<Page>
CERTIFICATE OF AMENDMENT
OF
SIXTH RESTATED CERTIFICATE OF INCORPORATION
OF
NITROMED, INC.
Pursuant to Section 242 of the
General Corporation Law of the State of Delaware
------------------------
NitroMed, Inc. (hereinafter called the "Corporation"), organized and
existing under and by virtue of the General Corporation Laws of the State of
Delaware, does hereby certify as follows:
At a meeting of the Board of Directors of the Corporation a resolution was
duly adopted, pursuant to Section 242 of the General Corporation Law of the
State of Delaware, setting forth amendments to the Sixth Restated Certificate of
Incorporation of the Corporation and declaring said amendments to be advisable.
The stockholders of the Corporation duly adopted said amendments by written
consent in accordance with Sections 228 and 242 of the General Corporation Law
of the State of Delaware. Said amendments have been duly adopted in accordance
with Section 242 of the General Corporation Law of the State of Delaware. The
resolution setting forth the amendments is as follows:
RESOLVED: That the Sixth Restated Certificate of Incorporation of the
Corporation (the "Restated Certificate") be amended as follows:
(1) Article III(a) of the Restated Certificate is deleted in its entirety
and the following new paragraph is inserted in lieu thereof:
"(a) AUTHORIZATION. The total number of shares of all classes of
stock which the Corporation shall have authority to issue is
69,688,320 consisting of:
(i) 34,688,320 shares of Preferred Stock, par value $.01 per
share (the "Preferred Stock"), of which:
(A) 5,000,000 shares shall be designated "Series A
Convertible Preferred Stock" (the "Series A Stock");
(B) 17,005,330 shares shall be designated "Series B
Convertible Preferred Stock" (the "Series B Stock");
(C) 3,157,895 shares shall have been designated "Series
C Convertible Preferred Stock" (the "Series C Stock");
(D) 2,137,791 shares shall have been designated "Series
D Convertible Preferred Stock" (the "Series D Stock");
(E) 7,137,304 shares shall have been designated "Series
E Convertible Preferred Stock" (the "Series E Stock");
(F) 250,000 shares shall have been designated "Series F
Junior Convertible Preferred Stock" (the "Series F Junior Stock"); and
<Page>
(ii) 35,000,000 shares of Common Stock, par value $.01 per
share (the "Common Stock")."
(2) Article III, Section A.7, of the Restated Certificate shall be amended
by adding the following new Section A.7(k):
"A.7(k) All holders of record of shares of Series Preferred Stock
shall be given written notice of the mandatory conversion of Series
Preferred Stock pursuant to Section A.7(j) above and such notice shall
designate the place for such mandatory conversion. Such notice need
not be given in advance of the mandatory conversion date. Such notice
shall be sent by first class or registered mail, postage prepaid, or
given by electronic communication in compliance with the provisions of
the General Corporation Law, to each record holder of Series Preferred
Stock. Upon receipt of such notice, each holder of shares of Series
Preferred Stock shall surrender his or its certificate or certificates
for all such shares to the Corporation at the place designated in such
notice, and shall thereafter receive certificates for the number of
shares of Common Stock to which such holder is entitled pursuant to
Section A.7(j) above. As of the conversion date of the Series
Preferred Stock, all outstanding shares of Series Preferred Stock
shall be deemed to have been converted into shares of Common Stock,
which shall be deemed to be outstanding of record, and all rights with
respect to the Series Preferred Stock so converted, including the
rights, if any, to receive notices and vote (other than as a holder of
Common Stock), will terminate, except only the rights of the holders
thereof, upon surrender of their certificate or certificates therefor,
to receive certificates for the number of shares of Common Stock into
which such Series Preferred Stock has been converted. All certificates
evidencing shares of Series Preferred Stock converted into shares of
Common Stock pursuant to Section A.7(j) above shall, from and after
such conversion date, be deemed to have been retired and canceled,
notwithstanding the failure of the holder or holders thereof to
surrender such certificates to the Corporation in accordance with the
provisions hereof. Upon the closing of the sale of shares of Common
Stock in a firm commitment underwriting meeting the requirements of
Section A.7(j) above, the number of authorized shares of Series A
Stock, Series B Stock, Series C Stock, Series D Stock, Series E Stock
and Series F Junior Stock shall be automatically reduced by the number
of shares of Series A Stock, Series B Stock, Series C Stock, Series D
Stock, Series E Stock and Series F Junior Stock that had been
designated as Series A Stock, Series B Stock, Series C Stock, Series D
Stock, Series E Stock and Series F Junior Stock and all provisions
included under Article III(a)(i)(A)-(F) and all references to the
Series A Stock, Series B Stock, Series C Stock, Series D Stock, Series
E Stock and Series F Junior Stock in this Sixth Restated Certificate
of Incorporation shall be deleted and of no further force or effect.
(3) Article X of the Restated Certificate is deleted in its entirely and
the following is inserted in lieu thereof:
"ARTICLE X
LIMITATION OF LIABILITY
Except to the extent that the General Corporation Law of Delaware
prohibits the elimination or limitation of liability of directors for
breaches of fiduciary duty, no director of the Corporation shall be
personally liable to the Corporation or its stockholders for monetary
damages for any breach of fiduciary duty as a director,
notwithstanding any provision of law imposing such liability. No
amendment to or repeal of this provision shall apply to or have any
effect on the liability or alleged liability
-2-
<Page>
of any director of the Corporation for or with respect to any acts or
omissions of such director occurring prior to such amendment or
repeal."
(4) Article XI of the Restated Certificate is deleted in its entirely and
the following is inserted in lieu thereof:
"ARTICLE XI
INDEMNIFICATION
The Corporation shall provide indemnification as follows:
1. ACTIONS, SUITS AND PROCEEDINGS OTHER THAN BY OR IN THE RIGHT
OF THE CORPORATION. The Corporation shall indemnify each person who
was or is a party or threatened to be made a party to any threatened,
pending or completed action, suit or proceeding, whether civil,
criminal, administrative or investigative (other than an action by or
in the right of the Corporation) by reason of the fact that he or she
is or was, or has agreed to become, a director or officer of the
Corporation, or is or was serving, or has agreed to serve, at the
request of the Corporation, as a director, officer, partner, employee
or trustee of, or in a similar capacity with, another corporation,
partnership, joint venture, trust or other enterprise (including any
employee benefit plan) (all such persons being referred to hereafter
as an "Indemnitee"), or by reason of any action alleged to have been
taken or omitted in such capacity, against all expenses (including
attorneys' fees), judgments, fines and amounts paid in settlement
actually and reasonably incurred by or on behalf of Indemnitee in
connection with such action, suit or proceeding and any appeal
therefrom, if Indemnitee acted in good faith and in a manner which
Indemnitee reasonably believed to be in, or not opposed to, the best
interests of the Corporation, and, with respect to any criminal action
or proceeding, had no reasonable cause to believe his or her conduct
was unlawful. The termination of any action, suit or proceeding by
judgment, order, settlement, conviction or upon a plea of nolo
contendere or its equivalent, shall not, of itself, create a
presumption that Indemnitee did not act in good faith and in a manner
which Indemnitee reasonably believed to be in, or not opposed to, the
best interests of the Corporation, and, with respect to any criminal
action or proceeding, had reasonable cause to believe that his or her
conduct was unlawful.
2. ACTIONS OR SUITS BY OR IN THE RIGHT OF THE CORPORATION. The
Corporation shall indemnify any Indemnitee who was or is a party to or
threatened to be made a party to any threatened, pending or completed
action or suit by or in the right of the Corporation to procure a
judgment in its favor by reason of the fact that Indemnitee is or was,
or has agreed to become, a director or officer of the Corporation, or
is or was serving, or has agreed to serve, at the request of the
Corporation, as a director, officer, partner, employee or trustee of,
or in a similar capacity with, another corporation, partnership, joint
venture, trust or other enterprise (including any employee benefit
plan), or by reason of any action alleged to have been taken or
omitted in such capacity, against all expenses (including attorneys'
fees) and, to the extent permitted by law, amounts paid in settlement
actually and reasonably incurred by or on behalf of Indemnitee in
connection with such action, suit or proceeding and any appeal
therefrom, if Indemnitee acted in good faith and in a manner which
Indemnitee reasonably believed to be in, or not opposed to, the best
interests of the Corporation, except that no indemnification shall be
made under this Section 2 in respect of any claim, issue or matter as
to which Indemnitee shall have been adjudged to be liable to the
Corporation, unless, and only to the extent, that the Court of
Chancery of Delaware shall determine upon application that, despite
the adjudication of such liability but in view of all the
circumstances of the case,
-3-
<Page>
Indemnitee is fairly and reasonably entitled to indemnity for such
expenses (including attorneys' fees) which the Court of Chancery of
Delaware shall deem proper.
3. INDEMNIFICATION FOR EXPENSES OF SUCCESSFUL PARTY.
Notwithstanding any other provisions of this Article XI, to the extent
that an Indemnitee has been successful, on the merits or otherwise, in
defense of any action, suit or proceeding referred to in Sections 1
and 2 of this Article XI, or in defense of any claim, issue or matter
therein, or on appeal from any such action, suit or proceeding,
Indemnitee shall be indemnified against all expenses (including
attorneys' fees) actually and reasonably incurred by or on behalf of
Indemnitee in connection therewith. Without limiting the foregoing, if
any action, suit or proceeding is disposed of, on the merits or
otherwise (including a disposition without prejudice), without (i) the
disposition being adverse to Indemnitee, (ii) an adjudication that
Indemnitee was liable to the Corporation, (iii) a plea of guilty or
nolo contendere by Indemnitee, (iv) an adjudication that Indemnitee
did not act in good faith and in a manner he reasonably believed to be
in or not opposed to the best interests of the Corporation, and (v)
with respect to any criminal proceeding, an adjudication that
Indemnitee had reasonable cause to believe his conduct was unlawful,
Indemnitee shall be considered for the purposes hereof to have been
wholly successful with respect thereto.
4. NOTIFICATION AND DEFENSE OF CLAIM. As a condition precedent to
an Indemnitee's right to be indemnified, such Indemnitee must notify
the Corporation in writing as soon as practicable of any action, suit,
proceeding or investigation involving such Indemnitee for which
indemnity will or could be sought. With respect to any action, suit,
proceeding or investigation of which the Corporation is so notified,
the Corporation will be entitled to participate therein at its own
expense and/or to assume the defense thereof at its own expense, with
legal counsel reasonably acceptable to Indemnitee. After notice from
the Corporation to Indemnitee of its election so to assume such
defense, the Corporation shall not be liable to Indemnitee for any
legal or other expenses subsequently incurred by Indemnitee in
connection with such action, suit, proceeding or investigation, other
than as provided below in this Section 4. Indemnitee shall have the
right to employ his or her own counsel in connection with such action,
suit, proceeding or investigation, but the fees and expenses of such
counsel incurred after notice from the Corporation of its assumption
of the defense thereof shall be at the expense of Indemnitee unless
(i) the employment of counsel by Indemnitee has been authorized by the
Corporation, (ii) counsel to Indemnitee shall have reasonably
concluded that there may be a conflict of interest or position on any
significant issue between the Corporation and Indemnitee in the
conduct of the defense of such action, suit, proceeding or
investigation or (iii) the Corporation shall not in fact have employed
counsel to assume the defense of such action, suit, proceeding or
investigation, in each of which cases the fees and expenses of counsel
for Indemnitee shall be at the expense of the Corporation, except as
otherwise expressly provided by this Article XI. The Corporation shall
not be entitled, without the consent of Indemnitee, to assume the
defense of any claim brought by or in the right of the Corporation or
as to which counsel for Indemnitee shall have reasonably made the
conclusion provided for in clause (ii) above. The Corporation shall
not be required to indemnify Indemnitee under this Article XI for any
amounts paid in settlement of any action, suit, proceeding or
investigation effected without its written consent. The Corporation
shall not settle any action, suit, proceeding or investigation in any
manner which would impose any penalty or limitation on Indemnitee
without Indemnitee's written consent. Neither the Corporation nor
Indemnitee will unreasonably withhold or delay its consent to any
proposed settlement.
-4-
<Page>
5. ADVANCE OF EXPENSES. Subject to the provisions of Section 6 of
this Article XI, in the event that the Corporation does not assume the
defense pursuant to Section 4 of this Article XI of any action, suit,
proceeding or investigation of which the Corporation receives notice
under this Article XI, any expenses (including attorneys' fees)
incurred by or on behalf of Indemnitee in defending an action, suit,
proceeding or investigation or any appeal therefrom shall be paid by
the Corporation in advance of the final disposition of such matter;
provided, however, that the payment of such expenses incurred by or on
behalf of Indemnitee in advance of the final disposition of such
matter shall be made only upon receipt of an undertaking by or on
behalf of Indemnitee to repay all amounts so advanced in the event
that it shall ultimately be determined that Indemnitee is not entitled
to be indemnified by the Corporation as authorized in this Article XI;
and further provided that no such advancement of expenses shall be
made under this Article XI if it is determined (in the manner
described in Section 6) that (i) Indemnitee did not act in good faith
and in a manner he reasonably believed to be in, or not opposed to,
the best interests of the Corporation, or (ii) with respect to any
criminal action or proceeding, Indemnitee had reasonable cause to
believe his conduct was unlawful. Such undertaking shall be accepted
without reference to the financial ability of Indemnitee to make such
repayment.
6. PROCEDURE FOR INDEMNIFICATION. In order to obtain
indemnification or advancement of expenses pursuant to Section 1, 2, 3
or 5 of this Article XI, an Indemnitee shall submit to the Corporation
a written request. Any such advancement of expenses shall be made
promptly, and in any event within 30 days after receipt by the
Corporation of the written request of Indemnitee, unless the
Corporation determines within such 30-day period that Indemnitee did
not meet the applicable standard of conduct set forth in Section 1, 2
or 5 of this Article XI, as the case may be. Any such indemnification,
unless ordered by a court, shall be made with respect to requests
under Section 1 or 2 only as authorized in the specific case upon a
determination by the Corporation that the indemnification of
Indemnitee is proper because Indemnitee has met the applicable
standard of conduct set forth in Section 1 or 2, as the case may be.
Such determination shall be made in each instance (a) by a majority
vote of the directors of the Corporation consisting of persons who are
not at that time parties to the action, suit or proceeding in question
("disinterested directors"), whether or not a quorum, (b) by a
committee of disinterested directors designated by majority vote of
disinterested directors, whether or not a quorum, (c) if there are no
disinterested directors, or if the disinterested directors so direct,
be independent legal counsel (who may, to the extent permitted by law,
by regular legal counsel to the Corporation) in a written opinion, or
(d) by the stockholders of the Corporation.
7. REMEDIES. The right to indemnification or advancement of
expenses as granted by this Article XI shall be enforceable by
Indemnitee in any court of competent jurisdiction. Neither the failure
of the Corporation to have made a determination prior to the
commencement of such action that indemnification is proper in the
circumstances because Indemnitee has met the applicable standard of
conduct, nor an actual determination by the Corporation pursuant to
Section 6 of this Article XI that Indemnitee has not met such
applicable standard of conduct, shall be a defense to the action or
create a presumption that Indemnitee has not met the applicable
standard of conduct. Indemnitee's expenses (including attorneys' fees)
reasonably incurred in connection with successfully establishing
Indemnitee's right to indemnification, in whole or in part, in any
such proceeding shall also be indemnified by the Corporation.
8. LIMITATIONS. Notwithstanding anything to the contrary in this
Article XI, except as set forth in Section 7 of the Article XI, the
Corporation shall not indemnify an
-5-
<Page>
Indemnitee pursuant to this Article XI in connection with a proceeding
(or part thereof) initiated by such Indemnitee unless the initiation
thereof was approved by the Board of Directors of the Corporation.
Notwithstanding anything to the contrary in this Article XI, the
Corporation shall not indemnify an Indemnitee to the extent such
Indemnitee is reimbursed from the proceeds of insurance, and in the
event the Corporation makes any indemnification payments to an
Indemnitee and such Indemnitee is subsequently reimbursed from the
proceeds of insurance, such Indemnitee shall promptly refund
indemnification payments to the Corporation to the extent of such
insurance reimbursement.
9. SUBSEQUENT AMENDMENT. No amendment, termination or repeal of
this Article XI or of the relevant provisions of the General
Corporation Law of Delaware or any other applicable laws shall affect
or diminish in any way the rights of any Indemnitee to indemnification
under the provisions hereof with respect to any action, suit,
proceeding or investigation arising out of or relating to any actions,
transactions or facts occurring prior to the final adoption of such
amendment, termination or repeal.
10. OTHER RIGHTS. The indemnification and advancement of expenses
provided by this Article XI shall not be deemed exclusive of any other
rights to which an Indemnitee seeking indemnification or advancement
of expenses may be entitled under any law (common or statutory),
agreement or vote of stockholders or disinterested directors or
otherwise, both as to action in Indemnitee's official capacity and as
to action in any other capacity while holding office for the
Corporation, and shall continue as to an Indemnitee who has ceased to
be a director or officer, and shall inure to the benefit of the
estate, heirs, executors and administrators of Indemnitee. Nothing
contained in this Article XI shall be deemed to prohibit, and the
Corporation is specifically authorized to enter into, agreements with
officers and directors providing indemnification rights and procedures
different from those set forth in this Article XI. In addition, the
Corporation may, to the extent authorized from time to time by its
Board of Directors, grant indemnification rights to other employees or
agents of the Corporation or other persons serving the Corporation and
such rights may be equivalent to, or greater or less than, those set
forth in this Article XI.
11. PARTIAL INDEMNIFICATION. If an Indemnitee is entitled under
any provision of this Article to indemnification by the Corporation
for some or a portion of the expenses (including attorneys' fees),
judgments, fines or amounts paid in settlement actually and reasonably
incurred by or on behalf of Indemnitee in connection with any action,
suit, proceeding or investigation and any appeal therefrom but not,
however, for the total amount thereof, the Corporation shall
nevertheless indemnify Indemnitee for the portion of such expenses
(including attorneys' fees), judgments, fines or amounts paid in
settlement to which Indemnitee is entitled.
12. INSURANCE. The Corporation may purchase and maintain
insurance, at its expense, to protect itself and any director,
officer, employee or agent of the Corporation or another corporation,
partnership, joint venture, trust or other enterprise (including any
employee benefit plan) against any expense, liability or loss incurred
by him in any such capacity, or arising out of his status as such,
whether or not the Corporation would have the power to indemnify such
person against such expense, liability or loss under the General
Corporation Law of Delaware.
13. SAVINGS CLAUSE. If this Article or any portion hereof shall
be invalidated on any ground by any court of competent jurisdiction,
then the Corporation shall nevertheless indemnify each Indemnitee as
to any expenses (including attorneys'
-6-
<Page>
fees), judgments, fines and amounts paid in settlement in connection
with any action, suit, proceeding or investigation, whether civil,
criminal or administrative, including an action by or in the right of
the Corporation, to the fullest extent permitted by any applicable
portion of this Article that shall not have been invalidated and to
the fullest extent permitted by applicable law.
14. DEFINITIONS. Terms used herein and defined in Section 145(h)
and Section 145(i) of the General Corporation Law of Delaware shall
have the respective meanings assigned to such terms in such Section
145(h) and Section 145(i)."
(5) A new Article XII shall be inserted into the Restated Certificate as
follows:
"ARTICLE XII
STOCKHOLDER MEETINGS
Upon the closing of the sale of shares of Common Stock in a firm
commitment underwriting meeting the requirements of Section A.7(j),
Stockholders of the Corporation may not take any action by written
consent in lieu of a meeting. Notwithstanding any other provisions of
law, this Sixth Restated Certificate of Incorporation or the By-laws
of the Corporation, and notwithstanding the fact that a lesser
percentage may be specified by law, the affirmative vote of the
holders of at least seventy-five percent (75%) of the votes which all
the stockholders would be entitled to cast in any annual election of
directors or class of directors shall be required to amend or repeal,
or to adopt any provision inconsistent with, this Article XII."
IN WITNESS WHEREOF, the Corporation has caused this Certificate of
Amendment to be signed by its President and Chief Executive Officer on this ___
day of _________, 2003.
NITROMED, INC.
By:
---------------------------------------------
Name: Michael D. Loberg
Title: President and Chief Executive Officer
-7-