Exhibit 10.1


 


EXECUTION COPY


 


WAIVER AND THIRD
AMENDMENT TO LOAN AND SECURITY AGREEMENT


 


THIS
WAIVER AND THIRD AMENDMENT TO LOAN AND SECURITY AGREEMENT (this
“Amendment”) is dated as of December 29,
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 and that certain Second Amendment to Loan
and Security Agreement dated as of June 27, 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 will make a prepayment of $10,000,000 on or before December 31,
2008 (the “Pay Down Amount”) to Agent, for
the ratable benefit of the Lenders, that will be applied first to the
outstanding principal balance of the Initial Term Loan and then to the
outstanding principal balance of the Subsequent Term Loan; and


 


WHEREAS,
Borrower has requested that Agent and Lenders amend certain provisions of the
Loan Agreement, waive and defer certain fees and amend certain provisions of
the Loan Agreement, waive certain Events of Default that may have occurred
under the Debt Documents and waive certain other matters, 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 date hereof, prior
to giving effect to the payment of the Pay Down Amount, Borrower is indebted to
the Lenders in respect of the Term Loans in the aggregate principal amount of
$17,066,870.64.  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.                                      Waivers.


 


(a)                                  In
reliance upon the representations, warranties and covenants of the Borrower
contained in this Amendment, and subject to the terms and conditions of this
Amendment and any documents or instruments executed or delivered in connection
herewith, the Agent and each Lender hereby waives any Default or Event of Default that may have
occurred  under the Debt Documents
(collectively, the “Subject Events of Default”)
as a result of: (i) the failure of the Borrower to deliver (1) copies
of all statements, reports and notices made available generally by Borrower to
its securityholders or to any holders of Material Indebtedness and (2) copies
of all notices sent to Borrower or any Loan Party by the holders of Material
Indebtedness, and all documents filed with the Securities and Exchange
Commission or any securities exchange or governmental authority exercising a
similar function, in each case in accordance with Section 6.2(c) of
the Loan Agreement, for all periods from the Closing Date through the Amendment
Date, and (ii) the failure
of the Borrower to deliver notices relating to the Intellectual Property, in
accordance with Section 6.2(e) of the Loan Agreement, for all periods
from the Closing Date through the Amendment Date.  The waivers set forth in the
immediately preceding sentence relate solely to the Subject Events of Default,
and nothing in this Amendment is
intended (or shall be construed) to constitute a waiver by Agent or any Lender
of any other Default or Event of Default which may now or hereafter exist under
the Loan Agreement.


 


(b)                                 In
reliance upon the representations, warranties and covenants of the Borrower
contained in this Amendment, and subject to the terms and conditions of this
Amendment and any documents or instruments executed or delivered in connection
herewith, the Agent and Lenders hereby waive the prepayment premium payable
pursuant to Section 2.4 of the Loan Agreement solely with respect
to the Pay Down Amount.  The prepayment
premium payable pursuant to Section 2.4 of the Loan Agreement is
not hereby waived with respect to any prepayment other than the Pay Down
Amount.


 


3.                                      Amendments to Loan Agreement.  Subject
to the terms and conditions of this Amendment (including, without limitation,
the conditions to effectiveness set forth in Section 6 below), and
effective as of the Effective Date (as such term is defined in Section 6
below), the Loan Agreement is hereby amended as follows:


 


(a)                                  Section 2.4
of the Loan Agreement is hereby amended by deleting such section in its
entirety and replacing the following in lieu thereof:


 


“2.4. Prepayments.  Borrower
can voluntarily prepay, upon 5 Business Days’ prior written notice to Agent,
any Term Loan in full, but not in part (except for the portion of the Pay Down
Amount (as defined in that certain Waiver and Third Amendment to Loan Agreement
dated as of December 29, 2008 (the “Third Amendment”; and such
amount, the “Pay Down Amount”)) applied to the Subsequent Term Loan as a
prepayment in accordance with the terms of the Third Amendment).  Upon the date of (a) any voluntary
prepayment of a Term Loan in accordance with the


 


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immediately preceding
sentence or (b) any mandatory prepayment of a Term Loan required under
this Agreement (whether by acceleration of the Obligations pursuant to Section 8.2
or otherwise), Borrower shall pay to Agent, for the ratable benefit of the
Lenders, a sum equal to (i) all
outstanding principal plus accrued interest with respect to the such Term Loan,
(ii) the Final Payment Fee (as such term is defined in Section 2.7(b))
for such Term Loan, other than the deferred portion of the Final Payment Fee
solely with respect to the Pay Down Amount as set forth in Section 2.7(b),
which shall be payable in accordance with Section 2.7(b), and (iii) a
prepayment premium (as yield maintenance for the loss of a bargain and
not as a penalty) equal to: (A) 8.00%
of the outstanding principal of such Term Loan, if such payment is made on or
prior to the one year anniversary of the date such Term Loan was made (the “Applicable
First Anniversary”), (B) 2.00% of the outstanding principal amount of such Term Loan, if such
prepayment is made after the Applicable First Anniversary of such Term Loan but
on or before the two year anniversary of the date such Term Loan is made (the “Applicable
Second Anniversary”), and (C) 1.00% of the outstanding principal
amount of such Term Loan, if such prepayment is made after the Applicable Second
Anniversary but before the first day of the thirty-seventh month following the
date such Term Loan was made.”


 


(b)                                 Section 2.7
of the Loan Agreement is hereby amended by deleting clause (b) of such
section in its entirety and replacing the following in lieu thereof:


 


“(b)                           Final
Payment Fee.  Upon all outstanding principal amounts with
respect to any Term Loan being repaid, or being required to be repaid, in full
(whether voluntary, scheduled or mandatory or otherwise), for each Term Loan
Borrower shall pay to Agent, for the ratable accounts of Lenders, a fee equal
to 4.00% of the original principal amount of such Term Loan (the ‘Final
Payment Fee’); provided, however, notwithstanding the
foregoing, solely with respect to the Initial Term Loan, in lieu of the 4.00%
fee set forth above, Borrower shall pay to Agent, for the ratable accounts of
Lenders, a fee equal to 2.00% of the original principal amount of the Initial
Term Loan, which fee shall be fully earned on the Effective Date of (and as
such term is defined in) the Third Amendment, but shall be due and payable on
the earlier of (i) January 31, 2011 or (ii) the Applicable Term
Loan Maturity Date for the Subsequent Term Loan.”


 


(c)                                  Section 5.13
of the Loan Agreement is hereby amended by deleting such section in its
entirety and replacing the following in lieu thereof:


 


“5.13. Status of Helicos Biosciences Securities Corporation.  Borrower’s direct, wholly-owned Subsidiary,
Helicos Biosciences Securities Corporation, a Massachusetts corporation (“HBSC”),  has not engaged in any business (other than
establishing account number 1139758613 located at RBS Citizens, National
Association), does not own any assets and has not incurred any Indebtedness,
Liens or any other liabilities other than liabilities associated solely with
any taxes on HBSC and bank fees associated with HBSC’s bank account.”


 


(d)                                 Section 6.8(g) of
the Loan Agreement is hereby amended by deleting such clause in its entirety.


 


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(e)                                  Section 7.3
of the Loan Agreement is hereby amended by (i) deleting the comma at the
end of clause (d) of such section and replacing in lieu thereof, “and”,
and (ii) deleting clause (f) of such section in its entirety.


 


(f)                                    Section 7.7
of the Loan Agreement is hereby amended by deleting subclause (vi) of
clause (a) of such section and replacing in lieu thereof the following:


 


“(vi) [Reserved],”


 


(g)                                 Section 7.12
of the Loan Agreement is hereby amended by deleting such section in its
entirety and replacing the following in lie thereof:


 


 “7.12.  Helicos Biosciences
Securities Corporation.  HBSC
shall not (i) engage in any trade or business (other than maintaining an
account numbered 1139758613 located at RBS Citizens, National Association,
which account shall not contain any assets other than as expressly permitted by
Agent and Lenders in writing), (ii) own any assets or (iii) incur any
Indebtedness, Liens or any other liabilities other than liabilities associated
solely with any taxes on HBSC and bank fees associated with HBSC’s bank
account.”


 


(h)                                 Exhibit D
of the Loan Agreement is hereby amended by deleting clause (iii) of such
exhibit in its entirety and replacing the following in lieu thereof:


 


“(iii)  [Reserved]”


 


4.                                      No
Other Waivers or Amendments. 
Except for the waiver and amendments set forth and referred to in Section 2
and Section 3, respectively, 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.


 


5.                                      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 (other than the Subject Events of Default that
are waived in accordance with Section 2 hereof), (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, and (iv) attached
hereto as Exhibit A is a summary of all Intellectual Property of
the Borrower that 


 


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has been registered or abandoned during the period from the Closing
Date through the Amendment Date.


 


6.                                      Condition
Precedent to Effectiveness of this Amendment.  This Amendment shall become effective as of
the Amendment Date, and the waiver set forth in Section 2 and the
amendments set forth in Section 3 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 Pay Down Amount in immediately available funds; and


 


(c)  evidence satisfactory to Agent that Borrower
has received net cash proceeds of at least $15,000,000 from an issuance of
equity in form and substance, and subject to documentation, satisfactory to
Agent.


 


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, this Amendment 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 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 


 


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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 7 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 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 


 


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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 Waiver and Third 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:

  	
   

  
	
   

  	
  Name:

  
	
   

  	
  Title:

  



 


[Additional signature pages to
follow]


 

















 


	
   

  	
  AGENT AND LENDER:

  
	
   

  	
   

  
	
   

  	
  GENERAL ELECTRIC CAPITAL 

  
	
   

  	
  CORPORATION

  
	
   

  	
   

  
	
   

  	
   

  
	
   

  	
  By:

  	
   

  
	
   

  	
  Name:

  
	
   

  	
  Title: Duly Authorized
  Signatory

  
	
   

  	
   

  
	
   

  	
   

  
	
   

  	
  LENDER:

  
	
   

  	
   

  
	
   

  	
   

  
	
   

  	
  CIT HEALTHCARE LLC

  
	
   

  	
   

  
	
   

  	
   

  
	
   

  	
  By:

  	
   

  
	
   

  	
  Name:

  
	
   

  	
  Title:

  



 

















 


EXHIBIT A


 


Changes
to Intellectual Property