Exhibit 10.4

Amended and Restated as of May 22, 2006

Mr. Stephen Cohen

1000 Winter Street

Suite 2200

Waltham, MA 02451

Dear Steve:

This letter agreement constitutes the second amendment and restatement of the
original letter agreement of employment between you and Oscient Pharmaceuticals
Corporation (the “Company”), then known as Genome Therapeutics Corporation,
(which letter agreement of June 15, 2001, first amended and restated as of
February 27, 2003, is hereafter referred to as the “Original Agreement”). This
second amended and restated agreement (this “Agreement”) is as follows:

1. Position and Duties.

(a) As of the Effective Date of this Agreement, as set forth in the final
paragraph of this Agreement you will be employed by the Company on a limited
part-time basis to provide advice and other consulting services with respect to
your prior duties, transitional activities and responsibilities for the Company,
as requested from time to time by representatives of the Company. Your services
will be provided during normal business hours by telephone, in person or by
e-mail, as requested from time to time by the Company’s representatives. The
Company will make reasonable efforts to arrange your consulting services at
times that are mutually agreeable to you and the Company’s representatives.

(b) You also agree that, while employed by the Company hereunder, you will
devote your sufficient business time and your best efforts, business judgment,
skill and knowledge to the advancement of the business and interests of the
Company and its Affiliates and to the discharge of your duties and
responsibilities for them.

2. Compensation and Benefits. During your employment hereunder, as compensation
for all services performed by you for the Company and its Affiliates, the
Company will provide you the following pay and benefits:

(a) Compensation. As compensation for all services to be provided by you
hereunder and for your other agreements contained herein, the Company will pay
you two Fifty Thousand Dollar ($50,000) payments: the first payable within ten
(10) business days following the later of the Effective Date or the date this
Agreement, signed by you, is received by the Vice President of Human Resources
on behalf of the Company and the second payable on

 

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September 30, 2006. If your services are requested in excess of the limited
part-time basis as described herein, you and the Company will negotiate in good
faith a separate agreement to address such requests.

(b) Bonus. The Company will pay you a bonus for fiscal 2006 as determined by the
Board of Directors and prorated by multiplying the bonus compensation you would
have received had you continued employment until the end of the fiscal year by a
fraction, the numerator of which shall be the number of calendar days from
January 1 to the Effective Date and the denominator of which is 365. Payment
will be made at the time bonuses for fiscal 2006 are payable to executives of
the Company generally, but in no event later than April 30, 2007. You will not
be eligible to earn or receive any other bonus compensation on or after the
Effective Date unless mutually agreed by both parties pursuant to a separate
agreement or amendment to this Agreement.

(c) Option Grants. Any options granted to you during your employment with the
Company which have not yet vested and have not been exercised or cancelled and
have not expired shall continue to vest for the duration of time which you
provide services to the Company in accordance with the specified terms under
which each such options were granted. Provided that your employment hereunder is
not terminated by the Company for “Cause,” you shall have the requisite time in
accordance with the specified terms of such options to exercise any options
which are vested as of the date your employment with the Company terminates as
defined in paragraph 4 (the “Termination Date”) and have not then been exercised
or cancelled and have not yet expired, including options that had vested on or
before the Effective Date and those that vested after the Effective Date, but on
or before the Termination Date.

(d) Participation in Employee Benefit Plans. During your employment hereunder,
you will not be regularly scheduled to work sufficient hours to be eligible to
participate in the employee benefit plans of the Company, except that you and
your qualified beneficiaries, may elect to participate in the Company’s group
health and dental plans through the federal law known as COBRA.

(e) Employee Stock Purchase Program (“ESPP”). Your contribution for the first
half of 2006 into the ESPP will be considered complete and you will be afforded
all the benefits therein.

(f) Paid Time Off. You will not be eligible to earn vacation or other paid time
off on or after the Effective Date. At the time of the payment hereunder, in
accordance with paragraph 2(a) of this Agreement, the Company shall pay you, at
your base rate of pay in effect immediately prior to the Effective Date, for any
vacation that you had earned but not used as of that Date.

 

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(g) Business Expenses. The Company will pay or reimburse you for all reasonable
business expenses incurred or paid by you in the performance of your duties and
responsibilities for the Company, subject to any maximum annual limit and other
restrictions on such expenses set by the Company and to such reasonable
substantiation and documentation as it may specify from time to time.

3. Confidential Information, Restricted Activities and Protection of Documents.

(a) You acknowledge that, in consideration of your employment with the Company,
you agreed to and executed a joinder dated March 19, 2001 to the Company’s
Intellectual Property Policy, included Appendix I thereof (“Invention,
Assignment, Non-Disclosure and Covenant Not to Compete”), which imposes certain
non-competition, non-solicitation and non-disclosure restrictions on you (such
agreement being referred to herein as the “Intellectual Property and Non-Compete
Agreement”). The Intellectual Property and Non-Compete Agreement shall remain in
full force and effect during your employment with the Company hereunder and
shall survive termination of your employment with the Company, howsoever caused,
in accordance with its terms.

(b) All documents, records and files, in any media of whatever kind and
description, relating to the business, present or otherwise, of the Company or
any of its Affiliates, and any copies, in whole or in part, thereof (the
“Documents”), whether or not prepared by you shall be the sole and exclusive
property of the Company. You agree to safeguard all Documents and to surrender
to the Company, at the time your employment terminates or at such earlier time
or times as the Board or its designee may specify, all Documents then in your
possession or control.

4. Term and Termination of Employment. Unless earlier terminated in accordance
with this Agreement, your employment with the Company shall continue until
December 31, 2006, on which date it shall terminate by expiration of the term of
this Agreement. You may terminate your employment hereunder at any time upon
thirty (30) days’ notice to the Company; provided that such notice is
accompanied by your repayment to the Company of a pro-rated portion of the lump
sum paid to you under paragraph 2(a) hereof, determined by multiplying that
payment by a fraction, the numerator of which is the number of calendar days
between the effective date of your resignation and December 31, 2006 and the
denominator of which is the number of calendar days between the Effective Date
and December 31, 2006. This Agreement shall automatically terminate in the event
of your death during employment hereunder and, in that event, no repayment shall
be required.

 

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5. Matters Related to Termination.

(a) In the event of termination of your employment hereunder, whether by
expiration of the term of this Agreement or otherwise, the Company shall have no
further obligation to you.

(b) In signing this Agreement, you acknowledge that, as of the Effective Date,
you have received any and all compensation due to you from the Company through
that date and that, except for payments to be made to you or on your behalf in
accordance with this Agreement, nothing further is due to you from the Company
after the Effective Date.

6. Release of Claims.

(a) In consideration of the payment to be made to you under paragraph 2(a)
hereof and other good and valuable consideration to be provided you in
accordance with this Agreement, to which, you acknowledge, you would not
otherwise be entitled, you agree that this Agreement shall be in complete and
final settlement of any and all causes of action, rights or claims that you have
had in the past, now have, or might now have, in any way related to, connected
with or arising out of your employment or its termination or pursuant to Title
VII of the Civil Rights Act, the Americans with Disabilities Act, the Age
Discrimination in Employment Act, the Massachusetts fair employment practices
statute or any other federal, state or local law, regulation or other
requirement and you hereby release and forever discharge the Company and its
Affiliates and all of their respective past, present and future directors,
shareholders, officers, managers, members, general and limited partners,
employees, agents, representatives, successors and assigns, and all others
connected with any of them, all of the foregoing both individually and in their
official capacities, from any and all such causes of action, rights and claims.

(b) This Agreement, including the release of claims set forth directly above,
creates legally binding obligations and the Company therefore advises you to
consult an attorney before signing this Agreement. In signing this Agreement,
you give the Company assurance that you have signed it voluntarily and with a
full understanding of its terms; that you have had sufficient opportunity,
before signing this Agreement, to consider its terms and to consult with an
attorney, if you wished to do so, or to consult with any other person or
persons; and that, in signing this Agreement, you have not relied on any
promises or representations, express or implied, that are not set forth
expressly in this Agreement.

7. Definition. For purposes of this Agreement, “Affiliates” means all persons
and entities directly or indirectly controlling, controlled by or under common
control with the Company, where control may be by management authority, equity
interest or otherwise.

 

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8. Withholding. All payments made by the Company under this Agreement shall be
reduced by any tax or other amounts required to be withheld by the Company under
applicable law.

9. Assignment. Neither you nor the Company may make any assignment of this
Agreement or any interest in it, by operation of law or otherwise, without the
prior written consent of the other; provided, however, that the Company may
assign its rights and obligations under this Agreement without your consent to
one of its Affiliates or to any entity with whom the Company shall hereafter
affect a reorganization, consolidate with, or merge into or to whom it transfers
all or substantially all of its properties or assets. This Agreement shall inure
to the benefit of and be binding upon you and the Company, and each of our
respective successors, executors, administrators, heirs and permitted assigns.

10. Miscellaneous. This Agreement sets forth the entire agreement between you
and the Company and replaces all prior and contemporaneous communications,
agreements and understandings, written or oral, with respect to the terms and
conditions of your employment; provided, however, that this Agreement shall not
supercede the Intellectual Property and Non-Competition Agreement, any effective
assignment by you of any invention or other intellectual property to the Company
or any of its Affiliates in effect on the Effective Date, loans or other
obligations, if any, that you have to the Company or any of its Affiliates, or
to any of any of their benefit plans, which are outstanding on the Effective
Date or any obligations which you may have with respect to the securities of the
Company; and provided further, that this Agreement shall not constitute a waiver
by the Company of any right it now has or might now have under the Original
Agreement with respect to events occurring prior to the Effective Date. This
Agreement may not be modified or amended, and no breach shall be deemed to be
waived, unless agreed to in writing by you and an expressly authorized
representative of the Board. The headings and captions in this Agreement are for
convenience only and in no way define or describe the scope or content of any
provision of this Agreement. This Agreement may be executed in two or more
counterparts, each of which shall be an original and all of which together shall
constitute one and the same instrument. This is a Massachusetts contract and
shall be governed and construed in accordance with the laws of the Commonwealth
of Massachusetts, without regard to the conflict of laws principles thereof.

11. Notices. Any notices provided for in this Agreement shall be in writing and
shall be effective when delivered in person, consigned to a reputable national
courier service or deposited in the United States mail, postage prepaid, and
addressed to you at your last known address on the books of the Company or, in
the case of the Company, to it at its principal place of business, attention of
the Legal Department, or to such other address as either party may specify by
notice to the other actually received.

 

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If the terms of this Agreement are acceptable to you, please sign, date and
return it to me within twenty-one (21) days of the date you receive it. You may
revoke this Agreement at any time during the seven-day period immediately
following the date of your signing, provided that you do so to me in writing
prior to the last day of that period. If you do not revoke it, then, at the
later of (i) the expiration of that seven-day period or (ii) June 30, 2006 (the
“Effective Date”), this letter will take effect as a legally-binding agreement
between you and the Company on the basis set forth above. The enclosed copy of
this Agreement is for your records.

Sincerely yours,

OSCIENT PHARMACEUTICALS CORPORATION

/s/    Joseph A. Pane

Joseph A. Pane

Vice President, Human Resources

Accepted and Agreed:

/s/    Stephen Cohen

Stephen Cohen

Date: 5/22/06

 

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