<Page>

                                                                     Exhibit 4.4

                                                               EXECUTION VERSION

THIS WARRANT AND THE SHARES ISSUABLE HEREUNDER HAVE NOT BEEN REGISTERED UNDER
THE SECURITIES ACT OF 1933, AS AMENDED, OR ANY STATE SECURITIES LAWS, AND MAY
NOT BE SOLD, PLEDGED, OR OTHERWISE TRANSFERRED WITHOUT AN EFFECTIVE
REGISTRATION THEREOF UNDER SUCH ACT AND LAWS OR, SUBJECT TO SECTION 5.3 HEREOF,
AN OPINION OF COUNSEL REASONABLY SATISFACTORY TO THE CORPORATION AND ITS
COUNSEL, THAT SUCH REGISTRATION IS NOT REQUIRED

                            WARRANT TO PURCHASE STOCK

Issuer: ActivBiotics, Inc.
Number of Shares: 30,000, subject to adjustment
Class of Stock: Series B Convertible Preferred Stock, $O.01 par value per share
Exercise Price: $1.00 per share, subject to adjustment
Issue Date: November 12, 2003
Expiration Date: November 12, 2013

     FOR THE AGREED UPON VALUE of $1.00, and for other good and valuable
consideration, the receipt and sufficiency of which are hereby acknowledged,
this Warrant is issued to SILICON VALLEY BANK (together with its successors and
permitted assigns, "Holder") by ActivBiotics, Inc., a Delaware corporation (the
"Company").

     Subject to the terms and conditions hereinafter set forth, the Holder is
entitled upon surrender of this Warrant and a duly executed Notice of Exercise
in substantially the form attached hereto as Appendix 1 (the "Notice of
Exercise"), at the principal office of the Company, 128 Spring Street,
Lexington, Massachusetts 02421 or such other office as the Company shall notify
the Holder of in writing, to purchase from the Company up to thirty thousand
(30,000) fully paid and non-assessable shares (the "Shares") of the Company's
Series B Convertible Preferred Stock, $O.01 par value per share (the "Class"),
at a purchase price per Share of One Dollar ($1.00) (the "Exercise Price") This
Warrant may be exercised in whole or in part at any time and from time to time
until 5:00 PM, Eastern time, on the Expiration Date set forth above, and shall
be void thereafter. Until such time as this Warrant is exercised in full or
expires, the Exercise Price and the number of Shares are subject to adjustment
from time to time as hereinafter provided

     Notwithstanding the foregoing definition of Class, upon and after the
automatic or voluntary conversion, redemption or retirement of all (but not
less than all) of the outstanding shares of such Class, including without
limitation the Company's initial registered underwritten public offering and
sale of its securities ("IPO"), then from and after the date upon which all such
outstanding shares have been so converted, redeemed or retired, "Class" shall
mean the Company's common stock, $0.01 par value per share ("Common Stock"), and
this Warrant shall be exercisable for such number of shares of Common Stock as
shall equal the number of shares of Common Stock into which the Shares would
have been converted pursuant to the Company's Certificate of Incorporation, as

<Page>

amended, including without limitation the Certificate of Designation, if any,
applicable to the same class or series of preferred stock as the Shares (the
"Certificate") had the Shares been issued and outstanding immediately prior to
such conversion, redemption or retirement, and the Exercise Price shall be the
Common Stock conversion price as determined pursuant to the Certificate
immediately prior to such conversion, redemption or retirement (all subject to
further adjustment as provided herein).

ARTICLE 1. EXERCISE

          1.1 Method of Exercise. Holder may exercise this Warrant by delivering
this Warrant together with a duly executed Notice of Exercise to the principal
office of the Company. Unless Holder is exercising the conversion right set
forth in Section 1.2, Holder shall also deliver to the Company a bank or
certified check or wire transfer to an account specified by the Company for the
aggregate Exercise Price for the Shares being purchased.

          1.2 Conversion Right. In lieu of exercising this Warrant as specified
in Section 1.1, Holder may from time to time convert this Warrant, in whole
or in part, into a number of Shares determined as follows:

                X = Y (A-B)/A
     where:
                X = the number of Shares to be issued to the Holder

                Y = the number of Shares with respect to which this Warrant is
                being exercised

                A = the Fair Market Value (as determined pursuant to Section 1.3
                below) of one Share

                B = the Exercise Price

          1.3 Fair Market Value.

               1.3.1 If shares of the Class (or shares of the Company's stock
into which shares of the Class are convertible or exchangeable) are traded on a
nationally recognized securities exchange or over the counter market, the fair
market value of a Share shall be the closing price of a share of the Class (or
the closing price of a share of the Company's stock for which shares of the
Class are convertible or exchangeable, multiplied by the number of shares of
such stock into which one share of the Class is convertible or exchangeable)
reported for the business day immediately preceding the date of Holder's Notice
of Exercise to the Company.

               1.3.2 If shares of the Class (or shares of the Company's stock
into which shares of the Class are convertible or exchangeable) are not traded
on a nationally recognized


                                        2

<Page>

securities exchange or over the counter market, the Board of Directors of the
Company shall determine fail market value in its reasonable good faith judgment.

          1.4 Delivery of Certificate and New Warrant. Promptly after Holder
exercises or converts this Warrant, the Company at its sole expense shall
promptly deliver to Holder (i) certificates for the Shares acquired upon such
exercise, and (ii) if this Warrant has not been fully exercised or converted and
has not expired, a new warrant of like tenor representing the Shares for which
this Warrant is still exercisable.

          1.5 Replacement of Warrants. On receipt of evidence reasonably
satisfactory to the Company of the loss, theft, destruction or mutilation of
this Warrant and, in the case of loss, theft or destruction, on delivery of an
indemnity agreement reasonably satisfactory in form and amount to the Company
or, in the case of mutilation, on surrender and cancellation of this Warrant,
the Company at its expense shall execute and deliver, in lieu of this Warrant, a
new warrant of like tenor

          1.6 Assumption on Sale, Merger, or Consolidation of the Company

               16.1. "Acquisition". For the purpose of this Warrant,
"Acquisition" means any sale, assignment, transfer, exclusive license, or other
disposition of all or substantially all of the assets of the Company, or any
acquisition, reorganization, consolidation, or merger of the Company where the
holders of the Company's outstanding voting equity securities immediately prior
to the transaction beneficially own less than a majority of the outstanding
voting equity securities of the surviving or successor entity immediately
following the transaction

               1.6.2. Assumption of Warrant. Upon the closing of any Acquisition
(other than an Acquisition in which the consideration received by the Company's
stockholders consists solely of cash), and as a condition precedent thereto, the
successor or surviving entity shall assume the obligations of this Warrant, and
this Warrant shall be exercisable for the same securities and property as would
be payable for the Shares issuable upon exercise of the unexercised portion of
this Warrant as if such Shares were outstanding on the record date for the
Acquisition and subsequent closing. The Exercise Price shall be adjusted
accordingly, and the Exercise Price and number and class of Shares shall
continue to be subject to adjustment from time to time in accordance with the
provisions hereof.

ARTICLE 2. ADJUSTMENTS TO THE SHARES.

          2.1 Stock Dividends, Splits, Etc. If the Company declares or pays a
dividend on the outstanding shares of the Class, payable in shares of the Class,
Common Stock or other securities, or subdivides the outstanding shares of the
Class into a greater number of shares of the Class, or subdivides the shares of
the Class in a transaction that increases the amount of Common Stock into which
such shares are convertible, then upon exercise of this Warrant, for each Share
acquired, Holder shall receive, without additional cost to Holder, the total
number and kind of


                                        3

<Page>

securities to which Holder would have been entitled had Holder owned the Shares
of record as of the date the dividend or subdivision occurred.

          2.2 Reclassification, Exchange or Substitution. Upon any
reclassification, exchange, substitution, reorganization or other event that
results in a change of the number and/or class of the securities issuable upon
exercise or conversion of this Warrant, Holder shall be entitled to receive,
upon exercise or conversion of this Warrant, the number and kind of securities
and property that Holder would have received for the Shares if this Warrant had
been exercised immediately before such reclassification, exchange, substitution,
reorganization or other event. The Company or its successor shall promptly issue
to Holder a new warrant of like tenor for such new securities or other property.
The new warrant shall provide for adjustments which shall be as nearly
equivalent as may be practicable to the adjustments provided for in this Article
2 including, without limitation, adjustments to the Exercise Price and to the
number of securities or property issuable upon exercise of the new warrant. The
provisions of this Section 2.2 shall similarly apply to successive
reclassifications, exchanges, substitutions, reorganizations or other events.

          2.3 Adjustments for Combinations, Etc. If the outstanding shares of
the Class are combined or consolidated, by reclassification or otherwise, into a
lesser number of shares, the Exercise Price shall be proportionately increased
and the number of Shares issuable upon exercise or conversion of this Warrant
shall be proportionately decreased.

          2.4 No Impairment. The Company shall not, by amendment of the
Certificate or its by-laws or through a reorganization, transfer of assets,
consolidation, merger, dissolution, issue, or sale of securities or any other
voluntary action, avoid or seek to avoid the observance or performance of any of
the terms to be observed or performed under this Warrant by the Company, but
shall at all times in good faith assist in carrying out of all the provisions of
this Article 2 and in taking all such action as may be necessary or appropriate
to protect Holder's rights under this Article against impairment.

          2.5 Adjustments for Dilutive Issuances. The number of shares of Common
Stock for which the Shares are convertible shall be adjusted from time to time
in accordance with Section A.7 of Article 111 of the Certificate as if the
Shares were issued and outstanding on and as of the date of any such required
adjustment.

          2.6 Fractional Shares. No fractional Shares shall be issuable upon
exercise or conversion of the Warrant and the number of Shares to be issued
shall be rounded down to the nearest whole Share. If a fractional Share interest
arises upon any exercise or conversion of this Warrant, the Company shall
eliminate such fractional Share interest by paying Holder an amount computed by
multiplying such fractional interest by the Fair Market Value (determined in
accordance with Section 1.3 above) of one Share.

          2.7 Certificate as to Adjustments. Upon each adjustment of the
Exercise Price, number or class of Shares or number of shares of Common Stock or
other securities for which the


                                       -4-

<Page>

Shares are convertible or exchangeable, the Company at its expense shall
promptly compute such adjustment, and furnish Holder with a certificate of its
chief financial officer setting forth such adjustment and the facts upon which
such adjustment is based. The Company shall at any time and from time to time,
upon written request, furnish Holder with a certificate setting forth the
Exercise Price, number and class of Shares and conversion ratio in effect upon
the date thereof and the series of adjustments leading to such Exercise Price,
number and class of Shares and conversion ratio.

ARTICLE 3. REPRESENTATIONS AND COVENANTS OF THE COMPANY.

          3.1 Representations and Warranties. The Company hereby represents and
warrants to the Holder as follows:

               (a) All Shares which may be issued upon the due exercise of this
Warrant, and all Common Stock or other securities, if any, issuable upon due
conversion of the Shares, shall, upon issuance, be duly authorized, validly
issued, fully paid and non-assessable, and free of any liens and encumbrances
except for restrictions on transfer provided for herein or under applicable
federal and state securities laws.

               (b) The Company covenants that it shall at all times cause to be
reserved and kept available out of its authorized and unissued shares such
number of shares of its Series B Convertible Preferred Stock and shares of its
Common Stock and other securities as will be sufficient to permit the exercise
in full of this Warrant and the conversion of the Shares into shares of Common
Stock or such other securities.

               (c) On and as of the date hereof, (i) $1.00 is the lowest price
per share for which shares of the Class have been sold or issued by the Company,
and the lowest exercise or conversion price per share for which shares of the
Class may be purchased or acquired upon the exercise or conversion of
outstanding securities exercisable or convertible by their terms for shares of
the Class, and (ii) the Common Stock conversion price in effect for shares of
the Class as determined pursuant to the Certificate is $1.00.

               (d) The execution and delivery by the Company of this Warrant and
the performance of all obligations of the Company hereunder, including the
issuance to Holder of the right to acquire the Shares, have been duly authorized
by all necessary corporate action on the part of the Company, and this Warrant
is not inconsistent with the Certificate and/or the Company's by-laws, does not
contravene any law or governmental rule, regulation or order applicable to it,
does not and will not contravene any provision of, or constitute a default
under, any material indenture, mortgage, contract or other instrument to which
it is a party or by which it is bound, and constitutes a legal, valid and
binding agreement of the Company, enforceable in accordance with its terms.

          3.2 Notice of Certain Events. If the Company proposes at any time (a)
to declare any dividend or distribution upon any of its capital stock, whether
in cash, property, stock, or other securities and whether or not a regular cash
dividend; (b) to offer for subscription pro rata to the


                                       -5-

<Page>

holders of any class or series of its stock any additional shares of stock of
any class or series or other rights; (c) to effect any reclassification or
recapitalization of any of its securities; or (d) to merge or consolidate with
or into any other corporation, or sell, lease, license, or convey all or
substantially all of its assets, or to liquidate, dissolve or wind up; then, in
connection with each such event, the Company shall give Holder (1) at least 20
days prior written notice of the date on which a record will be taken for such
dividend, distribution, or subscription rights (and specifying the date on which
the holders of securities of the Company shall be entitled to receive such
dividend, distribution or rights) or for determining rights to vote, if any, in
respect of the matters referred to in (c) and (d) above; and (2) in the case of
the matters referred to in (c) and (d) above at least 20 days prior written
notice of the date when the same will take place (and specifying the date on
which the holders of securities of the Company will be entitled to exchange
their securities of the Company for securities or other property deliverable
upon the occurrence of such event).

          3.3 Registration Under Securities Act of 1933, as amended. The shares
of Common Stock issuable upon conversion of the Shares (and the Shares, at all
times when the Class is Common Stock) shall have certain incidental or
"piggyback" registration rights pursuant to, and as set forth in, that certain
Rights Agreement of even date herewith between the Company and Silicon Valley
Bank. The Company represents and warrants to Holder that the Company's foregoing
grant of registration rights and its execution, delivery and performance of the
aforementioned Rights Agreement (a) have been duly authorized by all necessary
corporate action of the Company's Board of Directors and shareholders, (b) will
not violate the Certificate or the Company's by-laws, each as amended, (c) will
not violate or cause a breach or default (or an event which with the passage of
time or the giving of notice or both, would constitute a breach or default)
under any agreement, instrument, mortgage, deed of trust or other arrangement to
which the Company is a party or by which it or any of its assets is subject or
bound, and (d) do not require the approval, consent or waiver of or by any
shareholder, registration rights holder or other third party which approval,
consent or waiver has not been obtained as of the date of issuance of this
Warrant.

ARTICLE 4. REPRESENTATIONS AND WARRANTIES OF THE HOLDER. Holder represents and
warrants to the Company as follows:

          4.1 Purchase for Own Account. Subject to Silicon Valley Bank's right
to transfer this Warrant and the Shares (and/or the securities, if any, issued
and issuable upon conversion of the Shares) to its parent corporation Silicon
Valley Bancshares and/or any other affiliate, this Warrant and the Shares to be
acquired upon exercise hereof will be acquired for investment for Holder's
account, not as nominee or agent, and not with a view to sale or distribution in
violation of applicable federal and state securities laws.

          4.2 Investment Experience. Holder understands that the purchase of
this Warrant and the Shares covered hereby involves substantial risk Holder (a)
has experience as an investor in unregistered securities, (b) has sufficient
knowledge and experience in financial and business affairs that it can evaluate
the risks and merits of its investment in this Warrant and the Shares, and (c)
can bear the economic risk of such Holder's investment in this Warrant and the
Shares


                                       -6-

<Page>

          4.3 Knowledge of Company Business. The Holder is aware of the
Company's business affairs and financial condition, and has acquired information
about the Company sufficient to reach an informed and knowledgeable decision to
acquire this Warrant.

          4.4 No Public Market. The Holder understands that this Warrant, the
Shares, and the Common Stock issuable upon conversion of the Shares must be held
indefinitely unless subsequently registered under the Securities Act of 1933, as
amended or unless exemptions from registration and qualification are otherwise
available.

          4.5 Accredited Investor. Holder is an "accredited investor" as such
term is defined in Regulation D under the Securities Act of 1933, as amended.

ARTICLE 5: MISCELLANEOUS.

          5.1 Automatic Conversion upon Expiration. In the event that, upon the
Expiration Date, the Fair Market Value of one Share (or other security issuable
upon the exercise hereof) as determined in accordance with Section 1.3 above is
greater than the Exercise Price in effect on such date, then this Warrant shall
automatically be deemed on and as of such date to be converted pursuant to
Section 1.2 above as to all Shares (or such other securities) for which it shall
not previously have been exercised or converted, and the Company shall promptly
deliver a certificate representing the Shares (or such other securities) issued
upon such conversion to the Holder.

          5.2 Legends. This Warrant and the Shares (and the securities issuable,
directly or indirectly, upon conversion of the Shares, if any) shall be
imprinted with a legend in substantially the following form:

     THIS SECURITY HAS NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS
     AMENDED, OR ANY STATE SECURITIES LAWS, AND MAY NOT BE SOLD, PLEDGED OR
     OTHERWISE TRANSFERRED WITHOUT AN EFFECTIVE REGISTRATION THEREOF UNDER SUCH
     ACT AND LAWS OR, SUBJECT TO SECTION 5.3 OF THAT CERTAIN WARRANT TO PURCHASE
     STOCK ISSUED BY THE CORPORATION TO SILICON VALLEY BANK DATED AS OF
     ________________, AN OPINION OF COUNSEL REASONABLY SATISFACTORY TO THE
     CORPORATION AND ITS COUNSEL THAT SUCH REGISTRATION IS NOT REQUIRED.
     ADDITIONALLY, THIS SECURITY IS SUBJECT TO THE PROVISIONS OF THE RIGHTS
     AGREEMENT DATED NOVEMBER __, 2003 BETWEEN ACTIVBIOTICS, INC. AND SILICON
     VALLEY BANK COPIES OF SUCH AGREEMENT MAY BE OBTAINED AT NO COST BY WRITTEN
     REQUEST MADE BY THE HOLDER OF RECORD OF THIS CERTIFICATE TO THE SECRETARY
     OF ACTIVBIOTICS, INC.


                                        7

<Page>

          5.3 Compliance with Securities Laws on Transfer. This Warrant and the
Shares (and the securities, if any, issued and issuable upon conversion of the
Shares) may not be transferred or assigned in whole or in part without
compliance with applicable federal and state securities laws by the transferor
and the transferee (including, without limitation, the delivery of investment
representation letters and legal opinions reasonably satisfactory to the
Company, as reasonably requested by the Company). The Company shall not require
Holder to provide an opinion of counsel if the transfer is to Silicon Valley
Bancshares or other affiliate of Holder.

          5.4 Transfer Procedure. Following its receipt of this executed
Warrant, Silicon Valley Bank will transfer same in whole or in part to its
parent corporation Silicon Valley Bancshares, and thereafter Holder and/or
Silicon Valley Bancshares may, subject to Section 5.3 above, transfer all or
part of this Warrant and/or the Shares (or the securities, if any, issued and
issuable upon conversion of the Shares) at any time and from time to time by
giving the Company notice of the portion of the Warrant and/or Shares (or the
securities, if any, issued and issuable upon conversion of the Shares) being
transferred setting forth the name, address and taxpayer identification number
of the transferee and surrendering this Warrant to the Company for reissuance to
the transferee(s) (and Holder if applicable); provided, that at all times prior
to the Company's IPO, Holder shall not, without the prior written consent of the
Company, transfer this Warrant (or any part hereof), any Shares, or any
securities issued or issuable upon conversion of the Shares, to any person who
directly competes with the Company, unless such transfer is in connection with
an Acquisition of the Company by any such person.

          5.5 Notices. All notices and other communications from the Company to
the Holder, or vice versa, shall be deemed delivered and effective when given
personally, or mailed by first-class registered or certified mail, postage
prepaid, or sent via reputable overnight courier service, fee prepaid, at such
address as may have been furnished to the Company or the Holder, as the case may
be, in writing by the Company or such holder from time to time, but in all
cases, unless instructed in writing otherwise, the Company shall deliver a copy
of all notices to Holder to Silicon Valley Bank, Treasury Department, 3003
Tasman Drive, HA 200, Santa Clara, California 95054.

          5.6 Waiver. This Warrant and any term hereof may be changed, waived,
discharged or terminated only by an instrument in writing signed by the party
against which enforcement of such change, waiver, discharge or termination is
sought.

          5.7 Attorneys Fees. In the event of any dispute between the parties
concerning the terms and provisions of this Warrant, the party prevailing in
such dispute shall be entitled to collect from the other party all costs
incurred in such dispute, including reasonable attorneys' fees.

          5.8 Governing Law. This Warrant shall be governed by and construed in
accordance with the laws of The Commonwealth of Massachusetts, without giving
effect to its principles regarding conflicts of law.


                                        8

<Page>

          5.9 No Rights as a Shareholder. Except as specifically provided in
this Warrant, Holder shall have no rights as a shareholder of the Company in
respect of the Shares issuable hereunder unless and until Holder exercises this
Warrant as to all or any of such Shares.

                  [REMAINDER OF PAGE LEFT BLANK INTENTIONALLY]


                                        9

<Page>

     IN WITNESS WHEREOF, the Company has caused this Warrant to Purchase Stock
to be executed as an instrument under seal by its duly authorized representative
as of the date first above written.

ATTEST:                                   "COMPANY"

                                          ACTIVBIOTICS, INC.


By: /s/ [ILLEGIBLE]                       By: /s/ J. L. Warren
    -----------------------------------       ----------------------------------
Name: [ILLEGIBLE]                         Name: J. L. WARREN
Title: WITNESS                            Title: C.E.O

"HOLDER"

SILICON VALLEY BANK


By: /s/ [ILLEGIBLE]
    -----------------------------------
Name: [ILLEGIBLE]
Title: Vice President


                                       10

<Page>

                                   APPENDIX 1

                               NOTICE OF EXERCISE

     1. The undersigned hereby elects to purchase ______ shares of the
__________ stock of ____________________ pursuant to Section 1.1 of the attached
Warrant, and tenders herewith payment of the Exercise Price of such shares in
full

     1. The undersigned hereby elects to convert the attached Warrant into
Shares in the manner specified in Section 1.2 of the attached Warrant. This
conversion is exercised with respect to ___________ of shares of the
________________________ Stock of ________________________

     [Strike paragraph that does not apply.]

     2. Please issue a certificate or certificates representing said shares in
the name of the undersigned or in such other name as is specified below:

                       ------------------------------------
                           (Name)

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

                       ------------------------------------
                           (Address)

     3. The undersigned represents it is acquiring the shares solely for its own
account and not as a nominee for any other party and not with a view toward the
resale or distribution thereof except in compliance with applicable securities
laws


                                          --------------------------------------
                                             (Signature)

-------------------
   (Date)

<Page>

                                   ASSIGNMENT

For value received, Silicon Valley Bank hereby sells, assigns and transfers
unto:

           NAME: SILICON VALLEY BANCSHARES
           ADDRESS: 3003 TASMAN DRIVE (HA-200)
           SANTA CLARA, CA 95054

           Taxid: 91-1962278

that certain Warrant to Purchase Stock issued by ActivBiotics, Inc.
(the "Company"), on November 12, 2003 (the "Warrant") together with all rights,
title and interest therein.

                                        SILICON VALLEY BANK


                                        By: /s/ R. Bryan Jadol
                                            ------------------------------------
                                        Name: R. Bryan Jadol
                                        Title :Vice President

Date November 12, 2003

By its execution below, and for the benefit of the Company, Silicon Valley
Bancshares makes each of the representations and warranties set forth in Article
4 of the Warrant as of the date hereof.

                                        SILICON VALLEY BANCSHARES


                                        By: /s/ Paulette Mehas
                                            ------------------------------------
                                        Name: Paulette Mehas
                                        Title: Treasurer