EXHIBIT 10.2


 


EXECUTION VERSION


 


THIS
INSTRUMENT AND THE INDEBTEDNESS, RIGHTS AND OBLIGATIONS EVIDENCED HEREBY AND
ANY LIENS OR OTHER SECURITY INTERESTS SECURING SUCH RIGHTS AND OBLIGATIONS ARE
SUBORDINATE (A) IN THE MANNER AND TO THE EXTENT SET FORTH IN THAT CERTAIN
SUBORDINATION AND INTERCREDITOR AGREEMENT (AS AMENDED, RESTATED, SUPPLEMENTED
OR MODIFIED FROM TIME TO TIME, THE “SENIOR SUBORDINATION AGREEMENT”) DATED AS
OF NOVEMBER 16, 2010, BY AND AMONG THE SUBORDINATED CREDITORS IDENTIFIED
THEREIN AND GENERAL ELECTRIC CAPITAL CORPORATION IN ITS CAPACITY AS AGENT FOR
CERTAIN LENDERS (TOGETHER WITH ITS SUCCESSORS AND ASSIGNS, “SENIOR CREDITOR
AGENT”), TO CERTAIN INDEBTEDNESS, RIGHTS, AND OBLIGATIONS OF HELICOS
BIOSCIENCES CORPORATION TO SENIOR CREDITOR AGENT AND SENIOR CREDITOR (AS
DEFINED THEREIN) AND LIENS AND SECURITY INTERESTS OF SENIOR CREDITOR AGENT
SECURING THE SAME ALL AS DESCRIBED IN THE SENIOR SUBORDINATION AGREEMENT AND (B) IN
THE MANNER AND TO THE EXTENT SET FORTH IN THAT CERTAIN SUBORDINATION AND
INTERCREDITOR AGREEMENT (AS AMENDED, RESTATED, SUPPLEMENTED OR MODIFIED FROM
TIME TO TIME, THE “JUNIOR SUBORDINATION AGREEMENT” AND TOGETHER WITH THE SENIOR
SUBORDINATION AGREEMENT, THE “SUBORDINATION AGREEMENTS”) DATED AS OF NOVEMBER 16,
2010, BY AND AMONG THE SUBORDINATED CREDITORS IDENTIFIED THEREIN AND GOODWIN
PROCTER LLP (TOGETHER WITH ITS SUCCESSORS AND ASSIGNS, “GOODWIN”), TO CERTAIN
INDEBTEDNESS, RIGHTS, AND OBLIGATIONS OF HELICOS BIOSCIENCES CORPORATION TO
GOODWIN AND LIENS AND SECURITY INTERESTS OF GOODWIN SECURING THE SAME ALL AS
DESCRIBED IN THE JUNIOR SUBORDINATION AGREEMENT, AND EACH HOLDER AND TRANSFEREE
OF THIS INSTRUMENT, BY ITS ACCEPTANCE HEREOF, IRREVOCABLY AGREES TO BE
BOUND BY THE PROVISIONS OF THE SUBORDINATION AGREEMENTS.


 


RISK PREMIUM PAYMENT AGREEMENT


 


THIS RISK PREMIUM PAYMENT AGREEMENT (this “Agreement”),
is made as of November 16, 2010 (the “Effective Date”),
by and among HELICOS
BIOSCIENCES CORPORATION, a Delaware corporation (the “Company”), and each of the Lenders identified on the
signature pages hereto (each individually a “Lender,”
and collectively the “Lenders”).


 


WHEREAS, the Company requires additional funds in order to
fund its operations;


 


WHEREAS, the Company desires to issue and sell certain
secured promissory notes in aggregate principal amount of up to $4,000,000 (the
“Notes”) to the Lenders in one or more
closings pursuant to a Subordinated Secured Note Purchase Agreement (the “Purchase Agreement”) to be entered into currently with this
Agreement;


 


WHEREAS, the Lenders would be unwilling to purchase any Notes
pursuant to the Purchase Agreement in the absence of a separate agreement
between the Company and the Lenders on the terms set forth in this Agreement;


 


NOW, THEREFORE, THE PARTIES HEREBY AGREE AS FOLLOWS:


 

















 


1.             DEFINITIONS.


 


1.1        “Affiliate”
shall mean, with respect to any person, any other person directly or indirectly
controlling, controlled by or under common control with such first person.


 


1.2        “Aggregate
Payment Consideration” shall mean, as of the time of any Liquidity
Transaction, the aggregate amount of all Payment Consideration with respect to
all Liquidity Transactions up to and including such Liquidity Transaction.


 


1.3        “Aggregate
Previous Risk Premium Payments” shall mean, with respect to any Risk
Premium Payment, the aggregate amount of all Risk Premium Payments previously
received by the Lenders, which shall be deemed to include any portions thereof
otherwise paid by, or invested in, the Company in accordance with written
instructions provided to the Company, pursuant to Section 2.6 of
this Agreement, by the Lender entitled to receive such amount.


 


1.4        “Agreement”
shall have the meaning ascribed to such term in the preamble to this Agreement.


 


1.5        “Business Day”
shall mean each day that is not a Saturday, Sunday or other day on which
banking institutions located in Boston, Massachusetts are authorized or
obligated by law or executive order to close.


 


1.6        “Change of
Control Liquidity Event” shall mean the first of the following
events occurring on or following the date of this Agreement:  (a) a merger or consolidation in which (i) the
Company is a constituent party or (ii) a Subsidiary of the Company is a
constituent party and the Company issues shares of its capital stock pursuant
to such merger or consolidation, except, in the case of either sub-clause (i) or
(ii) of this clause (a), any merger or consolidation in which the holders
of capital stock of the Company immediately prior to such merger or
consolidation continue to hold immediately following such merger or
consolidation, in approximately the same proportions as such shares were held
immediately prior to such merger or consolidation, at least a majority by
voting power and economic interest of the capital stock of the surviving or
resulting corporation, or if the surviving or resulting corporation is a wholly
owned Subsidiary of another corporation immediately following such merger or
consolidation, the parent corporation of such surviving or resulting
corporation, and (b) the sale or exclusive license, in a single
transaction or series of related transactions, by the Company or any of its
Subsidiaries of all or substantially all the assets or intellectual property of
the Company and its Subsidiaries taken as a whole.


 


1.7        “Company”
shall have the meaning ascribed to such term in the preamble to this Agreement.


 


1.8        “Company
Change of Control Notice” shall have the meaning ascribed to such
term in Section 2.5 of this Agreement.


 


1.9        “Company
Licensing Notice” shall have the meaning ascribed to such term in Section 2.3
of this Agreement.


 


1.10      “Contingent
and Contractual Arrangements” means any contingent fee agreement or
contractual obligation of the Company consented to by the Majority Lenders in
their sole discretion.


 


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1.11      “Effective
Date” shall have the meaning ascribed to such term in the preamble
to this Agreement.


 


1.12      “Lenders”
shall have the meaning ascribed to such term in the preamble to this Agreement.


 


1.13      “Liquidity
Payment Recipients” shall mean the Company, any Subsidiary of the
Company, any stockholders of the Company and any Affiliate of any of the
foregoing persons


 


1.14      “Liquidity
Transaction” shall mean any of the following events occurring on or
following the date of this Agreement until and including the first Change of
Control Liquidity Event:  (a) the
receipt by the Company of any payments, whether in cash or in any other form of
consideration, in any transaction or series of transactions at any time from
and after the execution of the Purchase Agreement, from any person, relating to
the intellectual property portfolio of the Company as such portfolio exists as
of the date of this Agreement, including payments, whether in cash or in any
other form of consideration, pursuant to any license, development, settlement,
right to use, joint venture or other similar agreement and (b) a Change of
Control Liquidity Event.


 


1.15      “Majority
Lenders” shall mean either (i) at least one of the Lenders
affiliated with Flagship Ventures and one of the Lenders affiliated with Atlas
Venture, or (ii) the holders of at least two-thirds of the aggregate
outstanding principal amount of all the Notes.


 


1.16      “Notes”
shall have the meaning ascribed to such term in the recitals to this Agreement.


 


1.17      “Objection
Notice” shall have the meaning ascribed to such term in Section 2.4
of this Agreement.


 


1.18      “Payment
Consideration” shall mean, with respect to any Liquidity
Transaction, the sum of any and all consideration paid or payable to the Liquidity
Payment Recipients on account of such Liquidity Transaction minus any amounts
required to be paid by the Liquidity Payment Recipients in connection with such
Liquidity Transaction under (a) Senior Facility (as defined in the
Purchase Agreement) as in effect following the modification thereof on the date
of this Agreement (b) the professional contingency arrangement between the
Company and Goodwin Procter LLP set forth in the letter dated October 22,
2010, (c) Contingent and Contractual Arrangements, (d) that certain
License Agreement dated March 15, 2005 by and between the Company and
Arizona Technology Enterprises, (e) that certain License Agreement dated June 7,
2004 by and between the Company, Roche Diagnostics GMBH and Roche Diagnostics
Corporation, and (f) that certain License Agreement dated November 30,
2003 by and between the Company and California Institute of Technology;
provided, however, that if such calculation yields an amount less than $0, the
Payment Consideration with respect to such Liquidity Transaction shall be $0;
and provided further that in the event that any or all of the consideration
paid or payable to the Liquidity Payment Recipients on account of such
Liquidity Transaction is in a form other than cash, then, for purposes of the calculation
of the Payment Consideration (including the calculation of any deductions under
clauses (a) through (c) of this sentence), all such non-cash
consideration shall be valued at cash amounts calculated in accordance with the
pricing mechanics of the applicable definitive transaction agreement with
respect to the Liquidity Transaction.


 


1.19      “Payment Date”
shall have the meaning ascribed to such term in Section 2.1 of this
Agreement.


 


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1.20      “Purchase Agreement”
shall have the meaning ascribed to such term in the recitals to this Agreement.


 


1.21      “Risk Premium
Payment” shall mean, with respect to any Liquidity Transaction:


 


(a)         If the Aggregate Payment
Consideration as of the time of such Liquidity Transaction (inclusive of the
Payment Consideration with respect to such Liquidity Event) is less than or
equal to $10,000,000, the amount yielded by the following formula, where “APC”
represents the Aggregate Payment Consideration as of the time of such Liquidity
Transaction, “APRPP” represents the amount of the Aggregate Previous Risk
Premium Payments and “IP” represents the aggregate amount of any interest that
has been paid, or, solely in the event that such Liquidity Transaction is a
Change of Control Liquidity Event, is otherwise payable, on the Notes as of the
time of such Liquidity Transaction, provided, however, that if the amount
yielded by such formula is less than $0, the Risk Premium Payment with respect
to such Liquidity Transaction shall be $0:


 


(0.6 * APC) - APRPP - IP


 


(b)        If the Aggregate Payment
Consideration as of the time of such Liquidity Transaction (inclusive of the
Payment Consideration with respect to such Liquidity Event) is greater than
$10,000,000 and less than or equal to $20,000,000, the amount yielded by the
following formula, where “APC” represents the Aggregate Payment Consideration
as of the time of such Liquidity Transaction, “APRPP” represents the amount of
the Aggregate Previous Risk Premium Payments and “IP” represents the aggregate
amount of any interest that has been paid, or, solely in the event that such
Liquidity Transaction is a Change of Control Liquidity Event, is otherwise
payable, on the Notes as of the time of such Liquidity Transaction, provided,
however, that if the amount yielded by such formula is less than $0, the Risk
Premium Payment with respect to such Liquidity Transaction shall be $0:


 


$6,000,000 + (0.5 * (APC -
$10,000,000)) - APRPP - IP


 


(c)         If the Aggregate Payment
Consideration as of the time of such Liquidity Transaction (inclusive of the
Payment Consideration with respect to such Liquidity Event) is greater than
$20,000,000 and less than or equal to $30,000,000, the amount yielded by the
following formula, where “APC” represents the Aggregate Payment Consideration
as of the time of such Liquidity Transaction, “APRPP” represents the amount of
the Aggregate Previous Risk Premium Payments and “IP” represents the aggregate
amount of any interest that has been paid, or, solely in the event that such
Liquidity Transaction is a Change of Control Liquidity Event, is otherwise
payable, on the Notes as of the time of such Liquidity Transaction, provided,
however, that if the amount yielded by such formula is less than $0, the Risk
Premium Payment with respect to such Liquidity Transaction shall be $0:


 


$11,000,000 + (0.4 * (APC -
$20,000,000)) - APRPP - IP


 


(d)        If the Aggregate Payment
Consideration as of the time of such Liquidity Transaction (inclusive of the
Payment Consideration with respect to such Liquidity Event) is greater than
$30,000,000 and less than or equal to $40,000,000, the amount yielded by the
following formula, where “APC” represents the Aggregate Payment Consideration
as of the time of such Liquidity Transaction, “APRPP” represents the amount of the
Aggregate Previous Risk Premium Payments and “IP” represents the aggregate
amount of any interest that has been paid, or, solely in the event that such
Liquidity Transaction is a Change of Control Liquidity Event, is otherwise
payable, on the Notes as of the time of such Liquidity Transaction, provided,
however, that if the amount yielded by such formula is less than $0, the Risk
Premium Payment with respect to such Liquidity Transaction shall be $0:


 


4

















 


$15,000,000 + (0.3 * (APC -
$30,000,000)) - APRPP - IP


 


(e)         If the Aggregate Payment
Consideration as of the time of such Liquidity Transaction (inclusive of the
Payment Consideration with respect to such Liquidity Event) is greater than
$40,000,000, the amount yielded by the following formula, where “APC”
represents the Aggregate Payment Consideration as of the time of such Liquidity
Transaction, “APRPP” represents the amount of the Aggregate Previous Risk
Premium Payments and “IP” represents the aggregate amount of any interest that
has been paid, or, solely in the event that such Liquidity Transaction is a
Change of Control Liquidity Event, is otherwise payable, on the Notes as of the
time of such Liquidity Transaction, provided, however, that if the amount
yielded by such formula is less than $0, the Risk Premium Payment with respect
to such Liquidity Transaction shall be $0:


 


$18,000,000 + (0.1 * (APC -
$40,000,000)) - APRPP - IP


 


1.22      “Subsidiary”
means, with respect to any person, any other person the management of which is
directly or indirectly controlled by, or of which an aggregate of more than 50%
of the outstanding voting capital stock (or other voting equity interest) is,
at the time, owned or controlled, directly or indirectly by, such first person.


 


2.             PAYMENT OF RISK PREMIUM


 


2.1        Risk Premium Entitlement.  Subject to the terms and conditions of the
Senior Subordination Agreement, upon the occurrence of a Liquidity Transaction
other than a Change of Control Liquidity Event, the Lenders shall be entitled
to receive from the Company a Risk Premium Payment with respect to such
Liquidity Transaction on the forty-fifth (45th) calendar day (or, if such day is not a Business
Day, the next Business Day immediately following such day) following the
closing of the Liquidity Transaction, and upon the occurrence of a Change of
Control Liquidity Event, the Lenders shall be entitled to receive from the
Company a Risk Premium Payment with respect to such Liquidity Transaction
concurrently with the closing of such Liquidity Transaction (the date on which
any such payment is due, a “Payment Date”).  This Risk Premium Payment shall be allocated
among the Lenders pro rata in accordance with the aggregate principal amount of
Notes purchased by each of the Lenders (regardless of whether all or any of
such Notes are then outstanding) prior to or concurrently with the occurrence
of the Liquidity Transaction. 
Notwithstanding anything to the contrary provided in this agreement and
for the avoidance of doubt, from and after a Change of Control Liquidity Event,
the Lenders shall be entitled to the Risk Premium Payment with respect to such
Change of Control Liquidity Event and shall not be entitled to Risk Premium
Payments with respect to any subsequent event (including, without limitation,
Risk Premium Payments that would otherwise subsequently be payable in respect
of licensing agreements entered into prior to the Change of Control Liquidity
Event that resulted in the occurrence of Licensing Liquidity Events prior to
such Change of Control Liquidity Event).


 


2.2        Consideration of Securities.  In the event that the Payment Consideration
with respect to a Liquidity Transaction consists, in whole or in part, of
securities, then the Risk Premium Payment to which the Lenders are entitled
with respect to such Liquidity Transaction shall be payable in the form of such
securities in a percentage that is equal to the percentage that the securities
included in such Payment Consideration represent of the total amount of such
Payment Consideration, with such securities valued in accordance with the
pricing mechanics of the definitive transaction agreement for the Liquidity
Transaction.  The balance of the Risk
Premium Payment not payable in the form of such securities shall be payable in
cash and not in any other form of asset. 
Notwithstanding the other provisions of this Section 2.2, if
distribution of any such securities to a Lender in accordance with this Section 2.2
would, in the reasonable opinion of counsel to such Lender or counsel to the
Company, violate applicable securities law, the portion of the Risk Premium
Payment that would otherwise be 


 


5

















 


payable in the form of such
securities to such Lender shall be payable in such other form of consideration
as shall be mutually agreed between such Lender and the Company.


 


2.3        Notice of Licensing Event.  Within two (2) Business Days following
the occurrence of a Liquidity Transaction other than a Change of Control
Liquidity Event (a “Licensing Liquidity Event”),
the Company shall deliver written notice to the Lenders of such event (a “Company Licensing Notice”), which shall include a brief
description of the Liquidity Transaction, including without limitation (a) the
identity of any parties that entered into one or more agreements with any of
the Liquidity Payment Recipients in connection with the Liquidity Transaction, (b) the
material terms of the Liquidity Transaction, (c) the Company’s calculation
of the amount of Payment Consideration occurring with respect to the Liquidity
Transaction, including a description of how such Payment Consideration was
payable as divided among the Liquidity Payment Recipients, (d) the Company’s
calculation of the Risk Premium Payment with respect to the Liquidity Transaction,
including without limitation, the Company’s calculations of (i) the
Aggregate Payment Consideration, (ii) the Aggregate Previous Risk Premium
Payments and (iii) the aggregate amount of any interest that has been paid
on the Notes as of the time of such Liquidity Transaction, (e) if
applicable, the Company’s calculation of the value of the Payment Consideration
that is in the form of securities and the portion of the Risk Premium Payment
that is consequently payable in the form of such securities pursuant to this
Agreement and (f) reasonable back-up documentation supporting such
calculations that would enable a reasonable person to review and evaluate such
calculations.


 


2.4        Verification and Contesting of
Company Calculations Regarding Licensing Events.  During the twenty (20) calendar days
following receipt of a Company Licensing Notice, each Lender shall have the
right to request further reasonable documentation from the Company with respect
to the Liquidity Transaction described in such Company Licensing Notice and the
calculations of the Company set forth in such Company Licensing Notice and the
Company shall provide such requested documentation to the requesting Lender
promptly following any such request. 
Each Lender shall have the right, at any time on or prior to the
thirtieth (30th) calendar day
following receipt of a Company Licensing Notice to object to any calculation of
the Company set forth in such Company Licensing Notice, which right shall be
exercisable by delivery of a written notice of such objection (an “Objection Notice”) to the Company and each other Lender
specifying in reasonable detail the reasons for the Lender’s objection and the
alternative calculations that the Lender believes to be correct.  In the event that any Lender delivers any
such Objection Notice, the Lenders and the Company shall attempt in good faith
to agree upon the appropriate calculation of any contested amounts.  If no such agreement can be reached prior to
the Payment Date with respect to such Liquidity Transaction, the Company shall
deliver to the Lenders on the Payment Date the full amount of the Risk Premium
Payment set forth in the Company Licensing Notice in accordance with the
procedures specified in Section 2.6 of this Agreement, and any of
the Company or the Lenders may demand arbitration as to the remainder of the
Risk Premium Payment that is demanded by the Lenders by delivering written
notice of such demand to each of the other parties hereto.  The arbitrator for such arbitration shall be
mutually agreed upon by the parties, and in the event that, within thirty (30)
calendar days after submission of any dispute to arbitration, the parties
cannot mutually agree on one arbitrator, then, within fifteen (15) calendar
days after the end of such thirty (30) calendar-day period, the Lenders, taken
together, shall select one (1) arbitrator and the Company shall select one
(1) arbitrator.  The two (2) arbitrators
so selected shall select a third arbitrator to participate in the conduct the
arbitration.  Any such arbitration shall
be held in Suffolk County, Massachusetts under the rules then in effect of
the American Arbitration Association. 
The decision of the arbitrator or a majority of the three arbitrators,
as the case may be, as to the appropriate calculation of the contested amounts
shall be final, binding, and conclusive upon the parties.  Such decision shall be written and shall be
supported by written findings of fact and conclusions which shall set forth the
judgment of the arbitrator(s).  Within
two (2) Business Days following any judgment of the arbitrator(s) requiring
additional payments by the Company to the Lenders, the Company shall 


 


6

















 


deliver such amounts to the
Lenders in accordance, mutatis mutandis,
with the procedures specified in Section 2.6 of this Agreement.


 


2.5        Advance Notice of Change of
Control Liquidity Event; Certification.  The Company shall deliver written notice to
the Lenders at least twenty (20) Business Days prior to the closing of any
Change of Control Liquidity Event (a “Company Change of Control
Notice”), which Company Change of Control Notice shall include a
brief description of the anticipated Change of Control Liquidity Event,
including without limitation (a) the material terms of the Change of
Control Liquidity Event (notice of which terms shall be deemed satisfied if
such terms are described in a Current Report on Form 8-K filed with the
Securities and Exchange Commission on or prior to the date on which the Company
shall deliver such Change of Control Liquidity Notice), (b) the Company’s
best estimated calculation of the amount of Payment Consideration that will
occur with respect to the Liquidity Transaction, including a description of how
such Payment Consideration will be payable as divided among the Liquidity
Payment Recipients, (c) the Company’s best estimated calculation of the
Risk Premium Payment that will occur with respect to the Change of Control
Liquidity Event, including without limitation, the Company’s calculations of (i) the
anticipated Aggregate Payment Consideration, (ii) the anticipated
Aggregate Previous Risk Premium Payments and (iii) the aggregate
anticipated amount of any interest that will have been paid on the Notes as of
the time of such Liquidity Transaction, (d) if applicable, the Company’s
best estimated calculation of the value of the Payment Consideration that is in
the form of securities and the portion of the Risk Premium Payment that is
consequently payable in the form of such securities pursuant to this Agreement
and (e) reasonable back-up documentation supporting such calculations that
would enable a reasonable person to review and evaluate such calculations.  From and after the delivery of a Company
Change of Control Notice until the closing of the Liquidity Transaction to
which such notice relates, each Lender shall have the right to request further
reasonable documentation from the Company with respect to the Change of Control
Liquidity Event described in such Company Change of Control Notice and the
calculations of the Company set forth in such Company Change of Control Notice
and the Company shall provide such requested documentation to the requesting
Lender promptly following any such request. 
One Business Day prior to the closing of a Change of Control Liquidity
Event, the Chief Financial Officer of the Company, or the person holding the
equivalent office with the Company in the event that the Company does not then
have an officer with such a title, shall deliver to the Lenders a certification
setting forth the Company’s final definitive calculations for all calculations
required to be included in a Company Change of Control Notice with respect to
such Change of Control Liquidity Event along with reasonable back-up
documentation supporting such calculations that would enable a reasonable
person to review and evaluate such calculations, and which shall certify that
all such calculations are true, correct and complete in all respects and that
the back-up documentation provided with the certificate in support of such
calculations is true, correct and complete in all respects.


 


2.6        Risk Premium Payment.  Subject to the terms
and conditions of the Subordination Agreement, on the Payment Date relating to
each Liquidity Transaction, the Company shall deliver to the Lenders the Risk
Premium Payment to which the respective Lenders are entitled pursuant to Section 2.1
of this Agreement, such payment to be delivered (a) to the extent in the
form of cash, by wire transfer of immediately available funds to the respective
accounts designated by the Lenders by written notice to the Company given on or
prior to the Payment Date and (b) to the extent in the form of securities,
by physical delivery of certificates representing such securities to the
Lenders at their respective addresses specified on the signature pages hereto
as the same may be updated from time to time by the Lenders upon the furnishing
of written notice to the Company, or by such other means as may be mutually
agreed to between the applicable Lender and the Company.  At any time prior to the delivery by the
Company of payment pursuant to the preceding sentence, the Lender entitled to
receive such payment may, upon the furnishing of written notice to the Company,
request that any payment that such Lender is entitled to receive pursuant to
this Agreement be instead directed to any other person 


 


7

















 


(provided that a Lender may
not require that payment in the form of securities be directed to any person
where such payment would, in the reasonable opinion of counsel to the Company,
result in a violation of applicable securities law) or be reinvested in the
Company upon terms and conditions acceptable to such Lender in its sole
discretion.


 


3.             MISCELLANEOUS.


 


3.1        Successors and Assigns.  Except as otherwise provided herein, the
terms and conditions of this Agreement shall inure to the benefit of and be
binding upon the respective successors and assigns of the parties, provided,
however, that the Company may not assign its obligations under this
Agreement without the written consent of each of the Lenders and no Lender may
assign its obligations under this Agreement other than to its Affiliates
(which, for the avoidance of doubt, shall include any management company of a
Lender that is a venture capital fund) without the written consent of the
Company.  Nothing in this Agreement,
express or implied, is intended to confer upon any party other than the parties
hereto or their respective successors and assigns any rights, remedies,
obligations or liabilities under or by reason of this Agreement, except as
expressly provided in this Agreement.


 


3.2        Governing Law.  This Agreement shall be governed by and
construed under the laws of the Commonwealth of Massachusetts.


 


3.3        Counterparts.  This Agreement may be executed in two or more
counterparts, each of which shall be deemed an original, but all of which
together shall constitute one and the same instrument.


 


3.4        Titles and Subtitles.  The titles and subtitles used in this
Agreement are used for convenience only and are not to be considered in
construing or interpreting this Agreement.


 


3.5        Interpretation.  For all purposes hereof, the terms “include,”
“includes” and “including” shall be deemed followed by the words “without
limitation.”  The definitions contained
in this Agreement are applicable to the singular as well as the plural forms of
such terms.  Any agreement or instrument
defined or referred to in this Agreement or in any agreement or instrument that
is referred to in this Agreement means such agreement or instrument as from
time to time amended, modified or supplemented. 
References to a person are also to its permitted successors and assigns.


 


3.6        Notices.  All
notices and other communications given or made pursuant to this Agreement shall
be in writing and shall be deemed effectively given:  (a) upon personal delivery to the party
to be notified, (b) when sent by confirmed facsimile if sent during normal
business hours of the recipient, if not so confirmed, then on the next Business
Day, (c) five (5) calendar days after having been sent by registered
or certified mail, return receipt requested, postage prepaid or (d) one (1) Business
Day after deposit with a nationally recognized overnight courier, specifying
next day delivery, with written verification of receipt.  All communications shall be sent to the
respective parties at the following addresses (or at such other addresses as
shall be specified by notice given in accordance with this Section 3.6):


 


If to the Company:


 


HELICOS BIOSCIENCES
CORPORATION.

One Kendall Square


Suite 7301


Cambridge,
MA 02139

Attention:  Chief Financial Officer


 


8

















 


With
a copy, delivery of which shall not constitute notice to the Company hereunder,
to:


 


Goodwin
Procter LLP


53 State Street


Boston, MA 02109


Attention:     Stuart Cable, Esq.


James
Matarese, Esq.


 


If to the Lenders:


 


At
the respective addresses shown on the signature pages of this Agreement
(provided that for Purchasers sharing a single address as shown on the
signature pages of this Agreement, delivery of a single notice or other
communication, as applicable, addressed to all such Purchasers, to such address
in accordance with the remainder of this Section 3.6, shall be sufficient
to for compliance with this Section 3.6), with a copy, delivery of which
shall not constitute notice to any Lender hereunder, to:


 


Wilmer
Cutler Pickering Hale and Dorr LLP


60
State Street


Boston,
MA 02109


Attn:  Philip P. Rossetti, Esq.


Facsimile:  617-526-5000


 


3.7        Entire Agreement; Amendments and
Waivers.  This Agreement constitutes the
full and entire understanding and agreement between and among the parties with
regard to the subject hereof. 
Notwithstanding anything to the contrary set forth herein, any term of
this Agreement may be amended and the observance of any term of this Agreement
may be waived (either generally or in a particular instance and either
retroactively or prospectively) with the written consent of the Majority
Lenders and the Company.


 


3.8        Severability.  If one or more provisions of this Agreement
are held to be unenforceable under applicable law, such provision shall be
excluded from this Agreement and the balance of the Agreement shall be
interpreted as if such provision were so excluded and shall be enforceable in
accordance with its terms.


 


3.9        Indemnity; Costs, Expenses and
Attorneys’ Fees.  The Company
shall pay all costs and expenses that it incurs with respect to the
negotiation, execution and delivery of this Agreement.  The Company shall indemnify and hold each
Lender harmless from any loss, cost, liability and legal or other expense,
including reasonable attorneys’ fees of such Lender’s counsel, which a Lender
may directly or indirectly suffer or incur by reason of the failure of the
Company to perform any of its obligations under this Agreement.


 


3.10      Further Assurance.  From time to time, the Company shall execute
and deliver to the Lenders such additional documents and shall provide such
additional information to the Lenders as any Lender may reasonably require to
carry out the terms of this Agreement.


 


3.11      Amendments and Waivers.  Notwithstanding anything to the contrary set
forth herein, any term of this Agreement may be amended and the observance of
any term of this Agreement may be waived (either generally or in a particular
instance and either retroactively or prospectively), with the written consent
of all parties hereto.


 


9

















 


3.12      Waiver of Jury Trial.  TO THE EXTENT EACH MAY LEGALLY DO SO,
EACH PARTY HERETO HEREBY EXPRESSLY WAIVES ANY RIGHT TO TRIAL BY JURY OF ANY
CLAIM, DEMAND, ACTION, CAUSE OF ACTION, OR PROCEEDING ARISING UNDER OR WITH
RESPECT TO THIS AGREEMENT, OR IN ANY WAY CONNECTED WITH, OR RELATED TO, OR
INCIDENTAL TO, THE DEALING OF THE PARTIES HERETO WITH RESPECT TO THIS
AGREEMENT, OR THE TRANSACTIONS RELATED THERETO, IN EACH CASE WHETHER NOW
EXISTING OR HEREAFTER ARISING, AND IRRESPECTIVE OF WHETHER SOUNDING IN
CONTRACT, TORT, OR OTHERWISE.  TO THE EXTENT
EACH MAY LEGALLY DO SO, EACH PARTY HERETO HEREBY AGREES THAT ANY SUCH
CLAIM, DEMAND, ACTION, OR PROCEEDING SHALL BE DECIDED BY A COURT TRIAL WITHOUT
A JURY AND THAT EITHER PARTY HERETO MAY FILE AN ORIGINAL COUNTERPART OR
A COPY OF THIS AGREEMENT WITH ANY COURT AS WRITTEN EVIDENCE OF THE CONSENT OF
ANY OTHER PARTY HERETO TO THE WAIVER OF ITS RIGHT TO TRIAL BY JURY.


 


[Signature pages follow]


 


10
















 


IN WITNESS WHEREOF, the parties have executed
this Risk Premium Payment Agreement as of the date first above written.


 


	
   

  	
  COMPANY:

  
	
   

  	
   

  
	
   

  	
  HELICOS
  BIOSCIENCES CORPORATION

  
	
   

  	
   

  
	
   

  	
  By:

  	
  /s/
  Ivan Trifunovich

  
	
   

  	
   

  	
  Name:
  Ivan Trifunovich

  
	
   

  	
   

  	
  Title:
  Chairman, President and Chief Executive Officer

  



 


[Signature Page to Risk
Premium Payment Agreement]


 

















 


	
   

  	
  LENDERS:

  
	
   

  	
   

  
	
   

  	
  APPLIED GENOMIC
  TECHNOLOGY CAPITAL FUND, L.P.;

  
	
   

  	
  AGTC ADVISORS
  FUND, L.P.

  
	
   

  	
  Each by AGTC Partners, L.P., its General Partner

  
	
   

  	
  By NewcoGen Group Inc. its General Partner

  
	
   

  	
   

  
	
   

  	
   

  
	
   

  	
  By:

  	
  /s/ Noubar Afeyan

  
	
   

  	
   

  	
  Name: Noubar
  Afeyan

  
	
   

  	
   

  	
  Title: President

  
	
   

  	
   

  	
   

  
	
   

  	
   

  	
   

  
	
   

  	
  Notice
  Address:

  
	
   

  	
   

  
	
   

  	
  One
  Memorial Drive, Seventh Floor

  
	
   

  	
  Cambridge,
  MA 02142

  
	
   

  	
  Attn:

  
	
   

  	
   

  
	
   

  	
   

  
	
   

  	
  NEWCOGEN
  GROUP LLC;

  
	
   

  	
  NEWCOGEN
  EQUITY INVESTORS LLC;

  
	
   

  	
  NEWCOGEN-ELAN
  LLC;

  
	
   

  	
  NEWCOGEN-PE
  LLC;

  
	
   

  	
  NEWCOGEN-LONG
  REIGN HOLDING LLC;

  
	
   

  	
  ST
  NEWCOGEN LLC

  
	
   

  	
   

  
	
   

  	
  Each
  by its Manager NewcoGen Group Inc.

  
	
   

  	
   

  
	
   

  	
  By:

  	
  /s/
  Noubar Afeyan

  
	
   

  	
   

  	
  Name:
  Noubar Afeyan

  
	
   

  	
   

  	
  Title:
  President

  
	
   

  	
   

  	
   

  
	
   

  	
   

  	
   

  
	
   

  	
  Notice
  Address:

  
	
   

  	
  One Memorial Drive, Seventh Floor

  
	
   

  	
  Cambridge, MA 02142

  
	
   

  	
  Attn:

  
				



 


[Signature Page to Risk
Premium Payment Agreement]


 

















 


	
   

  	
  LENDERS:

  
	
   

  	
   

  
	
   

  	
  FLAGSHIP VENTURES FUND 2004, L.P.

  
	
   

  	
   

  
	
   

  	
  By its General Partner

  
	
   

  	
  Flagship Ventures General
  Partner

  
	
   

  	
  LLC

  
	
   

  	
   

  
	
   

  	
  By:

  	
  /s/ Noubar Afeyan

  
	
   

  	
   

  	
  Manager

  
	
   

  	
   

  
	
   

  	
   

  
	
   

  	
  Notice
  Address:

  
	
   

  	
   

  
	
   

  	
  One
  Memorial Drive, Seventh Floor

  
	
   

  	
  Cambridge,
  MA 02142

  
	
   

  	
  Attn:

  



 


[Signature Page to Risk
Premium Payment Agreement]


 

















 


	
   

  	
  LENDERS:

  
	
   

  	
   

  
	
   

  	
  ATLAS VENTURE FUND
  VI, L.P.

  
	
   

  	
  ATLAS VENTURE
  ENTREPRENEURS’ FUND VI, L.P.

  
	
   

  	
  By:

  	
  Atlas Venture
  Associates VI, L.P.

  
	
   

  	
   

  	
  Their General
  Partner

  
	
   

  	
  By:

  	
  Atlas Venture
  Associates VI, Inc.

  
	
   

  	
   

  	
  Its General
  Partner

  
	
   

  	
   

  
	
   

  	
  By:

  	
  /s/ Kristen Laguerre

  
	
   

  	
   

  	
  Name: Kristen
  Laguerre

  
	
   

  	
   

  	
  Title: Vice
  President

  
	
   

  	
   

  	
   

  
	
   

  	
  Notice Address:

  
	
   

  	
   

  
	
   

  	
  25 First Street,
  Suite 303

  
	
   

  	
  Cambridge, MA
  02141

  
	
   

  	
  Attention: General
  Counsel

  
	
   

  	
   

  
	
   

  	
   

  
	
   

  	
  ATLAS VENTURE FUND
  VI, GMBH & CO. KG

  
	
   

  	
  By:

  	
  Atlas Venture
  Associates VI, L.P.

  
	
   

  	
   

  	
  Its Managing
  Limited Partner

  
	
   

  	
  By:

  	
  Atlas Venture
  Associates VI, Inc.

  
	
   

  	
   

  	
  Its General
  Partner

  
	
   

  	
   

  
	
   

  	
  By:

  	
  /s/ Kristen Laguerre

  
	
   

  	
   

  	
  Name: Kristen Laguerre

  
	
   

  	
   

  	
  Title: Vice
  President

  
	
   

  	
   

  
	
   

  	
  Notice Address:

  
	
   

  	
   

  
	
   

  	
  25 First Street,
  Suite 303

  
	
   

  	
  Cambridge, MA
  02141

  
	
   

  	
  Attention: General
  Counsel

  



 


[Signature Page to Risk
Premium Payment Agreement]


 

















 


	
   

  	
  LENDERS:

  
	
   

  	
   

  
	
   

  	
  ATLAS VENTURE FUND
  V, L.P.

  
	
   

  	
  ATLAS VENTURE
  ENTREPRENEURS’ FUND V, L.P.

  
	
   

  	
  By:

  	
  Atlas Venture
  Associates V, L.P.

  
	
   

  	
   

  	
  Their General
  Partner

  
	
   

  	
  By:

  	
  Atlas Venture
  Associates V, Inc.

  
	
   

  	
   

  	
  Its General
  Partner

  
	
   

  	
   

  	
   

  
	
   

  	
  By:

  	
  /s/ Kristen Laguerre

  
	
   

  	
   

  	
  Name: Kristen
  Laguerre

  
	
   

  	
   

  	
  Title: Vice
  President

  
	
   

  	
   

  	
   

  
	
   

  	
  Notice Address:

  
	
   

  	
   

  
	
   

  	
  25 First Street,
  Suite 303

  
	
   

  	
  Cambridge, MA
  02141

  
	
   

  	
  Attention: General
  Counsel

  



 


[Signature Page to Risk
Premium Payment Agreement]