<PAGE>
                                                                    Exhibit 10.6


                                 HYBRIDON, INC.
                                345 Vassar Street
                         Cambridge, Massachusetts 02139

                                  May 20, 2005



Pillar Investments Limited
St. James' Chambers
Douglas
Isle of Man

Gentlemen:

         This letter sets forth the terms and conditions of the engagement of
Pillar Investments Limited (the "Advisor") as a non-exclusive financial advisor
to Hybridon, Inc. (the "Company") in connection with the arrangement and
negotiation of a private placement of the Company's convertible subordinated
notes outside of the United States (the "Transaction"). The Advisor, in its
capacity as financial advisor to the Company, has identified and will identify
potential non-U.S. investors and, subject to the Company's prior written
approval, has contacted or will contact such potential investors on behalf of
the Company and has provided and will provide such other services in connection
with the Transaction as the Company may from time to time reasonably request.

         The Advisor has not contacted or initiated and shall not contact or
initiate any discussions with any party or prospective investor without first
identifying such party or prospective investor to the Company and obtaining the
Company's prior written approval to make such contact or initiate such
discussions (such parties and prospective investors that are approved by the
Company are referred to herein as the "Approved Investors"). The Advisor shall
not have authority under this letter to bind the Company in any way to any
party, and nothing contained in this letter shall require the Company to accept
the terms of any proposal or undertake any other action that would result in the
receipt by the Advisor of a fee hereunder.

         The Advisor represents, warrants and covenants to the Company that:

                  (a)      It has not offered, offered to sell or sold and shall
         not offer, offer to sell or sell any securities of the Company on the
         basis of any written communications or documents relating to the
         Company or its business other than written materials furnished by the
         Company or previously approved by the Company in writing, including
         without limitation the Company's filings under the Securities Exchange
         Act of 1934, as amended (the "Offering Materials"). No communications
         (whether oral or written) or documents relating to the Company or its
         business made or delivered by the Advisor have been or shall be
         inconsistent with the Offering Materials.


<PAGE>

                  (b)      It has not offered, offered to sell or sold and shall
         not offer, offer to sell or sell any securities of the Company to any
         investor in the United States or to any United States person outside
         the United States.

                  (c)      It has not engaged and shall not engage in any form
         of general solicitation or general advertising which is prohibited by
         Regulation D ("Regulation D") promulgated under the Securities Act of
         1933, as amended (the "Securities Act"), in connection with the
         Transaction or any directed selling efforts in the United States (as
         such term is defined in Regulation S ("Regulation S") promulgated under
         the Securities Act). In addition, such Advisor has not taken and shall
         not take any action that might reasonably be expected to jeopardize the
         availability for the Transaction of the exemption from registration
         provided by Regulation S or the qualification of securities of the
         Company for offer and sale under any applicable foreign securities
         laws.

                  (d)      It shall make reasonable inquiry to determine that
         each investor is acquiring the securities of the Company for his or its
         own account for investment.

                  (e)      In the performance of its services hereunder, it has
         complied and shall comply with the U.S. securities laws and the
         securities laws in effect in any jurisdiction in which securities of
         the Company are offered by it and the rules, regulations and orders of
         any securities administrator existing or adopted thereunder.

                  (f)      It shall not receive, directly or indirectly, any
         remuneration in respect of any issuance and sale by the Company of its
         securities in the United States or to any U.S. person.

         In the event a Transaction with Approved Investors is completed during
the term of this letter, the Company will (i) pay the Advisor a fee in an amount
equal to 5.25% of the Aggregate Value (as defined below) of the Transaction
received from Approved Investors and (ii) issue to the Advisor a five-year
warrant or warrants (in a form containing antidilution protection for stock
splits and other similar events and other customary provisions as agreed by the
Company and the Advisor) to purchase such number of shares of common stock of
the Company (the "Warrant Shares") as is equal to 10% of the Issued Shares (as
defined below) at an exercise price per share equal to the conversion price of
the convertible subordinated notes issued to Approved Investors in the
Transaction.

         For the purposes of this letter, (i) the term "Aggregate Value" shall
mean the total amount of cash and the fair market value of all other property
paid by Approved Investors to the Company in consideration for the convertible
subordinated notes of the Company to be issued in the Transaction, and (ii) the
term "Issued Shares" shall mean the total number of shares of common stock of
the Company issuable, as of the closing, upon conversion of the convertible
subordinated notes of the Company issued to the Approved Investors, which
Approved Investors were introduced to the Company by the Advisor, in the
Transaction.


                                       -2-
<PAGE>

         The Advisor recognizes that the Company is subject to the rules of the
American Stock Exchange, including Section 711 of the American Stock Exchange
Company Guide. Accordingly, the Advisor agrees that notwithstanding the
foregoing the Company shall have no obligation hereunder to pay any fees or
issue any Warrants to the Advisor that would not comply with the rules of the
American Stock Exchange or that would require the Company to obtain stockholder
approval. In the event of such a conflict, the Company and the Advisor agree to
negotiate in good faith new compensation terms for the Advisor.

         In addition to any fees payable to the Advisor under the terms of this
letter, the Company agrees to reimburse the Advisor for its reasonable
out-of-pocket expenses incurred in connection with the Advisor's activities
under this letter, which shall not exceed $35,000, in the aggregate, without the
Company's prior approval.

         The Company agrees to indemnify the Advisor and its affiliates,
directors, officers, employees, agents and controlling persons (each such person
being an "Indemnified Party") from and against any and all losses, claims,
damages and liabilities, joint or several, to which such Indemnified Party may
become subject under any applicable federal or state law, or otherwise, related
to or arising out of the engagement of the Advisor pursuant to, and the
performance by the Advisor of the services contemplated by, this letter and
will, subject to the limitation set forth below, reimburse any Indemnified Party
for all expenses (including reasonable counsel fees and expenses, whether
incurred in connection with third party claims or direct claims against the
Company) as they are incurred in connection with the investigation of,
preparation for or defense of any pending or threatened claim or any action or
proceeding arising therefrom, whether or not such Indemnified Party is a party.
The Company will not be liable under the foregoing indemnification provision to
the extent that any loss, claim, damage, liability or expense is found in a
final judgment by a court of competent jurisdiction to have resulted from an
Indemnified Party's breach of this letter, bad faith, willful misfeasance, gross
negligence or reckless disregard of its obligations or duties. No Indemnified
Party shall settle any claim for which indemnification may be sought by him or
it hereunder without the prior written consent of the Company. The Company's
obligations to indemnify pursuant hereto shall be limited to the Indemnified
Party's actual liabilities, losses, damages or expenses incurred and shall not
include any consequential damages or damages for loss of business or reputation.

         The Company will have the right, at its option, to assume the defense
of any litigation or proceeding in respect of which indemnity may be sought
hereunder, including the employment of counsel reasonably satisfactory to the
Advisor (the Advisor hereby agrees that Wilmer Cutler Pickering Hale and Dorr
LLP is satisfactory to the Advisor) and the payment of the fees and expenses of
such counsel, in which event, except as provided below, the Company shall not be
liable for the fees and expenses of any other counsel retained by any
Indemnified Person in connection with such litigation or proceeding. In any such
litigation or proceeding the defense of which the Company shall have so assumed,
any Indemnified Person shall have the right to participate in such litigation or
proceeding and to retain its own counsel.


                                       -3-
<PAGE>

         Upon receipt by an Indemnified Person of actual notice of a claim,
action or proceeding against such Indemnified Person in respect of which
indemnity may be sought hereunder, such Indemnified Person shall promptly notify
the Company with respect thereto. In addition, an Indemnified Person shall
promptly notify the Company after any action is commenced (by the way of service
with a summons or other legal process giving information as to the nature and
basis of the claim) against such Indemnified Person in respect of which
indemnity may be sought hereunder. In any event, failure to notify the Company
shall not relieve the Company from any liability which the Company may have on
account of this indemnity or otherwise, except to the extent the Company shall
have been prejudiced by such failure.

         In the course of its services, the Advisor has had and will have access
to Confidential Information (as defined below) concerning the Company. The
Advisor agrees that all Confidential Information has been and will be treated by
the Advisor as confidential in all respects. The term "Confidential Information"
shall mean all information, whether written or oral, which is disclosed by the
Company or its affiliates, agents or representatives to the Advisor or is
otherwise learned of by the Advisor in connection with its role as financial
advisor to the Company which information is not in the public domain, but shall
not include: (i) information which, prior to disclosure to the Advisor, was
already in the Advisor's possession and was not otherwise subject to an
obligation of confidentiality; (ii) information which is publicly disclosed
other than by the Advisor in violation of this letter; (iii) information which
is obtained by the Advisor from a third party that (x) the Advisor does not know
to have violated, or to have obtained such information in violation of, any
obligation to the Company or its affiliates with respect to such information,
and (y) does not require the Advisor to refrain from disclosing such
information; and (iv) information which is required to be disclosed by the
Advisor or its outside counsel under compulsion of law (whether by oral
question, interrogatory, subpoena, civil investigative demand or otherwise) or
by order of any court or governmental or regulatory body to whose supervisory
authority the Advisor is subject; provided that, in such circumstance, the
Advisor will give the Company prior written notice of such disclosure and
cooperate with the Company to minimize the scope of any such disclosure. Each
Advisor's obligation under this paragraph shall survive the expiration,
termination or completion of this letter or the Advisor's engagement hereunder.

         The Advisor's engagement hereunder and this letter shall terminate on
the earlier of (i) May 30, 2005 or (ii) written notice of termination by the
Company to the Advisor or by the Advisor to the Company, it being understood
that the provisions relating to confidentiality and indemnification will survive
any such termination.

         This letter shall be construed and interpreted in accordance with the
laws of the Commonwealth of Massachusetts. This letter constitutes the entire
agreement of the parties with respect to the subject matter hereof.

         If the foregoing is in accordance with your understanding, please
confirm acceptance by signing and returning to us the duplicate of this letter
attached herewith.


                                       -4-
<PAGE>

                                        Sincerely,

                                        HYBRIDON, INC.



                                        By: /s/ R. Andersen
                                           --------------------
                                           Name:  R.G. Andersen
                                           Title: CFO

AGREED AND ACCEPTED AS OF
THE DATE SET FORTH ABOVE BY:

PILLAR INVESTMENTS LIMITED



By: /s/ Youssef El Zein
   --------------------
    Title: Director


                                       -5-