Exhibit
10.1


 


EXECUTION COPY


 


 


SECOND AMENDMENT TO LOAN
AND SECURITY AGREEMENT


 


THIS
SECOND AMENDMENT TO LOAN AND SECURITY AGREEMENT (this “Amendment”) is
dated as of June 27, 2008 (the “Amendment Date”),
by and among HELICOS BIOSCIENCES
CORPORATION, a Delaware
corporation (“Borrower”), GENERAL
ELECTRIC CAPITAL CORPORATION, a Delaware corporation acting in its capacity as
agent (the “Agent”) for the lenders under the
Loan Agreement (as defined below) (the “Lenders”), and
the Lenders.


 


W  I  T  N  E
S  S  E  T  H:


 


WHEREAS, Borrower, the Lenders and Agent are
parties to that certain Loan and Security Agreement, dated as of December 31,
2007, as amended by that certain First Amendment to Loan and Security Agreement
and Post-Closing Obligations Letter dated as of February 14, 2008 (as so
amended and as the same may be further amended, supplemented and modified from
time to time, the “Loan Agreement”;
capitalized terms used herein have the meanings given to them in the Loan
Agreement except as otherwise expressly defined herein), pursuant to which
Lenders have agreed to provide to Borrower certain loans and other extensions
of credit in accordance with the terms and conditions thereof;


 


WHEREAS, Borrower has requested that Agent and
Lenders amend certain provisions of the Loan Agreement, in each case in
accordance with and subject to the terms and conditions set forth herein.


 


NOW,
THEREFORE, in
consideration of the premises, the covenants and agreements contained herein,
and other good and valuable consideration, the receipt and adequacy of which
are hereby acknowledged, Borrower, the Lenders and Agent hereby agree as
follows:


 


1.             Acknowledgment
of Obligations.  Borrower hereby
acknowledges, confirms and agrees that as of the close of business on the
Amendment Date, after giving effect to the making of the Subsequent Term Loan,
Borrower is indebted to the Lenders in respect of the Term Loans in the
aggregate principal amount of $20,000,000. 
All such Term Loans, together with interest accrued and accruing
thereon, and fees, costs, expenses and other charges owing by Borrower to Agent
and Lenders under the Loan Agreement and the other Debt Documents, are
unconditionally owing by Borrower to Agent and Lenders, without offset, defense
or counterclaim of any kind, nature or description whatsoever except as may be
limited by applicable bankruptcy, insolvency, reorganization, moratorium or
other similar laws relating to or affecting creditor’s rights generally.


 


2.             Amendments to Loan
Agreement.  Subject to the terms and conditions of
this Amendment (including, without limitation, the conditions to effectiveness
set forth in Section 5 below), and effective as of the Effective
Date (as such term is defined in Section 5 below), the Loan
Agreement is hereby amended as follows:


 


(a)           Section 2.3(a) of
the Loan Agreement is hereby amended by deleting such clause in its entirety
and replacing the following in lieu thereof:


 


 

















 


 


                “(a)         Interest.  Each Term Loan shall accrue
interest in arrears from the date made until such Term Loan is fully repaid at a fixed per annum rate of interest
equal to the sum of (x) with respect to the Initial Term
Loan, (i) the greater of (A) the Treasury Rate (as defined below) in effect on the day that is three (3) Business
Days prior to the making of such Term Loan as determined by Agent and (B) 3.84%
plus (ii) 6.11%, and (y) with respect to the Subsequent Term
Loan, (i) the greater of (A) the Treasury Rate (as defined below) in effect on the day that is three (3) Business
Days prior to the making of such Term Loan as determined by Agent and (B) 3.17%
plus (ii) 8.33%.  All computations of interest and
fees calculated on a per annum basis shall be made by Agent on the basis of a
360-day year, consisting of twelve 30-day months.  Each determination of an interest rate or the amount
of a fee hereunder shall be made by Agent and shall be conclusive, binding and
final for all purposes, absent manifest error. 
As used herein, the term “Treasury Rate” means a per annum rate of
interest equal to the rate published by the Board of Governors of the Federal
Reserve System in Federal Reserve Statistical Release H.15 entitled “Selected
Interest Rates” under the heading “U.S. Government Securities/Treasury Constant
Maturities” as the three year treasuries constant maturities rate.  In the event Release H.15 is no longer
published, Agent shall select a comparable publication to determine the U.S.
Treasury note yield to maturity.”


 


(b)           Section 2.3(b) of
the Loan Agreement is hereby amended by deleting such clause in its entirety
and replacing the following in lieu thereof:


 


                “(b)         Payments of Principal and Interest.  For the Initial Term Loan, Borrower shall pay
to the Agent, for the ratable benefit of the Lenders, (i) five (5) consecutive
payments of interest only (payable in arrears) at the rate of interest
determined in accordance with Section 2.3(a) on the first day of each
calendar month (a “Scheduled Payment Date”) commencing on February 1,
2008 and (ii) thirty-one
(31) equal consecutive payments of principal and interest (payable in arrears)
at the rate of interest determined in accordance with Section 2.3(a) on
each Scheduled Payment Date commencing on July 1, 2008.  For the Subsequent Term Loan, Borrower shall pay to
the Agent, for the ratable benefit of the Lenders, thirty-six (36) equal
consecutive payments of principal and interest (payable in arrears) at the rate
of interest determined in accordance with Section 2.3(a) on each
Scheduled Payment Date commencing on the first day of the calendar month
occurring after the month during which the Subsequent Term Loan was made (each
such payment made pursuant to each of the immediately preceding two sentences,
a “Scheduled Payment”).  The
amount of each such payment of principal and interest shall be calculated by
the Agent and shall be sufficient to fully amortize the principal and interest
due with respect to the applicable Term Loan over such repayment period.  Notwithstanding the foregoing, all unpaid
principal and accrued interest with respect to a Term Loan is due and payable
in full to Agent, for the ratable benefit of Lenders, on the earlier of (A) the
first day of the thirty-seventh month following the date such Term Loan was
made or (B) the date that such Term Loan otherwise becomes due and payable
hereunder, whether by acceleration of the Obligations pursuant to Section 8.2
or otherwise (the earlier of (A) or (B), the “Applicable Term Loan
Maturity Date”). Each Scheduled Payment, when paid, shall be applied first
to the payment of accrued and unpaid interest on the applicable Term Loan 


 


 


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and then to unpaid principal balance of such Term Loan.  Without limiting the foregoing, all
Obligations shall be due and payable on the Applicable Term Loan Maturity Date
for the last Term Loan made.”


 


(c)           A
new Section 2.9 to the Loan Agreement shall be added to read as
follows:


 


                “2.9        Authorization and Issuance of the
Warrants.  As of June 27,
2008, Borrower has
duly authorized the issuance to Lenders (or their respective affiliates or designees)
of stock purchase warrants substantially in the form of the warrant attached
hereto as Exhibit F (collectively, the “Warrants”)
evidencing Lenders’ (or their respective affiliates or designees) right to
acquire their respective Pro Rata Share of up to 110,000 shares of Common Stock
of Borrower at an
exercise price of $4.80 per share.  The
exercise period shall expire six (6) years from the date such Warrant is
issued.”


 


(d)           Section 4.2(c) of
the Loan Agreement is hereby amended by deleting such clause in its entirety
and replacing the following in lieu thereof:


 


                                “(c)         [Reserved.]”


 


(e)           Section 5.5
of the Loan Agreement is hereby amended by adding the following new sentence at
the end of such section:


 


“For the purposes
of the immediately preceding sentence, the revised annual operating plan of
Borrower delivered to Agent and Lenders in connection with that certain Second
Amendment to Loan and Security Agreement, dated as of June 27, 2008, among
Borrower, Agent and Lenders, shall constitute the most recent annual operating
plan of Borrower until such time as a more recent annual operating plan of
Borrower is provided in accordance with Section 6.3.”


 


(f)            Section 6.6
of the Loan Agreement is hereby amended by deleting such section in its
entirety and replacing the following in lieu thereof:


 


“6.6        Agreement with
Landlord/Bailee.  Each Loan
Party shall use commercially reasonable efforts to obtain and maintain such
Access Agreement(s) with respect to any real property on which (a) a
Loan Party’s principal place of business, (b) a Loan Party’s books or
records or (c) Collateral (other than finished commercial products which
are under contract for sale with a third party in the ordinary course of
business but which are classified as inventory pursuant to GAAP) with an
aggregate value in excess of $250,000 is located (other than real property
owned by such Loan Party) as Agent may reasonably require provided, however,
that the Agent shall not exercise any of its rights under such Access
Agreements unless entitled to do so pursuant to this Agreement.


 


(g)           Section 6.8(c) of
the Loan Agreement is hereby amended by deleting such clause in its entirety
and replacing the following in lieu thereof:


 


 


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“(c)         Agent and Lenders do not authorize and
each Loan Party agrees it shall not (i) part with possession of any of the
Collateral (except (A) to Agent (on behalf of itself and Lenders), (B) for
maintenance and repair (C) or for a Permitted Disposition), or (ii) remove
any of the Collateral from the continental United States other than (x) Inventory
with a value not to exceed $1,000,000, (y) finished commercial products
which are under contract for sale or collaboration with a third party but which
are classified as inventory pursuant to GAAP in an amount not to exceed 5 units
of  the Helicos Genetic Analysis Systems
(which includes the HeliScope Single Molecule Sequencer), and (z) cash not
to exceed $100,000.


 


(h)           Section 6.8(g) of
the Loan Agreement is hereby amended by deleting such clause in its entirety
and replacing the following in lieu thereof:


 


“(g)         Borrower agrees to
maintain, at all times, unrestricted cash in account number                 
of Borrower at RBS Citizens, National Association (the “Cash Account”) equal
to at least ten million dollars ($10,000,000.00).  Borrower shall provide Agent and each Lender
with (i) within five Business Days after the end of each month, a summary
of cash balances in form and substance satisfactory to Agent located in any
deposit accounts (including the Cash Account) of the Borrower or any of its
Subsidiaries and (ii) such other information as Agent may reasonably
request from time to time to evidence compliance with this Section 6.8(g).  The Cash Account shall be subject to an Account
Control Agreement pursuant to Section 7.10.”


 


(i)            The
Loan Agreement is hereby further amended by adding new Exhibit F,
which is attached to this Amendment as Exhibit F.


 


3.             No
Other Amendments.  Except for the amendments set
forth and referred to in Section 2 above, the Loan Agreement shall
remain unchanged and in full force and effect. 
Nothing in this Amendment is intended, or shall be construed, to
constitute a novation or an accord and satisfaction of any of Borrower’s
Obligations or to modify, affect or impair the perfection or continuity of
Agent’s security interests in, security titles to or other liens, for the
benefit of itself and the Lenders, on any Collateral for the Obligations.


 


4.             Representations
and Warranties.  To induce Agent and Lenders to enter into
this Amendment, Borrower does hereby warrant, represent and covenant to Agent
and Lenders that after giving effect to this Amendment (i) each
representation or warranty of the Borrower set forth in the Loan Agreement is
hereby restated and reaffirmed as true and correct in all material respects on
and as of the Amendment Date as if such representation or warranty were made on
and as of the date hereof (except to the extent that any such representation or
warranty expressly relates to a prior specific date or period), (ii) no
Default or Event of Default has occurred and is continuing as of the date
hereof and (iii) Borrower has the power and is duly authorized to enter
into, deliver and perform this Amendment and this Amendment is the legal, valid
and binding obligation of the Borrower enforceable against the Borrower in
accordance with its terms.


 


5.             Condition
Precedent to Effectiveness of this Amendment. 
This Amendment shall become effective as of the Amendment Date, and the
amendments set forth in Section 2  


 


 


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hereof shall be deemed to be effective as of the Amendment Date (the “Effective Date”), upon
the satisfaction in full of each of the following conditions precedent:


 


                                (a) receipt
by the Agent of one or more counterparts of this Amendment duly executed and
delivered by the Borrower, Agent and Lenders, in form and substance
satisfactory to Agent and Lenders;


 


                                (b) receipt
by the Agent of payment by the Borrower of the Amendment Fee (defined below) in
immediately available funds; and


 


                                (c) receipt
by Agent of such certificates, documents and other information necessary or
required by Agent and Lenders to satisfy the conditions set forth in Sections
4.2(a) and 4.2(b) of the Loan Agreement, including,
without limitation, the following documents:


 


(i) an officer’s certificate in form and substance satisfactory to
Agent;


 


(ii) a secretary’s certificate, in form and
substance satisfactory to Agent;


 


(iii) an updated Perfection Certificate, in form and substance
satisfactory to Agent; and


 


(iv) a disbursement instruction letter, in form and substance
satisfactory to Agent.


 


6.             The
Amendment Fee.  The Borrower hereby agrees to pay to the
Agent, for the ratable benefit of the Lenders, an amendment fee (the “Amendment
Fee”) in an amount equal to $150,000.00, as of the date of this Agreement.


 


7.             Release.


 


(a)           In
consideration of the agreements of Agent and Lenders contained herein and for
other good and valuable consideration, the receipt and sufficiency of which is
hereby acknowledged, Borrower, on behalf of itself and its successors, assigns,
and other legal representatives, hereby absolutely, unconditionally and
irrevocably release, remise and forever discharge Agent and Lenders and their
respective successors and assigns, and their respective present and former
shareholders, affiliates, subsidiaries, divisions, predecessors, directors,
officers, attorneys, employees, the agents and other representatives (Agent and
Lenders, and all such other Persons being hereinafter referred to collectively
as the “Releasees” and
individually as a “Releasee”), of
and from all demands, actions, causes of action, suits, covenants, contracts,
controversies, agreements, promises, sums of money, accounts, bills,
reckonings, damages and any and all other claims, counterclaims, defenses,
rights of set-off, demands and liabilities whatsoever other than with
respect to any claims made to correct manifest errors with respect to amounts
owing pursuant to the Loan Agreement or other Debt Documents (individually, a “Claim”
and collectively, “Claims”) of
every name and nature, known or unknown, suspected or unsuspected, both at law
and in equity, which Borrower or any of their respective successors, assigns,
or other legal representatives may now or hereafter own, hold, have or claim to
have against the Releasees or any of them for, upon, or by reason of any
circumstance, action, cause 


 


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or thing whatsoever which arises at any time on or prior to the day and
date of this Amendment, for or on account of, or in relation to, or in any way
in connection with the Loan Agreement, this Amendment or any of the other Debt
Documents or transactions thereunder or related thereto.


 


(b)           Borrower
understands, acknowledges and agrees that its release set forth above may be
pleaded as a full and complete defense and may be used as a basis for an
injunction against any action, suit or other proceeding which may be
instituted, prosecuted or attempted in breach of the provisions of such
release.


 


(c)           Borrower
agrees that no fact, event, circumstance, evidence or transaction which could
now be asserted or which may hereafter be discovered shall affect in any manner
the final, absolute and unconditional nature of the release set forth above.


 


8.             Covenant Not To Sue.         Borrower,
on behalf of itself and its respective successors, assigns, and other legal
representatives, hereby absolutely, unconditionally and irrevocably, covenants
and agrees with and in favor of each Releasee that it will not sue (at law, in
equity, in any regulatory proceeding or otherwise) any Releasee on the basis of
any Claim released, remised and discharged by Borrower pursuant to Section 6
above.  If Borrower or any of its
respective successors, assigns or other legal representatives violates the
foregoing covenant, Borrower, for itself and its successors, assigns and legal
representatives, jointly and severally agrees to pay, in addition to such other
damages as any Releasee may sustain as a result of such violation, all
attorneys’ fees and costs incurred by any Releasee as a result of such
violation.


 


9.             Advice
of Counsel.  Each of the parties represents to each other
party hereto that it has discussed this Amendment with its counsel.


 


10.          Severability of
Provisions.  In case any provision of or obligation under
this Amendment shall be invalid, illegal or unenforceable in any applicable
jurisdiction, the validity, legality and enforceability of the remaining
provisions or obligations, or of such provision or obligation in any other
jurisdiction, shall not in any way be affected or impaired thereby.


 


11.          Counterparts.  This
Amendment may be executed in multiple counterparts, each of which shall be
deemed to be an original and all of which when taken together shall constitute
one and the same instrument.  Delivery of
an executed signature page of this Amendment by facsimile transmission or
electronic transmission shall be as effective as delivery of a manually
executed counterpart hereof.


 


12.          GOVERNING
LAW.  THIS AGREEMENT SHALL BE GOVERNED BY, AND
CONSTRUED IN ACCORDANCE WITH, THE INTERNAL LAWS OF THE STATE OF NEW YORK
APPLICABLE TO CONTRACTS MADE AND PERFORMED IN SUCH STATE WITHOUT REGARD TO THE
PRINCIPLES THEREOF REGARDING CONFLICTS OF LAWS.


 


13.          Entire Agreement. 
The Loan Agreement as and when amended through this Amendment embodies
the entire agreement between the parties hereto relating to the subject 


 


 


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matter thereof and supersedes all prior agreements, representations and
understandings, if any, relating to the subject matter thereof.


 


14.          No Strict Construction,
Etc.  The parties hereto have participated jointly
in the negotiation and drafting of this Amendment.  In the event an ambiguity or question of
intent or interpretation arises, this Amendment shall be construed as if
drafted jointly by the parties hereto and no presumption or burden of proof
shall arise favoring or disfavoring any party by virtue of the authorship of
any provisions of this Amendment.  Time
is of the essence for this Amendment.


 


15.          Costs and Expenses. 
Borrower absolutely and unconditionally agree to reimburse Agent and
Lenders for all reasonable out-of-pocket fees, costs and expenses, including
all reasonable fees and expenses of counsel, incurred in the preparation,
negotiation, execution and delivery of this Amendment and any other Debt
Documents or other agreements prepared, negotiated, executed or delivered in
connection with this Amendment or transactions contemplated hereby, all in accordance
with Section 10.5 of the Loan Agreement.


 


 


[Signature
Page to Follow]


 


 


 


 


 


 


 


 


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                IN WITNESS WHEREOF, the parties hereto have caused this
Second Amendment to Loan and Security Agreement to be duly executed and
delivered as of the day and year specified at the beginning hereof.


 


 


 


	
   

  	
  BORROWER:

  	 

	
   

  	
   

  	 

	
   

  	
  HELICOS
  BIOSCIENCES CORPORATION

  	 

	
   

  	
   

  	 

	
   

  	
   

  	 

	
   

  	
  By:

  	
  /s/ Stephen J. Lombardi

  
	
   

  	
  Name:

  	
  Stephen J. Lombardi

  
	
   

  	
  Title:

  	
  President

  
					



 


 


 


 


 


 


 


[Additional signature pages to
follow]


 


 


 


 


 


 


 


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  AGENT AND LENDER:

  
	
   

  	
   

  
	
   

  	
  GENERAL ELECTRIC CAPITAL
  CORPORATION

  
	
   

  	
   

  
	
   

  	
   

  
	
   

  	
  By:

  	
  /s/ Danijela Gjenero

  
	
   

  	
  Name:

  	
  Danijela Gjenero

  
	
   

  	
  Title:

  	
  Duly Authorized
  Signatory

  
				



 


 


 


 


	
   

  	
  LENDER:

  
	
   

  	
   

  
	
   

  	
  CIT HEALTHCARE LLC

  
	
   

  	
   

  
	
   

  	
  By:

  	
  /s/ Jonathan L. Domm

  
	
   

  	
  Name:

  	
  Jonathan L. Domm

  
	
   

  	
  Title:

  	
  Senior Vice President

  
				



 


 


 


 


 


 


 


 


 


 


9

















 


 


 


EXHIBIT F


 


FORM OF
WARRANT


 


 


 


 


 


 


 


 


 


 


 


 


 


 


 


 


 


 


 


 


 


 


 


 


 


 


 


 


10