<PAGE>


                                                                    EXHIBIT 10.1





                      AMENDED AND RESTATED PROMISSORY NOTE

$4.0 MILLION                                                    OCTOBER 26, 2006

         WHEREAS, Boston Life Sciences, Inc., a Delaware corporation (the
"MAKER"), and Robert Gipson (the "LENDER"), are parties to that certain
Promissory Note, dated August 8, 2006 and made by the Maker in favor of the
Lender for the principal sum $3,000,000.00 (the "ORIGINAL NOTE");

         WHEREAS, in accordance with the terms of the Original Note, Lender has
made those Advances (as defined in Section 1 below) set forth on the schedule
attached hereto; and

         WHEREAS, the Lender and the Maker desire to amend and restate the
Original Note as set forth herein.

         NOW THEREFORE, in consideration of the premises and mutual promises and
covenants contained herein, and on the terms herein set forth, the parties
hereto, intending to be legally bound, hereby agree to amend and restate the
Original Note in its entirety to read as follows:

         FOR VALUE RECEIVED, Maker, hereby unconditionally promises to pay to
the order of Lender, in lawful money of the United States of America and in
immediately available funds, the principal sum of Four Million Dollars
($4,000,000), or, if less, the aggregate unpaid principal amount of all Advances
(the "LOAN"), together with accrued and unpaid interest thereon, each due and
payable on the dates and in the manner set forth below.

         1.       ADVANCES. From time to time prior to the Maturity Date
(defined in Section 2 below), and so long as no Event of Default exists, the
Lender shall make advances (the "ADVANCES") to the Maker, and the Maker may
borrow funds from the Lender hereunder, provided that the aggregate principal
amount of all Advances shall in no event exceed $4,000,000. Each request for an
Advance shall be made by the Maker in writing, delivered to the Lender at least
seven (7) business days prior the requested date of such Advance and shall
specify the date of such Advance, and the amount of such Advance. Each Advance
shall be in the minimum amount of $1,000,000. The Lender shall, and is hereby
authorized to, record on the schedule attached hereto, or to otherwise record in
accordance with its usual practice, the date and amount of each Advance and the
date and amount of each principal payment hereunder, provided, however, that any
failure to so record any Advance or Payment shall not in any manner affect the
obligation of the Maker to repay any Advance in accordance with the terms
hereof.

         2.       PRINCIPAL REPAYMENT. The outstanding principal amount of the
Loan shall be due and payable on the earliest to occur of (i) June 30, 2007,
(ii) the date on which the Maker consummates an equity financing in which the
aggregate gross proceeds to the Maker total at least $10,000,000 and (iii) the
date on which the Lender declares an Event of Default (as defined in Section 8
below) to have occurred (the first of the events set forth in Section 2(i),
2(ii) and 2(iii) to occur being referred to herein as the "MATURITY DATE"). This
Amended and Restated Note may be prepaid in whole or in part at any time without
premium or penalty.

         3.       INTEREST RATE AND PAYMENTS. Interest shall accrue on each
Advance from the date of such Advance and all unpaid interest shall be due and
payable on the Maturity Date. The Maker

                                                                 Promissory Note

<PAGE>

promises to pay interest on the outstanding principal amount of each Advance
until payment in full of such Advance at a per annum interest rate equal to (i)
nine percent (9%) from the date of each Advance to the Maturity Date, (ii) from
and after the Maturity Date, or during the continuance of an Event of Default
(as defined below), at the rate set forth in clause (i) plus two percent (2%),
or (iii) if less than the rates applicable under both clauses (i) and (ii), the
maximum rate permissible by law. Interest shall be calculated on the basis of a
360-day year for the actual number of days elapsed.

         4.       PLACE OF PAYMENT. All amounts payable hereunder shall be
payable in immediately available funds at the office of the Lender, c/o Ingalls
& Snyder, 61 Broadway, New York, NY, unless another place of payment shall be
specified in writing by the Lender.

         5.       APPLICATION OF PAYMENTS. Payment on this Amended and Restated
Note shall be applied first to costs and expenses due hereunder, if any, then to
accrued interest, and thereafter to the outstanding principal balance hereof.
Any principal repayment or interest payment hereunder not paid when due, whether
at stated maturity, by acceleration or otherwise, shall bear interest at the
rate set forth in clause (ii) of Section 2 hereof (or, if such rate exceeds the
maximum rate permitted by law, then at such maximum rate permitted by law) until
paid in full.

         6.       REPRESENTATIONS AND WARRANTIES. The Maker represents and
warrants to the Lender that:

                  (a)      the Maker is duly organized, validly existing, and in
                           good standing under the laws of its jurisdiction of
                           incorporation and is duly qualified and in good
                           standing in every other jurisdiction where the nature
                           of its business or the location or ownership of its
                           properties requires such qualification and where the
                           failure to be so qualified would reasonably be
                           expected to have a material adverse effect on the
                           Maker's business, operations, properties, assets or
                           condition (financial or otherwise);

                  (b)      the Maker has the full corporate power and authority
                           to execute and deliver this Amended and Restated Note
                           and to perform all of the obligations hereunder, and
                           all necessary corporate action has been taken to
                           execute and deliver this Amended and Restated Note
                           and to make the borrowings hereunder;

                  (c)      this Amended and Restated Note constitutes the legal,
                           valid, and binding obligations of the Maker,
                           enforceable against the Maker in accordance with its
                           terms, subject to applicable bankruptcy, insolvency,
                           reorganization or similar laws generally affecting
                           the enforcement of the rights of creditors; and

                  (d)      the execution, delivery and performance by the Maker
                           of this Amended and Restated Note does not (i)
                           violate any provisions of the Maker's Certificate of
                           Incorporation, as amended, bylaws, as amended, or any
                           contract, agreement, law, regulation, order, decree
                           or writ to which the Maker or any


                                                                 Promissory Note

                                      -2-
<PAGE>

                           of its properties are subject or (ii) require the
                           consent or approval of any person, entity or
                           authority, including, without limitation, any
                           regulatory authority or governmental body of the
                           United States of America or any state thereof or any
                           political subdivision of any of the foregoing.

         7.       NEGATIVE COVENANTS. So long as any principal and interest
remains outstanding under this Amended and Restated Note, the Maker shall not:

                  (a)      create, incur, assume, guaranty, become liable with
                           respect to (contingently or otherwise), or permit to
                           be outstanding any indebtedness for money borrowed
                           (including, without limitation, any indebtedness
                           evidenced by any notes, instruments or agreements or
                           in connection with any capitalized lease), except for
                           the obligations under this Amended and Restated Note
                           or a promissory note of even date herewith pursuant
                           to which the Maker shall be permitted to borrow up to
                           an additional principal sum of $4,000,000 together
                           with interest thereon;

                  (b)      (i) declare or pay any cash dividend, or make a
                           distribution on, repurchase, or redeem, any class of
                           stock of the Maker, other than pursuant to repurchase
                           obligations under existing employee stock purchase or
                           option plans or (ii) sell, lease, transfer or
                           otherwise dispose of any material assets or property
                           of the Maker; or

                  (c)      dissolve or liquidate.

         8.       DEFAULT. Each of the following events shall be an "EVENT OF
DEFAULT" hereunder:

                  (a)      the Maker fails to pay any of the principal, interest
                           or any other amounts payable under this Amended and
                           Restated Note when and as the same becomes due and
                           payable;

                  (b)      the Maker files any petition or action for relief
                           under any bankruptcy, reorganization, insolvency or
                           moratorium law or any other law for the relief of, or
                           relating to, Maker, now or hereafter in effect, or
                           seeks the appointment of a custodian, receiver,
                           trustee (or other similar official) of the Maker or
                           all or any substantial portion of the Maker's assets,
                           or makes any assignment for the benefit of creditors
                           or takes any action in furtherance of any of the
                           foregoing, or fails to generally pay its debts as
                           they become due;

                  (c)      an involuntary petition is filed, or any proceeding
                           or case is commenced, against the Maker (unless such
                           proceeding or case is dismissed or discharged within
                           ninety (90) days of the filing or commencement
                           thereof) under any bankruptcy, reorganization,
                           arrangement, insolvency, adjustment of debt,
                           liquidation or moratorium statute now or hereafter in
                           effect, or a custodian, receiver, trustee, assignee
                           for the benefit of creditors (or other similar
                           official) is applied for, appointed for the Maker or
                           to take

                                                                 Promissory Note

                                      -3-
<PAGE>

                           possession, custody or control of any property of the
                           Maker, or an order for relief is entered against the
                           Maker in any of the foregoing; or

                  (d)      any representation or warranty made or deemed made by
                           the Maker under this Amended and Restated Note shall
                           have been false or misleading in any material respect
                           when made or deemed made.

         9.       REMEDIES. Upon the occurrence and during the continuance of an
Event of Default hereunder:

                  (a)      all unpaid principal, accrued interest and other
                           amounts owing hereunder shall, at the option of the
                           Lender, and, in the case of an Event of Default
                           pursuant to Section 8(b) or (c) above, automatically,
                           be immediately due, payable and collectible by the
                           Lender pursuant to applicable law;

                  (b)      any and all unpaid principal, interest or other
                           amounts due under this Amended and Restated Note
                           shall thereafter bear interest at the maximum rate
                           set forth in Section 3 hereof;

                  (c)      any and all of the Lender's obligations to make any
                           additional loans or advances hereunder shall
                           automatically terminate and expire; and

                  (d)      the Lender may exercise any and all rights and
                           remedies it may have under this Amended and Restated
                           Note or under applicable law.

         All rights and remedies shall be cumulative and not exclusive. The
failure of the holder hereof to exercise all or any of its rights, remedies,
powers or privileges hereunder or applicable law, in any instance shall not
constitute a waiver thereof in that or any other instance.

         10.      EXPENSES. The Maker agrees to and shall pay to the Lender on
demand, any and all expenses, including, without limitation, reasonable
attorney's fees and disbursements, incurred or paid by the Lender in connection
herewith, including, without limitation, such fees, costs and expenses incurred
for collection or enforcement of amounts outstanding hereunder, for protecting,
preserving or enforcing the Lender's rights or remedies (including fees, costs
and expenses relating to any proceedings with respect to the bankruptcy,
reorganization, insolvency, readjustment of debt, dissolution or liquidation of
the Maker).

         11.      WAIVER. The Maker, for itself and its legal representatives,
successors and assigns, hereby expressly waives demand, protest, presentment,
notice of dishonor, notice of acceptance, and notice of protest, and all other
demands and notices in connection with the delivery, acceptance, performance,
default or enforcement of this Amended and Restated Note and agrees that any
extension, renewal or postponement of the time of payment or any other
indulgence to, or release of any person now or hereafter obligated for the
payment of this Amended and Restated Note shall not affect the Maker's liability
hereunder.

         12.      NO RELIANCE. Lender hereby acknowledges (i) that Wilmer Cutler
Pickering Hale

                                                                 Promissory Note

                                      -4-
<PAGE>

and Dorr LLP has served as counsel solely to the Maker in connection with
entering into this Amended and Restated Note, the Loan and the transactions
contemplated hereby, and (ii) that Lender (a) has sought the advice of his own
legal counsel and has not relied upon Wilmer Cutler Pickering Hale and Dorr LLP,
(b) has had an opportunity to fully discuss and review the terms of this Amended
and Restated Note with Lender's counsel, (c) understands the contents herein and
freely and voluntarily assents to all of the terms and conditions hereof and the
transactions contemplated hereby

         13.      GOVERNING LAW; CONSENT TO JURISDICTION. THIS AMENDED AND
RESTATED NOTE IS INTENDED TO TAKE EFFECT AS A SEALED INSTRUMENT AND SHALL BE
GOVERNED BY, AND CONSTRUED IN ACCORDANCE WITH, THE LAWS (AND NOT THE LAWS OF
CONFLICT) OF THE COMMONWEALTH OF MASSACHUSETTS. THE MAKER HEREBY IRREVOCABLY
SUBMITS TO THE JURISDICTION OF THE COURTS OF THE COMMONWEALTH OF MASSACHUSETTS
AND THE UNITED STATES DISTRICT COURT FOR THE COMMONWEALTH OF MASSACHUSETTS FOR
THE PURPOSE OF ANY SUIT, ACTION OR OTHER PROCEEDING ARISING OUT OF OR RELATING
TO THIS AMENDED AND RESTATED NOTE AND THE MAKER HEREBY IRREVOCABLY AGREES THAT
ALL CLAIMS IN RESPECT OF SUCH ACTION OR PROCEEDING MAY BE HEARD AND DETERMINED
IN ANY SUCH COURT AND IRREVOCABLY WAIVES ANY OBJECTION IT MAY NOW OR HEREAFTER
HAVE AS TO THE VENUE OF ANY SUCH SUIT, ACTION OR PROCEEDING BROUGHT IN ANY SUCH
COURT OR THAT SUCH COURT IS AN INCONVENIENT FORUM. NOTHING HEREIN SHALL LIMIT
THE RIGHT OF THE LENDER TO BRING PROCEEDINGS AGAINST THE MAKER IN THE COURTS OF
ANY OTHER JURISDICTION. ANY JUDICIAL PROCEEDING BY THE MAKER AGAINST THE LENDER
OR ANY AFFILIATE OF THE LENDER INVOLVING, DIRECTLY OR INDIRECTLY, ANY MATTER IN
ANY WAY ARISING OUT OF, RELATED TO, OR CONNECTED WITH THIS AMENDED AND RESTATED
NOTE SHALL BE BROUGHT ONLY IN A COURT IN THE COMMONWEALTH OF MASSACHUSETTS.

         14.      SUCCESSORS AND ASSIGNS. This Amended and Restated Note and all
obligations of the Maker hereunder shall be binding upon the successors and
assigns of the Maker, and shall, together with the rights and remedies of the
Lender hereunder, inure to the benefit of the Lender, any future holder of this
Amended and Restated Note and their respective successors and assigns, provided,
however, the Maker may not transfer or assign its rights or obligations
hereunder without the express written consent of the Lender, and any purported
transfer or assignment by the Maker without the Lender's written consent shall
be null and void. The Lender may assign, transfer, participate or endorse its
rights under this Amended and Restated Note without the consent or approval of
the Maker, and all such rights shall inure to the Lender's successors and
assigns. No sales of participations, other sales, assignments, transfers,
endorsements or other dispositions of any rights hereunder or any portion
thereof or interest therein shall in any manner affect the obligations of the
Maker under this Amended and Restated Note. Upon request, the Maker shall, at
its own expense, execute and deliver to the assignee of this Amended and
Restated Note, a replacement Note of equal and like tenor in an amount assigned
to and assumed by such assignee.

                                                                 Promissory Note

                                      -5-
<PAGE>

         15.      WAIVER OF JURY TRIAL AND CERTAIN DAMAGES. THE MAKER AND THE
LENDER EACH WAIVES ITS RIGHT TO A JURY TRIAL WITH RESPECT TO ANY ACTION OR CLAIM
ARISING OUT OF ANY DISPUTE IN CONNECTION WITH THIS AMENDED AND RESTATED NOTE,
ANY RIGHTS OR OBLIGATIONS HEREUNDER OR THE PERFORMANCE OF ANY SUCH RIGHTS OR
OBLIGATIONS. Except as prohibited by law, the Maker waives any right which it
may have to claim or recover in any litigation referred to in the preceding
sentence any special, exemplary, punitive or consequential damages or any
damages other than, or in addition to, actual damages. The Maker (i) certifies
that neither the Lender nor any representative, agent or attorney of the Lender
has represented, expressly or otherwise, that the Lender would not, in the event
of litigation, seek to enforce the foregoing waivers and (ii) acknowledges that,
in entering into the Amended and Restated Note, the Lender is relying upon,
among other things, the foregoing waivers and certifications.

         16.      ENTIRE AGREEMENT; AMENDMENTS; INVALIDITY. This Amended and
Restated Note constitutes the entire agreement and understanding of the parties,
and supercedes and replaces in their entirety any prior discussions, agreements,
etc., all of which are merged herein and therein, including the Original Note.
None of the terms of this Amended and Restated Note may be amended or otherwise
modified except by an instrument executed by each of the Maker and the Lender.
If any term of this Amended and Restated Note shall be held to be invalid,
illegal or unenforceable, the validity of all other terms hereof shall in no way
be affected thereby, and this Amended and Restated Note shall be construed and
be enforceable as if such invalid, illegal or unenforceable term had not been
included herein. The Original Note is hereby terminated and of no further force
or effect.


                                     *****


                                                                 Promissory Note

                                      -6-
<PAGE>



         IN WITNESS WHEREOF, this Amended and Restated Note has been duly
executed as an instrument under seal as of the date first set forth above.


LENDER:                                 BOSTON LIFE SCIENCES, INC.


                                        By: /s/ Kenneth L. Rice
                                            ------------------------------------

                                        Printed Name: Kenneth L. Rice, Jr.
                                                      --------------------------

                                        Title: EVP & CFO
                                               ---------------------------------

                                        Address:

                                        ----------------------------------------

                                        ----------------------------------------

                                        ----------------------------------------

ATTEST:

By: /s/ Robert Gipson
   -----------------------------------

Title:
       -------------------------------


                                                                 Promissory Note

                                      -7-
<PAGE>


                                                                    EXHIBIT 10.1

                   SCHEDULE OF LOAN AND PAYMENTS OF PRINCIPAL
                     TO AMENDED AND RESTATED PROMISSORY NOTE
                             OF BOSTON LIFE SCIENCES




<Table>
<Caption>
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Principal                               Principal
Amount of            Date               Amount               Unpaid
Advance                                 Paid                 Balance
--------------------------------------------------------------------------------
<S>                  <C>                <C>                  <C>

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</Table>

                                                                 Promissory Note


                                      -8-