain, LESSOR may elect to terminate this lease. When such fire, casualty or taking renders the leased premises
substantially unsuitable for their intended use, a proportionate abatement of rent shall be made, and LESSEE may elect to terminate this lease if: (a) LESSOR fails to give written notice within
30 days after said fire, casualty or taking of its intention to restore the leased premises; or (b) LESSOR fails to restore the leased premises to a condition substantially suitable for
their intended use within 90 days after said fire, casualty or taking. LESSOR reserves all rights for damages or injury to the leased premises for any taking by eminent domain, except for
damage to LESSEE's property or equipment. 

        8.     FIRE INSURANCE. LESSEE shall not permit any use of the leased premises which will adversely affect or make voidable any
insurance on the property of which the leased premises are a part, or on the contents of said property, or which shall be contrary to any law, regulation or recommendation made by the Insurance
Services Office (or successor organization), state fire prevention agency, local fire department, LESSOR's insurer or any similar entity. LESSEE shall on demand reimburse LESSOR and all other tenants
all extra insurance premiums caused by LESSEE's use of the leased premises. LESSEE shall not vacate the leased premises or permit same to be unoccupied other than during LESSEE's customary
non-business days or hours, or cause or allow the utilities serving the leased premises to be terminated. 

        9.     SIGNS. LESSEE, at LESSEE's expense, shall erect promptly upon commencement of this lease, and then maintain signage for
the leased premises in accordance with building standards for style, size, wording, design, location, etc. now or hereafter made by LESSOR. LESSEE shall obtain LESSOR's prior written consent before
erecting any sign, and LESSOR may, at LESSEE's expense, remove and dispose of any sign not approved, erected, maintained or displayed in conformance with this lease. 

        10.   MAINTENANCE OF PREMISES. Except as otherwise provided below, LESSOR will be responsible for the structural maintenance of
the leased premises and for maintenance of the roof, landscaping, heating and cooling equipment, sprinklers, doors, locks, plumbing and electrical wiring, but specifically excluding damage caused by
the careless, malicious, willful or negligent acts of LESSEE or others, and chemical, corrosion or water damage from any source. LESSEE agrees to maintain at its expense all other aspects of the
leased premises in the same condition as they are at the commencement of the lease term or as they may be put in with LESSOR'S written consent during the 

term
of this lease, normal wear and tear only excepted, and whenever necessary, to replace light bulbs and glass, acknowledging that the leased premises are now in good order and the light bulbs and
glass whole. LESSEE shall properly control and vent all chemicals, radioactive materials, smoke, odors and other materials that may be harmful, and shall not cause the area surrounding the leased
premises or any other common area to be in anything other than a neat and clean condition, depositing all waste in appropriate receptacles. LESSEE shall be solely responsible for any damage to
plumbing equipment, sanitary lines or any other portion of the building which results from the discharge or use of any substance by LESSEE. LESSEE shall but permit the leased premises to be
overloaded, damaged, stripped or defaced, nor suffer any waste, and will not keep animals within the leased premises. If the leased premises include any wooden mezzanine-type space, the
floor capacity of such space is suitable only for office use, light storage or assembly work. LESSEE will protect any flooring with chair pads under any rolling chairs. Unless heat is provided at
LESSOR's expense, LESSEE shall maintain sufficient heat to prevent freezing of pipes or other damage. Notwithstanding the foregoing, any increase in heating. ventilating, air conditioning, plumbing or
electrical equipment or capacity, and any installation or maintenance of any "non-building standard" leasehold improvements or equipment which is associated with some specific aspect of
LESSEE's use, whether installed by LESSOR, LESSEE or a prior occupant, shall be LESSEE's sole responsibility, at LESSEE's expense, and subject to LESSOR's prior written consent. All maintenance
provided by LESSOR shall be during LESSOR's normal business hours. 

        11.   ASSIGNMENT OR SUBLEASE. Provided LESSEE is not in default of any terms or conditions hereof, LESSEE may assign this lease
or sublet or allow another entity or individual to occupy the whole or any part of the leased premises, but only with LESSOR's prior written consent in each and every instance. In no case may LESSEE
assign this lease or sublet the leased premises to any other current or prospective tenant of LESSOR, or any affiliate of such current or prospective tenant. As a condition to any assignment or
sublease, an additional security deposit shall be paid to and held by LESSOR. If LESSEE notifies LESSOR in writing of its desire to assign this lease or sublet the leased premises, LESSOR shall have
the option to terminate this lease, at an effective date to be determined by LESSOR, upon written notice to LESSEE. Notwithstanding LESSOR's consent to any assignment or sublease, LESSEE and GUARANTOR
shall remain liable to LESSOR for the payment of all rent and for the full performance of all covenants and conditions of this lease. 

        12.   ALTERATIONS. LESSEE shall not make structural alterations, additions or improvements of any kind to the leased premises,
but may make nonstructural alterations, additions or improvements with LESSOR's prior written consent. All such allowed alterations, additions and improvements shall be at LESSEE's expense and shall
conform with LESSOR's building standards and construction specifications. If LESSOR or its agent provides any services or maintenance for LESSEE in connection with such alterations, additions and
improvements or otherwise under this lease, LESSEE will promptly pay any just invoice. LESSEE shall obtain a lien waiver from any contractor it employs prior to commencement of any work. LESSEE shall
not permit any mechanics' liens, or similar liens, to remain upon the leased premises in connection with any work performed or claimed to have been performed at the direction of LESSEE and shall cause
any such lien to be released or removed forthwith without cost to LESSOR. Any alterations, additions and improvements shall become part of the leased premises and the property of LESSOR. LESSOR shall
have the right at any time to make additions to the building, change the arrangement of parking areas, stairs or walkways, or otherwise alter common areas or the exterior of the building. 

        13.   LESSOR'S ACCESS. LESSOR and its agents and designees may at any reasonable time enter to view the leased premises; to
show the leased premises to others; to make repairs and alterations as LESSOR or its designee should elect to do for the leased premises, the common areas, or any other portions of the building; and
without creating any obligation or liability for LESSOR, but at LESSEE's expense, to make repairs which LESSEE is required but has failed to do. 

        14.   SNOW REMOVAL. The plowing of snow from all roadways and unobstructed parking areas shall be at the sole expense of
LESSOR. The control of snow and ice on all walkways, steps and loading areas serving the leased premises and all other areas not readily accessible to plows shall be the 

sole
responsibility of LESSEE. Notwithstanding the foregoing, however, LESSEE shall hold LESSOR and OWNER harmless from any and all claims by LESSEE's employees, agents, callers or invitees for damage
or personal injury resulting in any way from snow or ice on any area serving the leased premises. 

        15.   ACCESS AND PARKING. Unless otherwise provided herein, LESSEE shall have the right without additional charge to use
parking facilities provided for the leased premises in common with others entitled to the use thereof. LESSEE shall not obstruct any portion of the building or its walkways and approaches. No
unattended parking will be permitted between 7:00 PM and 7:00 AM without LESSOR's prior written approval, and from November 15 through April 15 annually, such parking shall be permitted
only in those areas designated for assigned overnight parking. Unregistered or disabled vehicles, or storage trailers of any type, may not be parked at any time, LESSOR may tow, at LESSEE's sole risk
and expense, any misparked vehicle belonging to LESSEE or LESSEE's employees, agents, callers or invitees, at any time. LESSOR shall not provide, and shall not be responsible for providing, any
security services. 

        16.   LIABILITY. LESSEE shall be solely responsible as between LESSOR and LESSEE for deaths or personal injuries to all persons
and damage to any property, including damage by fire or other casualty, occurring in or on the leased premises (including any common areas as described below) and arising out of the use, control,
condition or occupancy of the leased premises by LESSEE, except for death, personal injuries or property damage directly resulting from the sole negligence of LESSOR. LESSEE agrees to indemnify and
hold harmless LESSOR and OWNER (as defined below) from any and all liability, including but not limited to costs, expenses, damages, causes of action, claims, judgments and attorney's fees caused by
or in any way arising out of any of the aforesaid matters. All common areas, including but not limited to any parking areas, stairs, corridors, roofs, walkways and elevators (herein collectively
called the common areas) shall be considered a part of the leased premises for liability and insurance purposes when they are used by LESSEE or LESSEE's employees, agents, callers, or invitees. 

        17.   INSURANCE. LESSEE shall secure and carry at its own expense a commercial general liability policy insuring LESSEE, LESSOR
and OWNER against any claims based on bodily injury (including death) or property damage arising out of the condition of the leased premises (including any common areas as described above) or their
use by LESSEE, including damage by fire or other casualty, such policy to insure LESSEE, LESSOR and OWNER against any claim up to $1,000,000 for each occurrence involving bodily injury (include
death), and $1,000,000 for each occurrence involving damage to property. This insurance shall be primary to and not contributory with any insurance carried by LESSOR, whose insurance shall be
considered excess. LESSOR and OWNER shall be included in each such policy as additional insureds using ISO Form CG 20 26 11 85 or some other form approved by LESSOR, and each such policy shall be
written by or with a company or companies satisfactory to LESSOR. Prior to occupancy, LESSEE shall deliver to LESSOR certificates and any applicable riders or endorsements showing that such insurance
is in force, and thereafter will provide renewal certificates at least 15 days prior to the expiration of any such policies. All such insurance certificates shall provide that such policies
shall not be cancelled without at least 10 days' prior written notice to each insured. If LESSEE fails to provide or maintain such insurance at any time during the term of this lease, LESSOR
may elect to contract for such insurance, and LESSEE shall pay LESSOR any costs that LESSEE would incur for such insurance in complying with this section, plus LESSOR's administrative expenses. 

        18.   BROKERAGE. LESSEE warrants and represents to LESSOR that LESSEE has dealt with no broker or third person with respect to
this lease and LESSEE agrees to indemnify LESSOR against any brokerage claims arising out of this lease. LESSOR warrants and represents to LESSEE that LESSOR has employed no exclusive broker or agent
in connection with this lease. If either party introduces a broker or third person on its behalf for any extension, renewal or expansion of this lease, any fees or commissions shall be the sole
responsibility of the party engaging such broker or third person. * except for Kevin Hanna of Cushman & Wakefield, Inc. to whom LESSOR shall pay a commission (estimated at $3,382.49) in
accordance with its standard fee schedule. 

        19.   SUBORDINATION. This lease shall be subject and subordinate to any and all mortgages and other instruments in the nature
of a mortgage, now or at any time hereafter, and LESSEE shall, when requested, promptly execute and deliver such written instruments as shall be necessary to show the subordination of this lease to
said mortgages or other such instruments in the nature of a mortgage. 

        20.   DEFAULT AND ACCELERATION OF RENT. In the event that (a) any assignment for the benefit of creditors, trust
mortgage, receivership or other insolvency proceeding shall be made or instituted with respect to LESSEE or LESSEE's property or (b) LESSEE shall default in the observance or performance of any
of LESSEE's covenants, agreements or obligations hereunder, and such default shall not be corrected within 10 days after written notice thereof, then LESSOR shall have the right thereafter,
while such default continues and without demand or further notice, to re-enter and take possession of the leased premises, to declare the term of this lease earned, and/or to remove
LESSEE's effects, without being guilty of trespass or conversion, and without prejudice to any remedies which might be otherwise used for arrears payment or other default or breach of the lease. If
LESSEE defaults in the payment of the security deposit, rent, taxes or substantial invoice from LESSOR or LESSOR's payment, and such default continues for 10 days after written notice thereof,
and, because both parties agree that nonpayment of said sums when due is a substantial breach or the lease, and, because the payment of rent in monthly installments is for the sole benefit and
convenience of LESSEE, then in addition to any other remedies, the net present value of the entire balance of rent due hereunder as of the date of LESSOR's notice, using the published prime rate then
in effect, shall immediately become due and payable as liquidated damages. No actions taken by LESSOR under this section shall terminate LESSEE's obligation to pay rent under this lease, as liquidated
damages or otherwise. Any sums received by LESSOR from or on behalf of LESSEE at any times shall be applied first to any unamortized improvements completed for LESSEE's occupancy, then to offset any
unpaid invoice or other payment due to LESSOR and then to unpaid rent. LESSEE shall pay any invoice within 10 days after receipt. If any rent and/or other payment is not received by LESSOR when
due, than LESSEE shall pay LESSOR a one-time late charge for each past due payment equal to one percent of such overdue amount or $35, whichever is greater. LESSEE shall also pay LESSOR
interest at the rate of 18 percent per annum on any past due payment. 

        21.   NOTICE. Any notice from LESSOR to LESSEE relating to the leased premises or this lease shall be deemed duly served when
left at the leased premises, or served by constable, or sent to the leased premises or to the last address designated by notice in accordance with this section, by certified or registered mail, return
receipt requested, postage prepaid, or by recognized courier service with a receipt therefor, addressed to LESSEE. Any notice from LESSEE to LESSOR relating to the leased premises or this lease shall
be deemed duly served when served by constable, or delivered to LESSOR by certified or registered mail, return receipt requested, postage prepaid, or by recognized courier service with a receipt
therefore, addressed to LESSOR at 200 West Cummings Park, Woburn, Massachusetts 01801 or at LESSOR's last designated address. No oral notice or representation shall have any force or effect. Time is
of the essence in the service of any notice. 

        22.   OCCUPANCY. If LESSEE takes possession of the leased premises prior to the start of the lease term, LESSEE will perform
and observe all of its covenants under this lease from the date upon which it takes possession. If LESSEE continues to occupy, control or encumber all or any part of the leased premises after the
termination of this lease without the written permission of LESSOR, LESSEE shall be liable to LESSOR for any and all loss, damages or expenses incurred by LESSOR, and all terms of this lease shall
continue to apply, except that use and occupancy payments shall be due in full monthly installments at a rate which shall be two times the greater of the monthly rent due under this lease immediately
prior to termination or LESSOR's then current published rent for the leased premises, it being understood that such extended occupancy is a tenancy at sufferance, solely for the benefit and
convenience of LESSEE and of greater rental value. LESSEE's control, occupancy or encumbrance of all or any part of the leased premises beyond noon on the last day of any monthly rental period shall
constitute LESSEE's occupancy for an entire additional month, and increased payment as provided in this section shall be due and payable immediately in advance. LESSOR's acceptance of any payments
from LESSEE during such extended occupancy shall not alter LESSEE's 

status
as a tenant at sufferance. LESSOR may require LESSEE to relocate to another similar facility at any time during the lease term upon prior written notice to LESSEE and on terms comparable to
those herein, and LESSEE shall be liable to LESSOR for any loss, damages or expenses incurred by LESSOR if LESSEE fails to relocate as required herein. 

        23.   FIRE PREVENTION. LESSEE agrees to use every reasonable precaution against fire, to provide and maintain approved, labeled
fire extinguishers, emergency lighting equipment and exit signs, and to complete any other modifications within the leased premises as required or recommended by the Insurance Services Office (or
successor organization), OSHA, the local fire department, LESSOR's insurer or any similar entity. 

        24.   OUTSIDE AREA. Anything held or stored by LESSEE in any common area without LESSOR's prior written consent shall be deemed
abandoned and may be removed by LESSOR at LESSEE's expense without notice. LESSEE shall maintain a building standard size dumpster in a location approved by LESSOR, which dumpster shall be provided
and serviced at LESSEE's expense by whichever disposal firm LESSOR may designate. Alternatively, if a shared dumpster or compactor is provided by LESSOR, LESSEE shall pay the disposal firm or LESSOR,
as applicable, LESSEE's proportionate share of any charges associated therewith. 

        25.   ENVIRONMENT. LESSEE will use the leased premises so as not to interfere in any way with the use and enjoyment of other
portions of the same or neighboring buildings by others by reason of odors, smoke, exhaust, smells, vibrations, noise, pets, accumulation of garbage or trash, vermin or other pests, or otherwise, and
will at its expense employ a professional pest control service if determined necessary by LESSOR. LESSEE agrees to maintain effective devices for preventing damage to plumbing and heating equipment
from deionized water, chemicals or hazardous materials which may be present at the leased premises. No hazardous materials or wastes shall be used, stored, disposed of, or allowed to remain at the
leased premises at any time without LESSOR's specific approval, and LESSEE shall be solely responsible for, and shall indemnify and hold harmless LESSOR and OWNER from, any and all corrosion or other
damage in any way associated with the use, storage and/or disposal of same by LESSEE. 

        26.   RESPONSIBILITY. Neither LESSOR nor OWNER shall be liable to anyone for, nor shall LESSEE's obligations under this lease
be reduced because of, loss or damage caused in any way by the use, leakage, seepage, flooding or escape of water or sewage in any form or from any source, by the interruption or cessation of any
service rendered customarily to the leased premises or building or agreed to by the terms of this lease, by any accident, the making of repairs, alterations or improvements, labor difficulties,
weather conditions, mechanical breakdowns, trouble or scarcity in obtaining fuel, electricity, service or supplies from the sources from which they are usually obtained, by any change in any utility
or service provider, or by any cause beyond LESSOR's immediate control. 

        27.   SURRENDER. On or before the termination of this lease, LESSEE shall remove all of LESSEE's goods and effects from the
leased premises, and shall deliver to LESSOR actual and exclusive possession of the leased premises and all keys and locks thereto, all fixtures, equipment and workstations of any type connected
therewith, and all alterations, additions and improvements made to or upon the leased premises, whether completed by LESSEE, LESSOR or others, including but not limited to any offices, window blinds,
floor coverings, computer floors, plumbing and plumbing fixtures, heating, ventilating and air conditioning equipment, ductwork, exhaust fans, water coolers, security, surveillance and fire protection
systems, telecommunications and data wiring, telephone equipment, air and gas distribution piping, compressors, overhead cranes, hoists, cabinets, counters, shelving, signs, electrical work, including
but not limited to lighting fixtures of any type, wiring, conduit, EMT, transformers, generators, distribution panels, but ducts, raceways, outlets and disconnects, and furnishings and equipment which
have been bolted, welded, nailed, screwed, glued or otherwise attached to any wall, floor, ceiling, roof, pavement or ground, or which have been directly wired or plumbed to any portion of any
building or other system serving the leased premises, including but not limited to water supply, drainage, venting or air or gas distribution systems. Notwithstanding the foregoing, prior to
termination of this lease, LESSEE shall, if requested by LESSOR, remove or tag for 

future
use any and all wiring and cabling installed and/or used by LESSEE. LESSEE shall deliver the leased premises fully sanitized from any chemicals or other contaminants, broom clean, and in at
least the same condition as they were at the commencement of the lease or any prior lease between the parties for the leased premises, or as they were modified during said term with LESSOR's written
consent, reasonable wear and tear only accepted, and LESSEE shall be deemed to be encumbering the leased premises until it delivers the leased premises to LESSOR in the condition required under this
lease. [Illegible] of LESSEE's property that remains in the leased premises upon termination of the lease shall be deemed abandoned and shall be disposed of as LESSOR sees fit,
[Illegible] no liability to LESSEE for loss or damage thereto, and at the sole risk or LESSEE. LESSOR may remove and store any such property at LESSEE's expense; retain same
under LESSOR's control; sell same at public or private sale (without notice) and apply the net proceeds of such safe to the payment of any sum due hereunder; or destroy same. In no case shall the
leased premises be deemed surrendered to LESSOR until the termination date provided herein or such other date as may be specified in a written agreement between the parties, notwithstanding the
delivery of any keys to LESSOR. 

        28.   GENERAL. (a) The invalidity or unenforceability of any clause or provision of this lease shall not affect or
render invalid or unenforceable any other clause or provision hereof. (b) The obligations of this lease shall run with the land, and this lease shall be binding upon and inure to the benefit of
the parties hereto and their respective successors and assigns, except that LESSOR and OWNER shall be liable for obligations occurring only while lessor or owner of the leased premises. (c) Any
action or proceeding arising out of the subject matter of this lease shall be brought by LESSEE within one year after the cause of action has occurred and only in a court within the commonwealth of
Massachusetts. (d) If LESSOR or OWNER is a trust, corporation, or other limited liability entity, the obligations of LESSOR shall be binding upon the trust, corporation, or other entity, but
not upon any trustee, officer, director, shareholder, member, limited partner or beneficiary individually. (e) If LESSOR is not the owner (OWNER) of the leased premises, LESSOR represents that
OWNER has agreed to be bound by the terms of this lease unless LESSEE is in default hereof. (f) This lease is made and delivered in the commonwealth of Massachusetts, and shall be interpreted,
construed, and enforced in accordance with the laws thereof. (g) This lease is the result of negotiations between parties of equal bargaining strength, and when executed by both parties shall
constitute the entire agreement between the parties, superseding all prior oral and written agreements, representations, statements and negotiations relating in anyway to the subject matter herein.
This lease may not be extended or amended except by written agreement signed by both parties, or as otherwise provided herein, and no other subsequent oral or written representation shall have any
effect hereon. (h) Notwithstanding any other statements herein, LESSOR makes no warranty, express or implied, concerning the suitability of the leased premises for LESSEE's intended use.
(i) LESSEE agrees that if LESSOR does not deliver possession of the leased premises as herein provided for any reason, LESSOR shall not be liable for any damages to LESSEE for such failure, but
LESSOR agrees to use reasonable efforts to deliver possession to LESSEE at the earliest practical date. A proportionate abatement of rent, excluding the cost of any amortized improvements to the
leased premises, for such time as LESSEE may be deprived of possession of the leased premises shall be LESSEE's sole remedy, except where a delay in delivery is caused in any way by LESSEE.
(j) Neither the submission of this lease form or any amendment hereof, nor the acceptance of the security deposit and/or rent shall constitute a reservation of or option for the leased
premises, or an offer to lease, it being expressly understood and agreed that neither this lease nor any amendment shall bind either party in any manner whatsoever unless and until it has been
executed by both parties. (k) LESSEE shall not be entitled to exercise any option in this lease, the attached Rider to Lease or any subsequent amendment or extension, or receive LESSOR's
consent as provided for herein, if LESSEE is at that time in default of any terms or conditions hereof. (i) Except as otherwise provided herein, neither LESSOR, nor OWNER, nor LESSEE shall be
liable for any special, incidental, indirect or consequential damages, including but not limited to lost profits or loss of business, arising out of or in any manner connected with performance or
nonperformance under this lease, even if any party has knowledge of the possibility of such damages. (m) The headings in this lease are for convenience only and shall not be considered part of
the terms hereof. (n) No restriction, condition or other endorsement by LESSEE on any check, nor LESSOR's deposit of any full or partial 

payment,
shall bind LESSOR in any way or limit LESSOR's rights under this lease. (o) LESSEE shall pay LESSOR for all legal and administrative fees and expenses incurred by LESSOR in connection
with any consent requested by LESSEE or in enforcing any or all obligations of LESEEE under this lease. (p) LESSEE will conform to all rules and regulations now or hereafter made by LESSOR for
parking, for the care, use or alteration of the building, its facilities and approaches, and for the administration of this lease, and will not permit any employee or visitor to violate this or any
other covenant or obligation of LESSEE. (q) LESSEE's covenants under this lease shall be independent of LESSOR's covenants, and LESSOR's failure to perform any of its covenants under this
lease, including a covenant constituting a significant inducement to LESSEE to enter into this lease, shall not excuse the payment of rent or any other charges by LESSEE or allow LESSEE to terminate
this lease.
(r) LESSOR, LESSEE, OWNER and GUARANTOR hereby waive any and all rights to a jury trial in any proceeding in any way arising out of the subject
matter of this lease. (s) See attached Rider to Lease for additional provisions.

        29.   SECURITY AGREEMENT. LESSEE hereby grants LESSOR a continuing security interest in all existing and hereafter acquired
property of LESSEE in any of LESSOR's building to secure the performance of all LESSEE's obligations under this lease or any subsequent lease between the parties. This provision shall survive
termination of this lease, shall continue under any subsequent lease between the parties, and shall not negate or replace any continuing security interest of LESSOR under any prior lease between the
parties. Default the payment or performance of any of LESSEE's obligations under this lease or any subsequent lease shall be a default under this security agreement, and shall entitle LESSOR to
immediately exercise all of the rights and remedies of a secured party under the Uniform Commercial Code. In the event of default, LESSEE agrees to assist and facilitate LESSOR's exercise of its
rights under the Uniform Commercial Code. LESSEE agrees to execute any security agreement or statement requested by LESSOR in connection with this security interest. 

        30.   WAIVERS, ETC. No consent or waiver, express or implied, by LESSOR to or of any breach of any covenant, condition or duty
of LESSEE shall be construed as a consent or waiver to or of any other breach of the same or any other covenant, condition or duty. If LESSEE is several persons, corporations, or other legal entities,
or a partnership, or some combination thereof, LESSEE's obligations are joint and several. Unless repugnant to the context, "LESSOR" and "LESSEE" mean the person or persons, natural or corporate,
named above as LESSOR and as LESSEE respectively, and their respective heirs, executors, administrators, successors and assigns. 

        31.   AUTOMATIC FIVE-YEAR EXTENSIONS. This lease, including all terms, conditions, escalations, etc. shall be
automatically extended for additional successive periods of five years each unless LESSOR or LESSEE serves written notice, either party to the other, of the other, of either party's option not to so
extend the lease. The time for serving such written notice shall be not more than 12 months or less than six months prior to the expiration of the then current lease term. Time is of the
essence. 

        IN
WITNESS WHEREOF, LESSOR and LESSEE have hereunto set their hands and common seals, intending to be legally bound hereby this 26th day of JANUARY, 2006. 

	LESSOR: CUMMINGS PROPERTIES, LLC	 	LESSEE: HELICOS BIOSCIENCES CORPORATION
	

By:	

/s/  E. N. AGRESTI, JR.      
	
 	

By:	

/s/  THOMAS MEYERS      

	 	Duly authorized	 	 	Duly authorized
	

 	

 	
 	

Print name:	

Thomas Meyers

 
 

GUARANTY    
    

        IN CONSIDERATION of LESSOR making this lease with LESSE, at the request of the undersigned (GURANTOR) and in reliance on this guaranty, GUARANTOR hereby
personally guarantees the prompt payment of rent by LESSEE and the performance by LESSEE of all terms, conditions, covenants and agreements of the lease, any amendments thereto and any extensions or 

assignments
thereof, with respect to the leased premises and any new premises that become subject to this lease, and the undersigned promises to pay all expenses, including reasonable attorney's fees,
incurred by LESSOR in enforcing all obligations of LESSEE under the lease or in enforcing this guaranty. LESSOR's consent to any assignments, subleases, amendments and extensions by LESSEE or to any
compromise or release of LESSEE's liability hereunder, with or without notice to the undersigned, or LESSOR's failure to notify the undersigned of any default and/or reinstatement of the lease by
LESSEE, shall not [ILLEGIBLE] the undersigned from liability as GUARANTOR. IN WITNESS WHEREOF, the undersigned GUARANTOR has hereunto set his/her/its hand and common seal,
[ILLEGIBLE] to be legally bound hereby on this            day
of                        ,            .
 

	 	 	 	Address:	 
	
 Signature	 	 	

	

Print name:	

 	
 	

 	

 
	 	
	 	 	

 
 

CUMMINGS PROPERTIES, LLC
  STANDARD FORM
  RIDER TO LEASE    
    

12050800-DJC-5 

The
following additional provisions are incorporated into and made a part of the attached lease: 

        A.    CONFLICTS. In the event of any conflict between any provision of this Rider to Lease and the attached lease, the
provisions of this Rider shall govern. 

        B.    SOUTH ESSEX SEWERAGE DISTRICT. With respect to leases at Cummings Center in Beverly (only), LESSEE shall fully comply with
all regulations of the South Essex Sewerage District (SESD) now or hereafter in effect, including prompt filing with LESSOR of any documents required by SESD regulations, and LESSEE agrees to
indemnify and hold harmless LESSOR and OWNER from any and all liability arising out of any noncompliance by LESSEE with such regulations. 

        C.    ACTIVITY AND USE RESTRICTION. With respect to leases at Cummings Center in Beverly and 10 and 18 Commerce Way in Woburn
(only), and except as provided below, the following activities and uses are expressly prohibited at the property of which the leased premises are a part residential uses (except for facilities for
adult congregate care or assisted living, senior housing, nursing home uses and other adult residential facilities in certain designated areas of the property); child care, day care, or public or
private elementary or secondary schools; a public park, playground or playing field, or other activities involving more than casual contact with the ground; cultivation
out-of-doors of fruits and vegetables destined for human consumption; and fishing or swimming in the ponds and other waterways on or adjacent to the property. In addition,
implementation of a health and safety plan is required for construction, utilities maintenance and other intrusive activities which are likely to involve extensive exposure to or contact with
subsurface soils at the property. Notices of Activity and Use Limitation providing further information have been recorded at the Essex South Registry of Deeds and the Middlesex South Registry of
Deeds, respectively, as well as recorded amendments authorizing both child care and a public elementary school in specific locations at Cummings Center. 

        D.    PARKING. LESSEE shall be entitled to use, in common with others, a proportionate share of the total number of common area
parking spaces provided for the building (based on square footage leased by LESSEE as compared with the total leasable square footage of the building). The number of spaces used by LESSEE's employees,
agents and invitees shall not at any time exceed LESSEE's proportionate share of the total spaces for the building. For purposes of determining LESSEE's compliance with this paragraph at any time, the
number of spaces used by LESSEE shall be presumed to equal the number of persons who are then present at the leased premises. 

        E.    REMEDIES. The parties agree that the actual damages to LESSOR as a result of nonpayment of rent by LESSEE would be
difficult to ascertain as of the execution of this lease; therefore, notwithstanding Section 20 above, the entire balance of unpaid rent, as a reasonable estimate of such actual damages, shall
become immediately due and payable, but only if LESSEE defaults in the payment of rent due under this lease and  not in the payment of any security deposit,
invoice, taxes or other charge which may also be due under this lease. The parties additionally agree that
in the event rent payments are accelerated, the total amount due shall be discounted to its net present value as of the date of LESSOR's notice of default, using the published prime rate then in
effect. Section 20 shall continue to apply in all other respects. 

        F.     RECORDING AND SECURITY. Although LESSOR may choose at any time to record activities at the building with unmonitored
remote television cameras, LESSEE acknowledges and agrees that, as provided in Section 15 above, LESSOR is not thereby or in any other way providing any security service for LESSEE or its
employees, agents, invitees, contractors and representatives, and that LESSOR has made no representations whatsoever, written or oral, concerning the safety of the leased premises or the presence,
effectiveness or operability of any security devices or security measures, or the safety or security of LESSEE, its employees, agents, invitees, callers, contractors and representatives, or LESSEE's
property, against the criminal or wrongful acts of third parties. 

Additionally,
LESSEE accepts full responsibility for protecting the persons and property of LESSEE and those of its employees, agents, Invitees, callers, contractors and representatives, and
(acknowledging that security devices or measures may fail or be thwarted by criminals, by other third parties or by electrical or mechanical malfunction), agrees not to rely on any such devices or
measures, and to protect itself, its property, and its employees, agents, invitees, callers, contractors and representatives as if such devices or measures did not exist. 

        G.    *
LESSEE agrees to take possession of the leased premises in "as is" condition. The parties acknowledge and agree that LESSOR has previously repaired and repainted all
drywall partitions, replaced glass and light bulbs as needed and cleaned the carpet. 

        H.    *
Notwithstanding monthly rent as provided in Section 1 above, LESSEE may deduct $1,206.33 per month from each monthly rental payment due from February 1,
2006 through January 30, 2007 (only), provided LESSOR receives each such monthly payment on or before the first day of the month for which such rent is due and LESSEE is not in arrears of any
rent or invoice payments or otherwise in default of this lease. Time is of the essence. 

        I.     *
The leased premises consist of approximately 5,475 square feet of ground level space and approximately 755 square feet of mezzanine level storage space. 

        J.     *
Notwithstanding the commencement date of this lease, LESSEE may occupy the leased premises one week following the full execution of this lease, including plans and
specifications if any, payment of the full security deposit and the first month's rent due for the month of February 2006, and production of all required insurance certificates, without further
obligation for the payment of monthly rent until March 1, 2006. All other terms, covenants and conditions of this lease shall apply during this rent-free period. 

        K.    During
the initial term of this lease, LESSEE may elect to cancel this lease for any reason or no reason at all effective as of the last day of any calendar month on or
after July 31, 2006, by serving LESSOR with not less than 45 days' prior written notice to that effect. LESSEE's notice to cancel shall only be effective if LESSEE is not then in arrears
of any rent or invoice payments or otherwise in default of this lease and if said notice is submitted to LESSOR along with simultaneous payment of $9,000 as a lease termination fee, however, in the
event said notice is properly submitted to LESSOR on or after September 30, 2006, said lease termination fee shall be $6,000. LESSEE shall also remain responsible for all damages to the leased
premises in accordance with this lease and for rent and all other charges due under this lease, including without limitation utility charges and real estate tax increases, through the revised lease
termination date. Time is of the essence. 

        L.    *
With respect to any condition existing prior to the commencement of LESSEE's occupancy under this lease, LESSOR shall hold LESSEE harmless from any and all suits,
judgments, or liabilities, for any "release," as defined in Section 101(22) of the Comprehensive Environmental Response, Compensation and Liability Act of 1980, as amended ("CERCLA") or in
Mass. G. L. c. 21E, §2 ("c. 21E"), of any "hazardous substance" as defined in Section 101(14) of CERCLA, any "hazardous material" as defined in Section 2 of c. 21E or any
petroleum (including crude oil or any fraction thereof) as a result of any activity on the property of which the leased premises are a part occurring prior to LESSEE's occupancy and not caused in any
way by LESSEE. 

        M.   *
Notwithstanding anything to the contrary in Section 25 above, LESSEE may use or store hazardous materials or hazardous wastes within the leased premises,
provided LESSEE fully complies with any applicable local, state, or federal law, regulation, ordinance and bylaw. LESSEE shall be solely responsible for and shall indemnify and hold LESSOR and OWNER
harmless from any and all liability, damage and personal injury in any way associated with any use, storage, or disposal of such materials. In the event any hazardous materials or hazardous wastes
remain in the leased premises after the termination of the lease or, if applicable, the date LESSEE relocates from the leased premises to new premises pursuant to an amendment to the lease
(collectively the "Vacate Date"), LESSEE authorizes LESSOR to properly dispose of them on LESSEE's behalf and at LESSEE's sole expense. 

        N.    Prior
to the Vacate Date, LESSEE, at LESSEE's sole expense, shall engage an independent and certified industrial hygienist ("the CIH") to prepare a decontamination work
plan ("work plan") for the leased premises in accordance with all CIH professional standards and all applicable laws to address all conditions arising out of LESSEE's tenancy. LESSEE shall complete
all measures specified in the work plan, including but not limited to, testing and cleaning of all surfaces, HVAC equipment, ductwork, and other building components recommended therein. The CIH shall
certify to LESSOR that as of the Vacate Date, the entire leased premises and any extension thereof used in any way by LESSEE are free from any harmful chemical, biological, or other contamination
arising out of LESSEE's tenancy, in accordance with all applicable CIH professional standards and all applicable laws, regulations, ordinances and bylaws. Said certification shall confirm the clean
condition of all HVAC equipment, ductwork, plumbing fixtures, drains, tanks, mechanical systems, cabinetry, countertops, walls, ceilings, floors, casework, pH adjustment tanks and acid neutralization
equipment, all other surfaces and the indoor air quality at the leased premises; that LESSEE has completed all measures specified in the work plan; and that there are no restrictions on future use and
occupation by others. A copy of the work plan shall be provided to LESSOR together with this certification. Also, in the event LESSEE uses or stores any radioactive materials within the leased
premises at any time, LESSEE shall obtain a written statement from the commonwealth of Massachusetts fully decommissioning the leased premises in accordance with all applicable laws, regulations,
ordinances and bylaws. LESSEE warrants and represents, however, that it will not use or store any radioactive materials at the leased premises. These certifications and all cleaning shall be completed
prior to the Vacate Date. The leased premises shall be deemed occupied by LESSEE unless and until LESSEE has fully vacated and returned the leased premises in accordance with the lease, has provided
the required certifications to LESSOR and completed all cleaning. 

        O.    *
LESSEE's maintenance obligations as provided in Section 10 above shall specifically include, without limitation, monthly inspections, and repair and replacement
as needed, of all acid neutralization, pH adjustment and other wastewater treatment tanks and equipment, and drain lines into which said tanks and equipment discharge; backflow preventers; air
filters; and all other exhaust and intake fan components, including belts. LESSEE shall be responsible for all maintenance and repairs of said equipment, both routine and otherwise, including
semiannual (or more frequent if necessary) cleaning and replenishment of neutralizing materials in pH adjustment tanks. LESSEE acknowledges and agrees that the plumbing, electrical, heating and
cooling systems provided and maintained by LESSOR are intended and sized only for office use, and any maintenance or additional equipment necessitated by LESSEE's use of and operations at the leased
premises shall be at LESSEE's sole expense. LESSEE agrees that all wastewater discharged from the leased premises shall be neutralized to a pH range between 6 and 9; or, in the case of deionized
water, shall be appropriately diluted or treated, and shall fully comply with all applicable state and local statutes, codes, regulations and/or ordinances. 

        P.     *
LESSEE shall notify LESSOR in writing upon LESSOR's request and 30 days prior to the Vacate Date of LESSEE's compliance with its inspection and maintenance
obligations as stated above. 

        Q.    LESSEE
shall provide prior to occupancy, and continue to maintain during the entire lease term, an irrevocable letter of credit in an amount not less than $25,000 for
LESSOR's benefit, in a form satisfactory to LESSOR's counsel, or an additional cash security deposit in the same amount securing LESSEE's performance of its obligations under the preceding four
paragraphs and Section 25 of this lease. Time is of the essence. 

        R.    *
The preceding five paragraphs regarding LESSEE's responsibility for the maintenance and condition of the leased premises are a key consideration of this lease. 

        S.     *
LESSOR consents to LESSEE's access to the roof of the building for the purpose of performing LESSEE's maintenance obligations as set forth above (only). LESSEE agrees
that no other work shall be carried on or any other equipment installed on the roof without the prior written consent of LESSOR. LESSEE shall be fully responsible for, and agrees to indemnify and hold
LESSOR harmless from, any and all property damage and personal injury associated in any way with the 

activities
of LESSEE and LESSEE's agents, employees and contractors on the roof and/or the location, installation or maintenance of LESSEE's equipment on the roof, including but not limited to, damage
to the watertight integrity of the roof and the roof membrane, from whatever cause. 

        T.     LESSOR
agrees to defer LESSEE's obligation to provide a letter of credit under Paragraph Q above because LESSEE agrees that it will limit its use of chemicals in
the leased premises to an aggregate of 20 gallons in total of all Class 1A, IB, 1C, 2, 3A and 3B chemicals, and represents that it will not use or store any radiological materials at the leased
premises. In the event LESSEE elects to use or store radiological materials or use a type or quantity of chemical in addition of those stated herein, then LESSEE shall notify LESSOR and provide LESSOR
with the letter of credit as described in Paragraph Q. 

	LESSOR: CUMMINGS PROPERTIES, LLC	 	LESSEE: HELICOS BIOSCIENCES CORPORATION
	

By:	

/s/  E. N. AGRESTI, JR.      
	
 	

By:	

/s/  THOMAS MEYERS      

	 	Duly authorized	 	 	Duly authorized
	

Date:	

1/26/06
	
 	

Print name:	

Thomas Meyers

	

 	

 	
 	

Title:	

VP and General Counsel

	 	 	 	 	08/04

QuickLinks

Exhibit 10.5

CUMMINGS PROPERTIES, LLC STANDARD FORM COMMERCIAL LEASE

GUARANTY

CUMMINGS PROPERTIES, LLC STANDARD FORM RIDER TO LEASE

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