Document:

exv4w1

Exhibit 4.1 

AMENDMENT

TO

RIGHTS AGREEMENT

     This Amendment to Rights Agreement (this “Amendment”) between Selectica, Inc., a Delaware
corporation (the “Company”), and U.S. Stock Transfer Corporation, as Rights Agent (the “Rights
Agent”), is effective this 17th day of November, 2008.

W I T N E S S E T H:

     WHEREAS, on February 4, 2003, the Company and the Rights Agent entered into that certain
Rights Agreement between the Company and the Rights Agent (the “Rights Agreement”);

     WHEREAS, the Company desires to amend the Rights Agreement pursuant to Section 27 thereof; and

     WHEREAS, as of the date hereof, the Rights (as defined in the Rights Agreement) are not
redeemable under the Rights Agreement, and the Company has satisfied all requirements to effect an
amendment to the Rights Agreement.

     NOW, THEREFORE, in consideration of the premises and of the mutual agreements herein set
forth, the parties hereto agree as follows:

     Section 1. Amendments.

(a) Section 1 of the Rights Agreement is hereby amended and restated to read as follows:

     “Section 1. Certain Definitions. For purposes of this Agreement, the
following terms have the meaning indicated:

     (a) “Acquiring Person” shall mean any Person (other than the Company, any
Related Person or any Exempt Person) that has become, in itself or, together with
all Affiliates and Associates of such Person, the Beneficial Owner of 4.99% or more
of the shares of Common Stock then outstanding; provided, however,
that any Person who would otherwise qualify as an Acquiring Person as of the Close
of Business on November 17, 2008 will not be deemed to be an Acquiring Person for
any purpose of this Agreement on and after such date unless and until such time as
such Person acquires beneficial ownership of additional shares of Common Stock
representing one-half of one percent (.5%) or more of the shares of Common Stock
then outstanding (provided, that such Person will be deemed to be an
Acquiring Person if, upon acquiring beneficial ownership of such
additional shares of Common Stock, such Person is the Beneficial
Owner of 15% or more of the shares of Common Stock then outstanding), unless, upon becoming the Beneficial Owner of such additional
shares of Common Stock, such Person is not then the Beneficial Owner of 4.99% or
more of the shares of Common Stock then outstanding; provided,
further, that a Person will not be deemed to have become an Acquiring Person
solely as a result of (i) a reduction in the number of shares of Common Stock
outstanding, (ii) the exercise of any options, warrants, rights or

 

 

similar interests (including restricted stock) granted by the Company to its
directors, officers and employees, (iii) any unilateral grant of any security by the
Company, or (iv) an Exempt Transaction, unless and until such time as such Person
acquires the beneficial ownership of one additional share of Common Stock.
Notwithstanding the foregoing, if the Board of Directors determines in good faith
that a Person who would otherwise be an “Acquiring Person” as defined pursuant to
the foregoing provisions of this Section 1(a), has become such inadvertently, and
such Person divests as promptly as practicable a sufficient number of shares of
Common Stock so that such Person would no longer be an “Acquiring Person” as defined
pursuant to the foregoing provisions of this Section 1(a), then such Person shall
not be deemed to be an “Acquiring Person” for any purposes of this Agreement.

     (b) “Affiliate” and “Associate” shall have the respective meanings ascribed to
such terms in Rule 12b-2 of the General Rules and Regulations under the Exchange
Act, as in effect on the date hereof, and to the extent not included within the
foregoing clause of this Section 1(b), shall also include, with respect to any
Person, any other Person (whether or not a Related Person or an Exempt Person) whose
shares of Common Stock would be deemed constructively owned by such first Person,
owned by a single “entity” as defined in Section 1.382-3(a)(1) of the Treasury
Regulations, or otherwise aggregated with shares owned by such first Person pursuant
to the provisions of the Code, or any successor provision or replacement provision,
and the Treasury Regulations thereunder, provided, however, that a
Person shall not be deemed to be the Affiliate or Associate of another Person solely
because either or both Persons are or were directors of the Company.

     (c) “Agreement” shall have the meaning ascribed thereto in the preamble to this
Agreement, and such term shall include all amendments to this Agreement.

     (d) A Person shall be deemed the “Beneficial Owner” of, and to “beneficially
own” any securities:

     (i) which such Person or any of such Person’s Affiliates or Associates,
directly or indirectly, has the right to acquire (whether such right is
exercisable immediately or only after the passage of time) pursuant to any
agreement, arrangement or understanding (whether or not in writing)
(including any purchase orders for shares of Common Stock initiated prior to
the first public announcement of the Amendment, dated November 17, 2008, of
this Agreement) or upon the exercise of conversion rights, exchange rights,
warrants, options, or other rights (in each case, other than upon exercise
or exchange of the Rights); provided, however, that a Person
shall not be deemed the “Beneficial Owner” of, or to “beneficially own”
securities (including rights, options or warrants) which are convertible or
exchangeable into Common Stock until such time

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as the convertible or exchangeable securities are exercised and
converted or exchanged into Common Stock except to the extent the
acquisition or transfer of such rights, options or warrants would be treated
as exercised on the date of its acquisition or transfer under Section
1.382-4(d) of the Treasury Regulations; provided, further,
that a Person shall not be deemed the Beneficial Owner of, or to
beneficially own, securities tendered pursuant to a tender or exchange offer
made by such Person or any of such Person’s Affiliates or Associates until
such tendered securities are accepted for purchase or exchange;

     (ii) which such Person or any of such Person’s Affiliates or
Associates, directly or indirectly, has or shares the right to vote or
dispose of, or has “beneficial ownership” of (as defined under Rule 13d-3 of
the General Rules and Regulations under the Exchange Act), including
pursuant to any agreement, arrangement or understanding (whether or not in
writing), but only if the effect of such agreement, arrangement or
understanding is to treat such Persons as an “entity” under Section
1.382-3(a)(1) of the Treasury Regulations; or

     (iii) of which any other Person is the Beneficial Owner, if such Person
or any of such Person’s Affiliates or Associates has any agreement,
arrangement or understanding (whether or not in writing) with such other
Person (or any of such other Person’s Affiliates or Associates) with respect
to acquiring, holding, voting or disposing of any securities of the Company,
but only if the effect of such agreement, arrangement or understanding is to
treat such Persons as an “entity” under Section 1.382-3(a)(1) of the
Treasury Regulations; provided, however, that a Person shall
not be deemed the Beneficial Owner of, or to beneficially own, any security
(A) if such Person has the right to vote such security pursuant to an
agreement, arrangement or understanding (whether or not in writing) which
(1) arises solely from a revocable proxy given to such Person in response to
a public proxy or consent solicitation made pursuant to, and in accordance
with, the applicable rules and regulations of the Exchange Act and (2) is
not also then reportable on Schedule 13D or Schedule 13G under the Exchange
Act (or any comparable or successor report), or (B) if such beneficial
ownership arises solely as a result of such Person’s status as a “clearing
agency,” as defined in Section 3(a)(23) of the Exchange Act;
provided, further, that nothing in this Section 1(d) shall
cause a Person engaged in business as an underwriter of securities or member
of a selling to group to be the Beneficial Owner of, or to beneficially own,
any securities acquired through such Person’s participation in good faith in
an underwriting syndicate until the expiration of 40 calendar days after the
date of such acquisition, or such later date as the directors of the Company
may determine in any specific case. Notwithstanding anything herein to the
contrary, to the extent not within the foregoing provisions of this Section
1(d), a Person shall be deemed the Beneficial Owner of, and shall

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be deemed to beneficially own or have beneficial ownership of,
securities which such Person would be deemed to constructively own or which
otherwise would be aggregated with shares owned by such pursuant to Section
382 of the Code, or any successor provision or replacement provision and the
Treasury Regulations thereunder.

     (e) “Business Day” shall mean any day other than a Saturday, a Sunday or a day
on which banking institutions in the State of California or the city in which the
principal office of the Rights Agent is located are authorized or obligated by law
or executive order to close.

     (f) “Close of Business” on any given date shall mean 5:00 p.m., New York time,
on such date; provided, however, that if such date is not a Business
Day it shall mean 5:00 p.m., New York time, on the next succeeding Business Day.

     (g) “Code” shall mean the Internal Revenue Code of 1986, as amended.

     (h) “Common Stock” when used with reference to the Company shall mean the
Common Stock, presently par value $.0001 per share, of the Company. “Common Stock”
when used with reference to any Person other than the Company shall mean the common
stock (or, in the case of an unincorporated entity, the equivalent equity interest)
with the greatest voting power of such other Person or, if such other Person is a
Subsidiary of another Person, the Person or Persons which ultimately control such
first-mentioned Person.

     (i) “Common Stock Equivalents” shall have the meaning set forth in Section
11(a)(iii) hereof.

     (j) “Current Value” shall have the meaning set forth in Section 11(a)(iii)
hereof.

     (k) “Distribution Date” shall have the meaning set forth in Section 3 hereof.

     (l) “Equivalent Preferred Shares” shall have the meaning set forth in Section
11(b) hereof.

     (m) “Exchange Act” shall mean the Securities Exchange Act of 1934, as amended.

     (n) “Exempt Person” shall mean a Person whose Beneficial Ownership (together
with all Affiliates and Associates of such Person) of 4.99% or more of the
then-outstanding Common Stock will not, as determined by the Board of Directors in
its sole discretion, jeopardize or endanger the availability to the Company of the
NOLs; provided, however, that such a Person will cease to be an

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“Exempt Person” if the Board of Directors makes a contrary determination with
respect to the effect of such Person’s Beneficial Ownership (together with all
Affiliates and Associates of such Person) upon the availability to the Company of
its NOLs.

     (o) “Exempt Transaction” shall mean any transaction that the Board of Directors
determines, in its sole discretion, is exempt, which determination shall be
irrevocable.

     (p) “Exchange Ratio” shall have the meaning set forth in Section 24 hereof.

     (q) “Expiration Date” shall have the meaning set forth in Section 7 hereof.

     (r) “Final Expiration Date” shall have the meaning set forth in Section 7
hereof.

     (s) “Flip-In Event” shall have the meaning set forth in Section 11(a)(ii)
hereof.

     (t) “NASDAQ” shall mean The Nasdaq Stock Market.

     (u) “NOLs” shall mean the Company’s net operating loss carryforwards.

     (v) “NYSE” shall mean the New York Stock Exchange.

     (w) “Person” shall mean any individual, firm, corporation, partnership, limited
liability company, limited liability partnership, trust or other legal entity, group
of persons making a “coordinated acquisition” of shares or otherwise treated as an
entity within the meaning of Section 1.382-3(a)(1) of the Treasury Regulations or
otherwise, and includes any successor (by merger or otherwise) of such individual or
entity.

     (x) “Preferred Stock” shall mean the Series A Junior Participating Preferred
Stock, par value $.0001 per share, of the Company having the rights and preferences
set forth in the Form of Certificate of Designation attached to this Agreement as
Exhibit A.

     (y) “Principal Party” shall have the meaning set forth in Section 13(b) hereof.

     (z) “Purchase Price” shall have the meaning set forth in Section 7(b) hereof.

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     (aa) “Redemption Date” shall have the meaning set forth in Section 7 hereof.

     (bb) “Redemption Price” shall have the meaning set forth in Section 23 hereof.

     (cc) “Related Person” shall mean (i) any Subsidiary of the Company or (ii) any
employee benefit or stock ownership plan of the Company or of any Subsidiary of the
Company or any entity holding shares of Common Stock for or pursuant to the terms of
any such plan

     (dd) “Right Certificate” shall have the meaning set forth in Section 3 hereof.

     (ee) “Securities Act” shall mean the Securities Act of 1933, as amended.

     (ff) “Section 11(a)(ii) Trigger Date” shall have the meaning set forth in
Section 11(a)(iii) hereof.

     (gg) “Spread” shall have the meaning set forth in Section 11(a)(iii) hereof.

     (hh) “Stock Acquisition Date” shall mean the first date of public announcement
(which, for purposes of this definition, shall include, without limitation, a report
filed pursuant to Section 13(d) of the Exchange Act) by the Company or an Acquiring
Person that an Acquiring Person has become such, or such earlier date as a majority
of the Board of Directors of the Company shall become aware of the existence of an
Acquiring Person.

     (ii) “Subsidiary” of any Person shall mean any corporation or other entity of
which securities or other ownership interests having ordinary voting power
sufficient to elect a majority of the board of directors or other persons performing
similar functions are beneficially owned, directly or indirectly, by such Person,
and any corporation or other entity that is otherwise controlled by such Person.

     (jj) “Substitution Period” shall have the meaning set forth in Section
11(a)(iii) hereof.

     (kk) “Summary of Rights” shall have the meaning set forth in Section 3 hereof.

     (ll) “Trading Day” shall have the meaning set forth in Section 11(d)(i) hereof.

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     (mm) “Treasury Regulations” shall mean final, temporary and proposed income tax
regulations promulgated under the Code, including any amendments thereto.”

     (b) The first sentence of Section 3(a) of the Rights Agreement is hereby amended to read as
follows:

“Until the earlier of (i) the Close of Business on the tenth Business Day after the
Stock Acquisition Date or (ii) the Close of Business on the tenth Business Day (or,
unless the Distribution Date shall have previously occurred, such later date as may
be specified by the Board of Directors of the Company) after the commencement of a
tender or exchange offer by any Person (other than the Company, any Related Person
or any Exempt Person), if upon the consummation thereof such Person would be the
Beneficial Owner of 4.99% or more of the then-outstanding Common Stock (the earlier
of such dates being referred to as the “Distribution Date”), (x) the Rights will be
evidenced (subject to the provisions of Section 3(b) hereof) by the certificates for
Common Stock registered in the names of the holders thereof and not by separate
Right Certificates, and (y) the Rights will be transferable only in connection with
the transfer of Common Stock.”

     (c) Section 9(b) of the Rights Agreement is hereby amended and restated to read as follows:

     “(b) So long as the shares of Preferred Stock issuable upon the exercise of
Rights may be listed or admitted to trading on any national securities exchange, the
Company shall use its best efforts to cause, from and after such time as the Rights
become exercisable, all shares reserved for such issuance to be listed or admitted
to trading on such exchange upon official notice of issuance upon such exercise.”

     (d) The penultimate sentence of Section 11(d)(i) of the Rights Agreement is hereby amended to
read as follows:

“The closing price for each day shall be the last sale price, regular way, or, in
case no such sale takes place on such day, the average of the closing bid and asked
prices, regular way, in either case as reported by the principal consolidated
transaction reporting system with respect to securities listed or admitted to
trading on the NYSE or NASDAQ or, if the Security is not listed or admitted to
trading on the NYSE or NASDAQ, as reported in the principal consolidated transaction
reporting system with respect to securities listed on the principal national
securities exchange on which the Security is listed or admitted to trading or, if
not listed on a national securities exchange, the last quoted price or, if not so
quoted, the average of the high and low asked prices in the over-the-counter market
as reported by any system then in use, or, if not so quoted, the average of the
closing bid and asked prices as furnished by a professional market maker making a
market in the Security selected by the Board of Directors of the Company.”

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     (e) Section 13(c)(ii) of the Rights Agreement is hereby amended and restated to read as
follows:

     “(ii) use its best efforts, if the Common Stock of the Principal Party shall be
listed or admitted to trading on the NYSE, NASDAQ or on another national securities
exchange, to list or admit to trading (or continue the listing of) the Rights and
the securities purchasable upon exercise of the Rights on the NYSE, NASDAQ or such
securities exchange, or, if the Common Stock of the Principal Party shall not be
listed or admitted to trading on the NYSE, NASDAQ or a national securities exchange,
to cause the Rights and the securities receivable upon exercise of the Rights to be
authorized for quotation on any system then in use;”

     (f) The penultimate sentence of Section 14(a) of the Rights Agreement is hereby amended to
read as follows:

“The closing price for any day shall be the last sale price, regular way, or, in
case no such sale takes place on such day, the average of the closing bid and asked
prices, regular way, in either case as reported in the principal consolidated
transaction reporting system with respect to securities listed or admitted to
trading on the NYSE or NASDAQ, if the Rights are not listed or admitted to trading
on the NYSE or NASDAQ, as reported in the principal consolidated transaction
reporting system with respect to securities listed on the principal national
securities exchange on which the Rights are listed or admitted to trading or, if the
Rights are not listed or admitted to trading on any national securities exchange,
the last quoted price or, if not so quoted, the average of the high bid and low
asked prices in the over-the-counter market, as reported by such system then in use
or, if on any such date the Rights are not so quoted, the average of the closing bid
and asked prices as furnished by a professional market maker making a market in the
Rights selected by the Board of Directors of the Company.”

     Section 2. Effect of this Amendment. It is the intent of the parties hereto that this
Amendment constitutes an amendment of the Rights Agreement as contemplated by Section 27 thereof.
This Amendment shall be deemed effective as of the date hereof upon execution and delivery by the
Board as if executed by both parties hereto on such date. Except as expressly provided in this
Amendment, the terms of the Rights Agreement remain in full force and effect. Unless the context
clearly provides otherwise, any reference to this “Agreement” or the “Rights Agreement” shall be
deemed to be a reference to the Rights Agreement as amended hereby.

     Section 3. Counterparts. This Amendment may be executed in any number of counterparts
and each of such counterparts shall for all purposes be deemed to be an original, and all such
counterparts shall together constitute one and the same instrument.

     Section 4. Governing Law. This Amendment shall be deemed to be a contract made
under the laws of the State of Delaware and for all purposes shall be governed by and construed

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in accordance with the laws of such state applicable to contracts to be made and performed
entirely within such state.

     Section 5. Severability. If any term, provision, covenant or restriction of this
Amendment is held by a court of competent jurisdiction or other authority to be invalid, illegal or
unenforceable, the remainder of the terms, provisions, covenants and restrictions of this Amendment
shall remain in full force and effect and shall in no way be affected, impaired or invalidated.

     Section 6. Descriptive Headings. The captions herein are included for convenience of
reference only, do not constitute a part of this Amendment and shall be ignored in the construction
and interpretation hereof.

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

	 	 	 	 	 	 	 
	 	 	SELECTICA, INC.	 	 
	 
	 	 	 	 	 	 
	 

	 	By:	 	/s/ Richard Heaps 	 	 
	 

	 	 	 	 

Name: Richard Heaps
	 	 
	 

	 	 	 	Title: CFO and General Counsel	 	 
	 
	 	 	 	 	 	 
	 	 	U.S. STOCK TRANSFER CORPORATION	 	 
	 
	 	 	 	 	 	 
	 

	 	By:	 	 	 	 
	 

	 	 	 	 

Name:
	 	 
	 

	 	 	 	Title:exv10w1

Exhibit 10.1

NitroMed,
Inc.

STOCKHOLDER AGREEMENT

     THIS STOCKHOLDER AGREEMENT (this “Agreement”), dated as of November           , 2008, is by
and among NitroMed, Inc., a Delaware corporation (“Public Company”) (only with respect to
Section 2(b) and Section 11 (and any provisions relating thereto)), Archemix Corp., a Delaware
corporation (“Merger Partner”), and the undersigned stockholder (“Stockholder”) of
Public Company.

     WHEREAS, concurrently with the execution and delivery of this Agreement, Public Company,
Newport Acquisition Corp., a Delaware corporation and a wholly owned subsidiary of Public Company
(the “Transitory Subsidiary”), and Merger Partner have entered into an Agreement and Plan
of Merger, dated as of the date hereof (as it may be amended or supplemented from time to time
pursuant to the terms thereof, the “Merger Agreement”), which provides for the merger (the
“Merger”) of the Transitory Subsidiary into Merger Partner in accordance with the terms of
the Merger Agreement;

     WHEREAS, Stockholder is the beneficial owner (as defined in Rule 13d-3 under the Exchange Act)
of such number of shares of each class of capital stock of Public Company as is indicated on the
signature page of this Agreement; and

     WHEREAS, in consideration of the execution and delivery of the Merger Agreement by Merger
Partner, Stockholder desires to agree to vote the Shares (as defined herein) over which Stockholder
has voting power so as to facilitate the consummation of the Merger;

     NOW, THEREFORE, in consideration of the foregoing, intending to be legally bound, the parties
hereto hereby agree as follows:

     1. Certain Definitions.

          (a) Capitalized terms used but not otherwise defined herein shall have the meanings ascribed
thereto in the Merger Agreement. For purposes of this Agreement, the following terms shall have
the following meanings:

          “Constructive Sale” means with respect to any security, a short sale with
respect to such security, entering into or acquiring an offsetting derivative contract with
respect to such security, entering into or acquiring a futures or forward contract to
deliver such security or entering into any other hedging or other derivative transaction
that has the effect of either directly or indirectly materially changing the economic
benefits or risks of ownership.

          “Shares” means (i) all shares of capital stock of Public Company owned,
beneficially or of record, by Stockholder as of the date hereof, and (ii) all additional
 shares of capital stock of Public Company acquired by Stockholder, beneficially or of
record, during the period commencing with the execution and delivery of this Agreement and
expiring on the Expiration Date (as such term is defined in Section 10 below).

          “Transfer” means, with respect to any security, the direct or indirect
assignment, sale, transfer, tender, exchange, pledge, hypothecation, or the grant, creation
or suffrage of a lien, security interest or encumbrance in or upon, or the gift, placement
in trust, or the Constructive Sale or other disposition of such security (including
transfers by testamentary or intestate succession or otherwise by operation of law) or any
right, title or interest therein (including, but not limited to, any right or power to vote
to which the holder thereof may be entitled, whether such right or power is granted by proxy
or otherwise), or the record or beneficial ownership thereof, the offer to make such a sale,
transfer, Constructive Sale or other disposition, and each

 

 

agreement, arrangement or understanding, whether or not in writing, to effect any of
the foregoing.

     2. Transfer and Voting Restrictions With Respect to the Shares.

          (a) At all times during the period commencing with the execution and delivery of this
Agreement and expiring on the Expiration Date, Stockholder shall not, except as the result of the
death of Stockholder or as otherwise permitted by this Agreement, Transfer any of the Shares, or
discuss, negotiate, make an offer or enter into an agreement, commitment or other arrangement with
respect thereto, unless the person to which such Shares are being Transferred shall have executed
and delivered a counterpart of this Agreement and agreed pursuant thereto, for the benefit of
Merger Partner, to hold such Shares subject to all terms and conditions of this Agreement.

          (b) Stockholder understands and agrees that if Stockholder attempts to Transfer, vote or
provide any other person with the authority to vote any of the Shares other than in compliance with
this Agreement, Public Company shall not, and Stockholder hereby unconditionally and irrevocably
instructs Public Company to not, (i) permit any such Transfer on its books and records, (ii) issue
a new certificate representing any of the Shares or (iii) record such vote, in each case, unless
and until Stockholder shall have complied with the terms of this Agreement.

          (c) Except as otherwise permitted by this Agreement or by order of a court of competent
jurisdiction, Stockholder will not commit any act that could restrict or affect Stockholder’s legal
power, authority and right to vote all of the Shares then owned of record or beneficially by
Stockholder or otherwise prevent or disable Stockholder from performing any of his, her or its
obligations under this Agreement. Without limiting the generality of the foregoing, except for
this Agreement and as otherwise permitted by this Agreement, Stockholder will not enter into any
voting agreement with any person or entity with respect to any of the Shares, grant any person or
entity any proxy (revocable or irrevocable) or power of attorney with respect to any of the Shares,
deposit any of the Shares in a voting trust or otherwise enter into any agreement or arrangement
with any person or entity limiting or affecting Stockholder’s legal power, authority or right to
vote the Shares in favor of the approval of the Proposed Transaction.

     3. Agreement to Vote Shares.

          (a) Prior to the Expiration Date, at every meeting of the stockholders of Public Company
called, and at every adjournment or postponement thereof, Stockholder (in Stockholder’s capacity
as such) shall appear at the meeting or otherwise cause the Shares to be present thereat for
purposes of establishing a quorum and, to the extent not voted by the persons appointed as proxies
pursuant to this Agreement, vote (i) in favor of adoption of the Merger Agreement and approval of
the transactions contemplated thereby (collectively, the “Proposed Transaction”), (ii)
against the approval or adoption of any proposal made in opposition to, or in competition with, the
Proposed Transaction, and (iii) against any of the following (to the extent unrelated to the
Proposed Transaction): (A) any merger, consolidation or business combination involving Public
Company or any of its subsidiaries other than the Proposed Transaction; (B) any sale, lease or
transfer of all or substantially all of the assets of Public Company or any of its subsidiaries;
(C) any reorganization, recapitalization, dissolution, liquidation or winding up of Public Company
or any of its subsidiaries that is prohibited by the Merger Agreement; or (D) any other action that
is a breach of any covenant, representation or warranty or any other obligation or agreement of
Public Company under the Merger Agreement or of Stockholder under this Agreement (each of (ii) and
(iii), a “Competing Transaction”).

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          (b) If Stockholder is the beneficial owner, but not the record holder, of the Shares,
Stockholder agrees to take all actions necessary to cause the record holder and any nominees to
vote all of the Shares in accordance with Section 3(a).

     4. Grant of Irrevocable Proxy.

          (a) Except as set forth in Section 4(f) hereof, Stockholder hereby irrevocably (to the fullest
extent permitted by law) grants to, and appoints, Merger Partner and each of its executive officers
and any of them, in their capacities as officers of Merger Partner (the “Grantees”), as
Stockholder’s proxy and attorney-in-fact (with full power of substitution and re-substitution), for
and in the name, place and stead of Stockholder, to vote the Shares, to instruct nominees or record
holders to vote the Shares, or grant a consent or approval in respect of such Shares in accordance
with Section 3 hereof and, in the discretion of the Grantees with respect to any proposed
adjournments or postponements of any meeting of stockholders at which any of the matters described
in Section 3 hereof is to be considered.

          (b) Except with respect to any proxy given by the Stockholder in connection with the BiDil
Sale, which shall remain in full force and effect and is not revoked or otherwise modified hereby,
Stockholder represents that any proxies heretofore given in respect of the Shares that may still be
in effect are not irrevocable, and such proxies are hereby revoked.

          (c) Stockholder hereby affirms that the irrevocable proxy set forth in this Section 4 is given
in connection with the execution of the Merger Agreement, and that such irrevocable proxy is given
to secure the performance of the duties of Stockholder under this Agreement. Stockholder hereby
further affirms that the irrevocable proxy is coupled with an interest and may under no
circumstances be revoked. Stockholder hereby ratifies and confirms all that such irrevocable proxy
may lawfully do or cause to be done by virtue hereof. Such irrevocable proxy is executed and
intended to be irrevocable in accordance with the provisions of Section 212 of the Delaware General
Corporation Law.

          (d) The Grantees may not exercise this irrevocable proxy on any other matter except as
provided above. Stockholder may vote the Shares on all other matters.

          (e) Merger Partner may terminate this proxy with respect to Stockholder at any time at its
sole election by written notice provided to Stockholder.

          (f) The proxy set forth in this Section 4 shall terminate upon the termination of this
Agreement in accordance with Section 10 hereof.

     5. No Solicitation. Stockholder, in his, her or its capacity as a Stockholder, shall
not directly or indirectly, (a) solicit, initiate, encourage, induce or knowingly facilitate the
communication, making, submission or announcement of any Acquisition Proposal or Acquisition
Inquiry or take any action that could reasonably be expected to lead to an Acquisition Proposal or
Acquisition Inquiry, (b) engage in discussions or negotiations with any Person with respect to any
Acquisition Proposal or Acquisition Inquiry, (c) approve, endorse or recommend any Acquisition
Proposal, or (d) enter into any letter of intent or similar document or any Contract contemplating
or otherwise relating to any Acquisition Transaction.

     6. Lock-Up With Respect to Public Company Common Stock.

          (a) Stockholder shall not Transfer any shares of Public Company Common Stock or any securities
convertible into or exercisable or exchangeable for Public Company Common Stock owned of record or
beneficially by Stockholder during the period commencing upon the Effective Time and ending 90 days
after the date on which the Effective Time occurs with respect to 50% of such shares and 180 days
after the Effective Time with respect to the remainder of such shares. The foregoing sentence

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shall not apply to (a) transactions relating to shares of Public Company Common Stock or other
securities acquired in open market transactions after the Effective Time; (b) transfers of shares
of Public Company Common Stock or other securities as a bona fide gift; (c) distributions of shares
of Public Company Common Stock or other securities to partners, members or shareholders of the
Stockholder or to the estate of any deceased partner or member of the Stockholder; (d) transfers to
any family limited partnership or family limited liability company whose partnership or equity
interests are owned by, or a trust for the direct or indirect benefit of, or controlled by, the
Stockholder or the immediate family of the Stockholder; (e) transfers to the Stockholder’s
Affiliates or to any investment fund or other entity controlled or managed by the Stockholder;
provided that in the case of any transfer or distribution pursuant to clause (b), (c), (d) or (e),
(i) each donee, distributee or transferee shall sign and deliver a lock-up letter containing
substantially similar provisions as are set forth in this Section 6; or (f) transfers to any
beneficiary of the Stockholder pursuant to will, intestacy, trust or other testamentary document or
applicable laws of descent. In addition, the Stockholder agrees that, without the prior written
consent of Public Company, it will not, during the period commencing on the Effective Time and
ending 180 days after the date on which the Effective Time occurs, make any demand for or exercise
any right with respect to, the registration of any shares of Public Company Common Stock or any
securities convertible into or exercisable or exchangeable for Public Company Common Stock. The
Stockholder also agrees and consents to the entry of stop transfer instructions with Public
Company’s transfer agent and registrar against the transfer of the undersigned’s shares of Public
Company Common Stock or any securities convertible into or exercisable or exchangeable for Public
Company Common Stock except in compliance with the foregoing restrictions.

          (b) In the event that Public Company releases any shares of Public Company Common Stock from
the lock-up restrictions set forth above, the same percentage of shares of Public Company Common
Stock held by such persons that are so released from the lock-up restrictions shall be immediately
and fully released with respect to shares of Public Company Common Stock held by the Stockholder.

     7. Action in Stockholder Capacity Only. Stockholder makes no agreement or
understanding herein as a director or officer of Public Company. Stockholder signs solely in
Stockholder’s capacity as a record holder and beneficial owner, as applicable, of Shares, and
nothing herein shall limit or affect any actions taken in Stockholder’s capacity as an officer or
director of Public Company. Nothing herein shall prevent or preclude an officer, director or
manager of the Stockholder who is serving as a director of Public Company from taking or not taking
any action in his capacity as a director of Public Company.

     8. Representations and Warranties of Stockholder.

          (a) Stockholder hereby represents and warrants to Merger Partner as follows: (i) Stockholder
is the beneficial or record owner of the shares of capital stock of Public Company indicated on the
signature page of this Agreement free and clear of any and all pledges, liens, security interests,
mortgage, claims, charges, restrictions, options, title defects or encumbrances except as provided
in the Voting Agreement; (ii) Stockholder does not beneficially own any securities of Public
Company other than the shares of capital stock and rights to purchase shares of capital stock of
Public Company set forth on the signature page of this Agreement; (iii) Stockholder has full power
and authority to make, enter into and carry out the terms of this Agreement and to grant the
irrevocable proxy as set forth in Section 4; and (iv) this Agreement has been duly and validly
executed and delivered by Stockholder and constitutes a valid and binding agreement of Stockholder
enforceable against Stockholder in accordance with its terms. Stockholder agrees to notify Merger
Partner promptly of any additional shares of capital stock of Public Company of which Stockholder
becomes the beneficial owner after the date of this Agreement.

- 4 -

 

          (b) As of the date hereof and for so long as this Agreement remains in effect, except for this
Agreement or as otherwise permitted by this Agreement, Stockholder has full legal power, authority
and right to vote all of the Shares then owned of record or beneficially by Stockholder, in favor
of the approval and authorization of the Proposed Transaction without the consent or approval of,
or any other action on the part of, any other person or entity (including, without limitation, any
governmental entity). Without limiting the generality of the foregoing, Stockholder has not
entered into any voting agreement (other than this Agreement and the Voting Agreement) with any
person with respect to any of the Shares, granted any person any proxy (revocable or irrevocable)
or power of attorney with respect to any of the Shares, deposited any of the Shares in a voting
trust or entered into any arrangement or agreement with any person limiting or affecting
Stockholder’s legal power, authority or right to vote the Shares on any matter (except, in each
case, with respect to the Voting Agreement and the Voting Agreement).

          (c) The execution and delivery of this Agreement and the performance by Stockholder of his,
her or its agreements and obligations hereunder will not result in any breach or violation of or be
in conflict with or constitute a default under any term of any agreement, judgment, injunction,
order, decree, law, regulation or arrangement to which Stockholder is a party and which Stockholder
is aware or by which Stockholder (or any of his, her or its assets) is bound and which Stockholder
is aware, except for any such breach, violation, conflict or default which, individually or in the
aggregate, would not materially impair or materially adversely affect Stockholder’s ability to
perform his, her or its obligations under this Agreement or render inaccurate any of the
representations made by Stockholder herein.

          (d) Stockholder understands and acknowledges that Public Company, the Transitory Subsidiary
and Merger Partner are entering into the Merger Agreement in reliance upon Stockholder’s execution
and delivery of this Agreement and the representations and warranties of Stockholder contained
herein.

     9. Confidentiality. Stockholder recognizes that successful consummation of the
Proposed Transaction may be dependent upon confidentiality with respect to the matters referred to
herein. In this connection, pending public disclosure thereof, and so that Public Company may rely
on the safe harbor provisions of Rule 100(b)(2)(ii) of Regulation FD promulgated under the Exchange
Act, Stockholder hereby agrees not to disclose or discuss such matters with anyone not a party to
this Agreement (other than its counsel and advisors, if any, and the officers, directors, counsel
and advisors of Public Company) without the prior written consent of Public Company and Merger
Partner, except for disclosures Stockholder’s counsel advises are required by applicable law, in
which case Stockholder shall give notice of such disclosure to Public Company and Merger Partner as
promptly as practicable so as to enable Public Company and Merger Partner to seek a protective
order from a court of competent jurisdiction with respect thereto. The parties understand and
agree that to the extent required by law Stockholder may make a filing on Schedule 13D (or an
amended filing) concerning this Agreement and that such filing will not constitute a violation of
this Section 9.

     10. Termination. This Agreement, including without limitation, Section 4, shall
terminate and be of no further force or effect whatsoever as of the earlier of (a) such date and
time as the Merger Agreement shall have been validly terminated pursuant to the terms of Article 9
thereof or (b) other than Sections 6, 11 and 12 hereof, the Effective Time (the “Expiration Date”).
Notwithstanding anything in this Agreement to the contrary, (i) Section 11 (and any provision
relating thereto) shall survive expiration or termination of this Agreement, (ii) Sections 6 and 12
hereof shall remain in full force and effect following the Effective Time for the time period
provided in Section 6 and (iii) if the Effective Time of the Merger has not occurred prior to June
30, 2009, this Agreement, including without limitation Sections 6 and 12 shall be of no further
force or effect.

- 5 -

 

     11. No Effect Upon Voting Agreement. Notwithstanding anything contained in this
Agreement or elsewhere to the contrary, each of the Merger Partner, the Public Company and the
Stockholder acknowledges and agrees that:

          (a) the sale of the BiDil and BiDil XR drug businesses and the other transactions contemplated
(the “BiDil Sale”) pursuant to the Purchase and Sale Agreement dated October 22, 2008 (the
“Purchase Agreement”) by and between the Public Company and JHP Pharmaceuticals, LLC (“JHP”) shall
not constitute a Competing Transaction for purposes of this Agreement and this Agreement shall not
apply to any action taken by Stockholder in connection with the BiDil Sale;

          (b) Stockholder is a party to that certain Voting Agreement, dated October 22, 2008, by and
among Stockholder, Public Company, JHP and certain other parties (the “Voting Agreement”) related
to the BiDil Sale;

          (c) all actions taken or refrained from by Stockholder in accordance with the terms of the
Voting Agreement shall be permitted under this Agreement regardless of any other provision hereof;

          (d) in no event shall this Agreement affect, limit or alter the rights or obligations of the
parties to the Voting Agreement, or the rights or obligations of the Public Company or JHP under
the Purchase Agreement, including, without limitation, the obligation of Stockholder to vote in
favor of the Voting Proposal, as such term is defined in the Purchase Agreement, for the Public
Company to consummate the Purchase Agreement in accordance with its terms or the rights of JHP to
take any action or exercise any right permitted under the Voting Agreement; and

          (e) to the extent that any provision of this Agreement can be viewed as inconsistent with any
right, power or privilege of the parties under the Voting Agreement, such provision of this
Agreement shall have no force and effect.

     12. Miscellaneous Provisions.

          (a) Amendments, Modifications and Waivers. This Agreement may not be amended or
modified except by an instrument in writing signed on behalf of each of the parties hereto. Any
agreement on the part of a party hereto to any waiver of any term or condition hereof shall be
valid only if set forth in a written instrument signed on behalf of such party. Such waiver shall
not be deemed to apply to any term or condition other than that which is specified in such waiver.
The failure of any party to this Agreement to assert any of its rights under this Agreement or
otherwise shall not constitute a waiver of such rights.

          (b) Entire Agreement. This Agreement constitutes the entire agreement among the
parties to this Agreement and supersedes any prior understandings, agreements or representations by
or among the parties hereto, or any of them, written or oral, with respect to the subject matter
hereof. In no event shall the parties have the right to amend, modify or delete, in whole or in
part, the provisions of Section 11 or any other provision that relates thereto without the written
consent of JHP.

          (c) Governing Law. All matters arising out of or relating to this Agreement and the
transactions contemplated hereby (including without limitation its interpretation, construction,
performance and enforcement) shall be governed by and construed in accordance with the internal
laws of the State of Delaware without giving effect to any choice or conflict of law provision or
rule (whether of the State of Delaware or any other jurisdiction) that would cause the application
of laws of any jurisdictions other than those of the State of Delaware.

- 6 -

 

          (d) Submission to Jurisdiction. Each of the parties to this Agreement (i) consents to
submit itself to the exclusive personal jurisdiction of the Court of Chancery of the State of
Delaware in any action or proceeding arising out of or relating to this Agreement or any of the
transactions contemplated by this Agreement, (ii) agrees that all claims in respect of such action
or proceeding may be heard and determined in such court, (iii) agrees that it shall not attempt to
deny or defeat such personal jurisdiction by motion or other request for leave from such court and
(d) agrees not to bring any action or proceeding arising out of or relating to this Agreement or
any of the transaction contemplated by this Agreement in any other court. Each of the parties
hereto waives any defense of inconvenient forum to the maintenance of any action or proceeding so
brought and waives any bond, surety or other security that might be required of any other party
with respect thereto. Any party may make service on another party by sending or delivering a copy
of the process to the party to be served at the address and in the manner provided for the giving
of notices in Section 12(m) hereof. Nothing in this Section 12(d), however, shall affect the right
of any party to serve legal process in any other manner permitted by law.

          (e) WAIVER OF JURY TRIAL. EACH OF THE PARTIES HERETO HEREBY IRREVOCABLY WAIVES ALL
RIGHT TO TRIAL BY JURY IN ANY ACTION, PROCEEDING OR COUNTERCLAIM (WHETHER BASED ON CONTRACT, TORT
OR OTHERWISE) ARISING OUT OF OR RELATING TO THIS AGREEMENT OR THE TRANSACTIONS CONTEMPLATED HEREBY
OR THE ACTIONS OF ANY PARTY IN THE NEGOTIATION, ADMINISTRATION, PERFORMANCE AND ENFORCEMENT OF THIS
AGREEMENT.

          (f) Attorneys’ Fees. In any action at law or suit in equity to enforce this Agreement
or the rights of any of the parties hereunder, the prevailing party in such action or suit shall be
entitled to receive its reasonable attorneys’ fees and all other reasonable costs and expenses
incurred in such action or suit.

          (g) Assignment and Successors. Except for any Transfer made in compliance with
Section 2(a) hereof, no party may assign any of its rights or delegate any of its performance
obligations under this Agreement, in whole or in part, by operation of law or otherwise without the
prior written consent of the other parties, except that Merger Partner, without obtaining the
consent of any other parties hereto, shall be entitled to assign this Agreement or all or any of
its rights or obligations hereunder to any one or more of its Affiliates. No assignment by Merger
Partner under this Section 12(g) shall relieve Merger Partner of its obligations under this
Agreement. Subject to the foregoing, this Agreement shall be binding upon, inure to the benefit
of, and be enforceable by, the parties hereto and their respective successors and permitted
assigns, including, without limitation, Stockholder’s estate and heirs upon the death of
Stockholder. Any purported assignment of rights or delegation of performance obligations in
violation of this Section 12(g) shall be null and void.

          (h) No Third Party Beneficiaries. This Agreement is not intended, and shall not be
deemed, to confer any rights or remedies upon any person other than the parties hereto, JHP as it
relates to Section 11 (or any other provision that relates thereto) and their respective successors
and permitted assigns, or to otherwise create any third-party beneficiary hereto.

          (i) Cooperation. Stockholder agrees to cooperate fully with Merger Partner and to
execute and deliver such further documents, certificates, agreements and instruments and to take
such other actions as may be reasonably requested by Merger Partner to evidence or reflect the
transactions contemplated by this Agreement and to carry out the intent and purpose of this
Agreement. Stockholder hereby agrees that Public Company and Merger Partner may publish and
disclose in the Registration Statement and any resale registration statement relating thereto
(including all documents and schedules filed with the SEC) and the Proxy Statement/Prospectus, such
Stockholder’s identity and ownership of Shares and the nature of such Stockholder’s commitments,
arrangements and understandings under this

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Agreement and may further file this Agreement as an exhibit to the Registration Statement or
in any other filing made by Public Company or Merger Partner with the SEC relating to the Proposed
Transaction.

          (j) Severability. Any term or provision of this Agreement that is invalid or
unenforceable in any situation in any jurisdiction shall not affect the validity or enforceability
of the remaining terms and provisions hereof or the validity or enforceability of the offending
term or provision in any other situation or in any other jurisdiction; provided however, that in
the event that any provision of Section 11 (or any provision relating thereto) is deemed invalid,
the parties will negotiate in good faith with JHP to agree upon replacement language that would
overcome invalidity to address the intention of Section 11 (or any provision relating thereto). If
the final judgment of a court of competent jurisdiction declares that any term or provision hereof
is invalid or unenforceable, the parties hereto agree that the court making such determination
shall have the power to limit the term or provision, to delete specific words or phrases, or to
replace any invalid or unenforceable term or provision with a term or provision that is valid and
enforceable and that comes closest to expressing the intention of the invalid or unenforceable term
or provision, and this Agreement shall be enforceable as so modified. In the event such court does
not exercise the power granted to it in the prior sentence, the parties hereto agree to replace
such invalid or unenforceable term or provision with a valid and enforceable term or provision that
will achieve, to the extent possible, the economic, business and other purposes of such invalid or
unenforceable term.

          (k) Time of Essence. With regard to all dates and time periods set forth or referred
to in this Agreement, time is of the essence.

          (l) Specific Performance; Injunctive Relief. The parties hereto acknowledge that
Public Company and Merger Partner shall be irreparably harmed and that there shall be no adequate
remedy at law for a violation of any of the covenants or agreements of Stockholder set forth in
this Agreement. Stockholder accordingly agrees that, in addition to any other remedies that may be
available to Public Company or Merger Partner, as applicable upon any such violation, such party
shall have the right to enforce such covenants and agreements by specific performance, injunctive
relief or by any other means available to such party at law or in equity without posting any bond
or other undertaking.

          (m) Notices. All notices and other communications hereunder shall be in writing and
shall be deemed duly delivered (i) four business days after being sent by registered or certified
mail, return receipt requested, postage prepaid, or (ii) one business day after being sent for next
business day delivery, fees prepaid, via a reputable nationwide overnight courier service, in each
case to the intended recipient as follows: (A) if to Public Company or Merger Partner, to the
address provided in the Merger Agreement, including to the persons designated therein to receive
copies, and (B) if to Stockholder, to Stockholder’s address shown below Stockholder’s signature on
the signature page hereof.

          (n) Counterparts and Signature. This Agreement may be executed in two or more
counterparts, each of which shall be deemed an original but all of which together shall be
considered one and the same agreement and shall become effective when counterparts have been signed
by each of the parties hereto and delivered to the other parties, it being understood that all
parties need not sign the same counterpart. The exchange of copies of this Agreement of amendments
thereto and of signature pages by facsimile transmission or by email transmission in portable
document format, or similar format, shall constitute effective execution and delivery of such
instrument(s) as to the parties and may be used in lieu of the original Agreement for all purposes.
Signatures of the parties transmitted by facsimile or by email transmission in portable document
format, or similar format, shall be deemed to be their original signatures for all purposes.

          (o) Headings. The headings contained in this Agreement are for convenience of
reference only and shall not affect in any way the meaning or interpretation of this Agreement.

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          (p) Legal Representation. This Agreement was negotiated by the parties with the
benefit of legal representation and any rule of construction or interpretation otherwise requiring
this Agreement to be construed or interpreted against any party shall not apply to any construction
or interpretation thereof.

          (q) Parallel Stockholder Agreements. The Public Company represents to the Stockholder
that each of the following stockholders have entered into Stockholder Agreements with Public
Company in connection with the Merger (the “Stockholder Agreements”): (i) HealthCare Ventures V,
L.P., (ii) HealthCare Ventures VI, L.P., (iii) Rho Ventures IV (QP), L.P., (iv) Rho Ventures IV,
L.P., (v) Rho Ventures IV GmbH & Co. Beteiligungs KG, (vi) Rho Management Trust II, (vii) Care
Capital, and (viii) Invus Public Equities L.P.. All of such Stockholder Agreements, including
without limitation this Agreement, have identical terms and the Public Company agrees not to amend
or waive any provision of any of such Stockholder Agreements without (i) providing Stockholder with
an opportunity to have the same amendment or waiver in connection with this Agreement and (ii) the
approval of JHP for any amendment or waiver in connection with Section 11 (or any provision
relating thereto).

- 9 -

 

     IN WITNESS WHEREOF, the undersigned have caused this Agreement to be duly executed as of the
date first written above.

	 	 	 	 	 	 	 
	ARCHEMIX CORP.:
	 	 	 	STOCKHOLDER:	 	 
	 
	 	 	 	 	 	 
	 	 	 	 	 	 	 
	Name:
	 	 	 	Name:	 	 
	Title:
	 	 	 	Title:	 	 
	 
	 	 	 	 	 	 
	 
	 	 	 	Address:	 	 
	 
	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 
	 	 	 	Telephone: (                    )                     -                    	 	 
	 
	 	 	 	Facsimile: (                       )                     -                    	 	 
	 
	 	 	 	E-Mail Address:                                          	 	 
	 
	 	 	 	 	 	 
	 
	 	 	 	Shares Beneficially Owned by Stockholder:	 	 
	 
	 	 	 	 	 	 
	 
	 	 	 	                     shares of Public Company Common Stock	 	 
	 
	 	 	 	 	 	 
	 
	 	 	 	                     Public Company Stock Options	 	 

With respect to Section 2(b) and Section 11 (and any provisions that relate thereto) only:

NITROMED, INC.:
                                        

Name:

Title:

[Signature Page to Stockholder Agreement]

- 10 -

 

Schedule
of Signatories to NitroMed Stockholder Agreement

	1.	 	Care Capital Investments II LP
	 
	2.	 	Care Capital Offshore Investments II LP
	 
	3.	 	CC/Q Partners LP
	 
	4.	 	CC/R Holdings LP
	 
	5.	 	HealthCare Ventures V, L.P.
	 
	6.	 	Healthcare Ventures VI, L.P.
	 
	7.	 	Invus Public Equities, L.P.
	 
	8.	 	Rho Management Trust II
	 
	9.	 	Rho Ventures IV GmbH & Co. Beteiligungs KG
	 
	10.	 	Rho Ventures IV, L.P.
	 
	11.	 	Rho Ventures IV (QP), L.P.

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