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                                                                     Exhibit 4.6

THIS WARRANT AND THE SHARES OF CAPITAL STOCK ISSUED UPON ANY EXERCISE HEREOF
HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE
"SECURITIES ACT"), OR ANY APPLICABLE STATE SECURITIES LAWS AND MAY NOT BE SOLD
OR OTHERWISE TRANSFERRED BY ANY PERSON, INCLUDING A PLEDGEE, UNLESS (1) EITHER
(A) A REGISTRATION WITH RESPECT TO THERETO SHALL BE EFFECTIVE UNDER THE
SECURITIES ACT, OR (B) THE COMPANY SHALL HAVE RECEIVED AN OPINION OF COUNSEL
SATISFACTORY TO THE COMPANY THAT AN EXEMPTION FROM REGISTRATION UNDER THE
SECURITIES ACT IS AVAILABLE, AND (2) THERE SHALL HAVE BEEN COMPLIANCE WITH ALL
APPLICABLE STATE SECURITIES OR "BLUE SKY" LAWS.

                                     For the purchase of up to 107,096 shares of
                                 shares of Series D Convertible Preferred Stock,
                                                       par value $.001 per share

No. W-03                                                         August 28, 2001

      PTC THERAPEUTICS, INC., a Delaware corporation (the "Company"), hereby
certifies that, for good and valuable consideration, Three Crowns Capital
(Bermuda) Ltd. or its permitted assigns (the "Warrant Holder") is entitled,
subject to the terms set forth below, to purchase from the Company at any time
on or before 5:00 p.m., eastern time, on August 28, 2011 (the "Exercise
Period"), up to 107,096 fully-paid and non-assessable shares of Series D
Convertible Preferred Stock, par value $.001 per share, of the Company (the
"Series D Preferred Stock"), or shares of the Common Stock, par value $.001 per
share, of the Company (the "Common Stock") upon a mandatory conversion of the
Series D Preferred Stock as provided in Section 3 hereof (the Series D Preferred
Stock and the Common Stock are hereinafter collectively referred to as
"Shares"), at a price per share (the "Exercise Price") which shall initially be
$3.25 per share and which shall be subject to adjustment as herein provided.

      1.    Exercise of Warrants.

      1.1. Exercise. Subject to the terms and conditions of this Warrant, this
Warrant shall become exercisable by the Warrant Holder on August 28, 2001.

      1.2. Procedure to Exercise. This Warrant may be exercised by the Warrant
Holder, in whole or in part, by surrendering this Warrant, with the purchase
form appended hereto as Exhibit A duly executed by such Warrant Holder or by
such Warrant Holder's duly authorized attorney, at the principal office of the
Company, or at such other office or agency as the Company may designate,
accompanied by payment in full by cash, check or wire transfer of the amount
obtained by multiplying the number of Shares in the notice of exercise by the
Exercise Price (the "Purchase Price").

      1.3. Net Issue Exercise. In lieu of exercising this Warrant in the manner
provided above in Section 1.2, the Warrant Holder may elect to receive shares
equal to the value of this Warrant (or the portion thereof being converted) by
surrender of this Warrant, in whole or in part, at the principal office of the
Company together with the notice of exercise attached hereto

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as Exhibit A, in which event the Company shall issue to the Warrant Holder the
number of Shares computed using the following formula (a "Net Issue Exercise"):

                                  X = Y (A - B)
                                      ---------
                                          A

Where:      X =         The number of Shares to be issued to the Warrant Holder.

            Y =         The number of Shares purchasable under this Warrant (at
                        the date of such calculation) that are being converted,
                        in whole or in part, hereunder.

            A =         The Fair Market Value of one Share (at the date of such
                        calculation).

            B =         The Exercise Price (as adjusted to the date of such
                        calculation).

      For purposes of this Section 1.3, if any Shares of the Warrant Holder or
any other shareholder of the Company are registered or publicly traded, then the
Fair Market Value of one Share shall mean the average of the closing bid and
asked prices of the Common Stock quoted in the over the counter market summary
or the closing price quoted by the Nasdaq National Market or any exchange on
which the Common Stock is listed, whichever is applicable, as published in the
Western Edition of The Wall Street Journal for the business day prior to the
date of determination of fair market value. If the Shares are not traded on the
Nasdaq National Market or on an exchange, the Fair Market Value of one Share
shall be determined in good faith by the Company's Board of Directors.

      1.4. Effectiveness. Each exercise or Net Issue Exercise of this Warrant
shall be deemed to have been effected immediately prior to the close of business
on the day on which this Warrant shall have been surrendered to the Company as
provided in Sections 1.2 or 1.3 above. At such time, the person or persons in
whose name or names any certificates for the Shares shall be issuable upon such
exercise or Net Issue Exercise as provided in Section 2 below shall be deemed to
have become the holder or holders of record of the Shares represented by such
certificates.

      2. Delivery of Stock Certificates, Etc. As soon as practicable after the
exercise or Net Issue Exercise of this Warrant in full or in part, and in any
event within 10 days thereafter, the Company at its expense will cause to be
issued in the name of, and delivered to, the Warrant Holder, or as such Warrant
Holder (upon payment by such Warrant Holder of any applicable transfer taxes)
may direct (i) a certificate or certificates for the number of fully paid and
non-assessable Shares to which the Warrant Holder shall be entitled upon such
exercise or Net Issue Exercise, and (ii) in case such exercise or Net Issue
Exercise is in part only, a new warrant or warrants (dated the date hereof) of
like tenor, calling in the aggregate on the face or faces thereof for the number
of Shares equal (without giving effect to any adjustment therein) to the number
of Shares called for on the face of this Warrant minus the number of Shares
purchased by the Warrant Holder upon such exercise or Net Issuance Exercise as
provided in Sections 1.2 or 1.3 herein.

      3. Adjustments Upon Mandatory Conversion of Series D Preferred Stock. Upon
any mandatory conversion of the Series D Preferred Stock pursuant to the
Company's Certificate of

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<PAGE>

Incorporation, as amended or amended and restated from time to time, this
Warrant shall cease to be exercisable for shares of Series D Preferred Stock and
shall become exercisable for that number of shares of Common Stock into which
the shares of Series D Preferred Stock purchasable hereunder would have been
convertible immediately prior to such mandatory conversion, and such that
payment of the Exercise Price, or any multiple thereof, shall entitle the
Warrant Holder to receive the number of shares of Common Stock as would have
been issued upon conversion of each share of Series D Preferred Stock
purchasable hereunder immediately prior to such mandatory conversion.

      4. Stock Splits, Stock Dividends and Combinations. If the Company at any
time subdivides the outstanding shares of Series D Preferred Stock, or issues a
stock dividend on the outstanding shares of Series D Preferred Stock, the
Exercise Price in effect immediately prior to such subdivision or the issuance
of such stock dividend shall be proportionately decreased, and the number of
Shares shall be proportionately increased, and if the Company at any time
combines the outstanding shares of Series D Preferred Stock, the Exercise Price
in effect immediately prior to such combination shall be proportionately
increased, and the number of shares shall be proportionately decreased,
effective at the close of business on the date of such subdivision, stock
dividend or combination, as the case may be. Upon any mandatory conversion of
the Series D Preferred Stock as provided in Section 3, each reference to Series
D Preferred Stock in this Section 4 shall be deemed to be Common Stock.

      5. Conversions; Reorganizations; Reclassification; Merger; Sales. In case
of any capital reorganization or any reclassification of the capital stock of
the Company or in case of the consolidation or merger of the Company with or
into another corporation or the conveyance of all or substantially all of the
assets of the Company to another corporation, this Warrant shall thereafter be
exercisable for the number of shares of stock or other securities or property to
which a holder of the number of Shares deliverable upon exercise of the Warrant
would have been entitled to upon such conversion, reorganization,
reclassification, consolidation, merger or conveyance and, in any such case,
appropriate adjustment as determined by the Board of Directors of the Company
shall be made in the application of the provisions herein set forth with respect
to the rights and interests thereafter of the Warrant Holder to the end that the
provisions set forth herein (including provisions with respect to changes in and
other adjustments of the Exercise Price and the number of Shares) shall
thereafter be applicable, as nearly as reasonably may be, in relation to any
shares of stock or other property thereafter deliverable upon the exercise of
the Warrant.

      6. Statement of Adjustment. Whenever the Exercise Price shall be adjusted
as provided herein, the Company shall promptly file with the Secretary of the
Company or at such other place as shall be designated by the Company, a
statement, signed by its chief financial officer, showing in detail the facts
requiring such adjustment, the Exercise Price in effect before and after such
adjustment and the kind and amount of shares of capital stock, securities or
other property thereafter to be received upon the exercise of this Warrant. The
Company shall also cause a copy of such statement to be sent in the manner
specified in Section 16.3 to the Warrant Holder.

      7. Notice of Adjustment. In the event the Company shall propose to take
any action of the types described in Sections 4 or 5, the Company shall give
notice to the Warrant Holder in

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the manner set forth in Section 16.3, which notice shall specify the record
date, if any, with respect to any such action and the date on which such action
is to take place. Such notice shall also set forth such facts with respect
thereto as shall be reasonably necessary to indicate the effect of such action
(to the extent such effect may be known at the date of such notice) on the
Exercise Price and the number, kind or class of shares or other securities or
property which shall be deliverable or purchasable upon the occurrence of such
action or deliverable upon the exercise hereof. In the case of any action which
would require the fixing of a record date, such notice shall be given at least
ten (10) days prior to the date so fixed, and in case of all other actions, such
notice shall be given at least twenty (20) days prior to the taking of such
proposed action. Failure to give such notice, or any defect therein, shall not
affect the legality or validity of any such action.

      8. Taxes. The Company shall pay all documentary, stamp or other
transactional taxes attributable to the issuance or delivery of shares of
capital stock of the Company upon the exercise or conversion hereof.

      9. No Fractional Shares. Each adjustment in the number of Shares
purchasable hereunder shall be calculated, to the nearest whole share with
fractional shares disregarded.

      10. Covenants as to Series D Preferred Stock and Common Stock. The Company
covenants and agrees that the shares of Series D Preferred Stock issuable
hereunder, and the Common Stock issuable upon conversion thereof, and the Common
Stock issuable hereunder, as the case may be, will, upon issuance in accordance
with the terms hereof, be validly issued and outstanding, fully paid and
nonassessable, with no personal liability attaching to the ownership thereof,
and free from all taxes, liens and charges with respect to the issuance thereof
imposed by or through the Company. The Company further covenants and agrees that
the Company will at all times have authorized and reserved, free from preemptive
rights imposed by or through the Company, a sufficient number of shares of
Series D Preferred Stock and Common Stock to provide for the exercise of the
rights represented by this Warrant. The Company further covenants and agrees
that if any shares of capital stock to be reserved for the purpose of the
issuance of shares upon the exercise of this Warrant require registration or
qualification with or approval by the Securities and Exchange Commission or any
state regulatory agency under Federal or state law before such shares may be
validly issued or delivered upon exercise, then the Company will in good faith
and as expeditiously as possible endeavor to secure such registration,
qualification or approval, as the case may be. Holders of Series D Preferred
Stock and Common Stock issuable upon exercise of this Warrant or conversion of
any such shares, as the case may be, shall be entitled to all the rights and
privileges of the Purchase Agreement and the Registration Rights Agreement dated
as of the date hereof between the Company and the Investors (as defined therein)
with respect to such shares.

      11. No Impairment. The Company will not, by amendment of its Certificate
of Incorporation or through any reorganization, transfer of assets,
consolidation, merger, dissolution, or any other similar voluntary action, avoid
or seek to avoid the observance or performance of any of the terms of this
Warrant, but will at all times in good faith assist in the carrying out of all
such terms and in the taking of all such action as may be necessary or
appropriate in order to protect the rights of the Warrant Holder against
impairment due to such event. Without limiting the generality of the foregoing,
the Company (a) will not increase the

                                       4
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par value of any shares of stock receivable on the exercise of the Warrant above
the amount payable therefor on such exercise, (b) will take all action that may
be necessary or appropriate in order that the Company may validly and legally
issue fully paid and nonassessable shares of stock, free from all taxes, liens
and charges with respect to the issue thereof, on the exercise of all of the
Warrants from time to time outstanding and (c) will not consolidate with or
merge into any other person or permit any such person to consolidate with or
merge into the Company (if the Company is not the surviving person), unless such
other person shall expressly assume in writing and will be bound by all the
terms of this Warrant.

      12. Compliance with Securities Act.

      12.1. Unregistered Securities. The Warrant Holder acknowledges that this
Warrant and the Shares have not been registered under the Securities Act of
1933, as amended, and the rules and regulations thereunder, or any successor
legislation (the "Securities Act"), and agrees not to sell, pledge, distribute,
offer for sale, transfer or otherwise dispose of this Warrant or any Shares in
the absence of (i) an effective registration statement under the Securities Act
covering this Warrant or such Shares and registration or qualification of this
Warrant or such Shares under any applicable "blue sky" or state securities law
then in effect, or (ii) an opinion of counsel, satisfactory to the Company, that
such registration and qualification are not required. The Company may delay
issuance of the Shares until completion of any action or obtaining of any
consent, which the Company deems necessary under any applicable law (including
without limitation state securities or "blue sky" laws).

      12.2. Investment Representation. The Warrant Holder represents to the
Company that this Warrant is being acquired for the Warrant Holder's own account
and for the purpose of investment and not with a present view to, or for sale in
connection with, the distribution thereof, nor with any present intention of
distributing or selling the Warrant or Common Stock issuable upon exercise of
the Warrant. The Warrant Holder acknowledges that it has been afforded the
opportunity to meet with the management of the Company and to ask questions of,
and receive answers from, such management and the Company's counsel about the
business and affairs of the Company and concerning the terms and conditions of
the offering of this Warrant, and to obtain any additional information, to the
extent that the Company possessed such information or could acquire it without
unreasonable effort or expense, necessary to verify the accuracy of the
information otherwise obtained by or furnished to the Warrant Holder. The Holder
has received all information which the Warrant Holder considered necessary to
form a decision concerning the purchase of this Warrant, and no valid request to
the Company by the Warrant Holder hereof for information of any kind about the
Company has been refused or denied by the Company or remains unfulfilled as of
the date hereof. The Warrant Holder attests that it may be considered to be a
sophisticated investor, is familiar with the risks inherent in speculative
investments such as in the Company, has such knowledge and experience in
financial business matters that he is capable of evaluating the merits and risk
of the investment in this Warrant and the Shares, and is able to bear the
economic risk of the investment. The Warrant Holder confirms that he is an
"accredited investor" as such term is defined in rule 501(a) of the Securities
Act.

      12.3. Investment Letter. Without limiting the generality of Section 12.1,
unless the offer and sale of any shares of Shares shall have been effectively
registered under the Securities Act, the Company shall be under no obligation to
issue the Shares unless and until the Warrant

                                       5
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Holder shall have executed an investment letter in form and substance
satisfactory to the Company, including a warranty at the time of such exercise
that the Warrant Holder is acquiring such shares for its own account, for
investment and not with a view to, or for sale in connection with, the
distribution of any such shares.

      12.4. Legend. Certificates delivered to the Warrant Holder pursuant to
Section 2 shall bear the following legend or a legend in substantially similar
form:

      "THE SECURITIES REPRESENTED BY THIS CERTIFICATE HAVE NOT BEEN REGISTERED
      UNDER THE SECURITIES ACT OF 1933 OR ANY OF THE SECURITIES LAWS. THESE
      SECURITIES HAVE BEEN ACQUIRED FOR INVESTMENT AND NOT WITH A VIEW TO
      DISTRIBUTION OR RESALE. SUCH SECURITIES MAY NOT BE OFFERED FOR SALE, SOLD,
      DELIVERED AFTER SALE, TRANSFERRED, PLEDGED OR HYPOTHECATED IN THE ABSENCE
      OF AN EFFECTIVE REGISTRATION STATEMENT COVERING SUCH SECURITIES UNDER THE
      SECURITIES ACT OF 1933 AND ANY OTHER APPLICABLE SECURITIES LAWS, UNLESS
      THE HOLDER SHALL HAVE OBTAINED AN OPINION OF COUNSEL REASONABLY
      SATISFACTORY TO THE CORPORATION THAT SUCH REGISTRATION IS NOT REQUIRED."

      13. Transferability. Without the prior written consent of the Company, the
Warrant shall not be assigned, pledged or hypothecated in any way (whether by
operation of law or otherwise) and shall not be subject to execution, attachment
or similar process. Any attempted transfer, assignment, pledge, hypothecation or
other disposition of the Warrant or of any rights granted hereunder contrary to
the provisions of this Section 13, or the levy of any attachment or similar
process upon the Warrant or such rights, shall be null and void.

      14. Lost, Stolen, Mutilated or Destroyed Warrant. If this Warrant is lost,
stolen, mutilated or destroyed, the Company may, on such terms as to indemnity
or otherwise as it may reasonably in its discretion impose (which shall in the
case of a mutilated Warrant, include the surrender thereof), issue a new Warrant
of like denomination and tenor as the Warrant so lost, stolen, mutilated or
destroyed.

      15. Register of Warrants. The Company shall maintain, at the principal
office of the Company (or such other office as it may designate by notice to the
Warrant Holder), a register for the Warrants in which the Company shall record
the name and address of the person in whose name a Warrant has been issued, as
well as the name and address of each transferee and each prior owner of such
Warrant.

      16. Miscellaneous.

      16.1. Waivers and Amendments. This Warrant or any provisions hereof may be
changed, waived, discharged or terminated only by a statement in writing signed
by the Company and by Warrant Holders who hold or have the right to acquire at
least two-thirds of the Shares at such time issued or issuable upon exercise of
the Warrants, provided that no change, addition, omission or waiver shall be
made without the written consent of the Warrant Holder(s)

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which affects (i) the number of Shares issuable on exercise of this Warrant,
(ii) the Exercise Price or (iii) any other provision other than in a manner in
which all the Warrants are affected.

      16.2. Governing Law. This Agreement shall be governed by and construed and
enforced in accordance with the laws of the State of Delaware without giving
effect to the conflicts of laws principles thereof.

      16.3. Notices. All notices or other communications required or permitted
hereunder shall be in writing and shall be hand delivered, sent by facsimile or
other electronic medium, or mailed, postage prepaid, or sent by reputable
overnight courier, delivery charges prepaid, addressed as follows or to such
other address as may be furnished in writing to the other parties hereto:

If to the Warrant Holder:           Three Crowns Capital (Bermuda) Ltd.
                                    Clarendon House
                                    PO Box HM 666
                                    2 Church Street
                                    Hamilton HM KX
                                    Bermuda
                                    441-292-4720 (Fax)
                                    Attention:  Peter Svennilson

With a copy to:                     Conyers Dill & Pearman
                                    Clarendon House
                                    2 Church Street
                                    Hamilton HM 11
                                    Bermuda
                                    441-292-4720 (Fax)
                                    Attention:  Peter A.S. Pearman

And:                                Nixon Peabody LLP
                                    101 Federal Street
                                    Boston, MA 02110
                                    617-345-1300
                                    Attention:  Carter S. Boom, Jr.

If to the Company:                  PTC Therapeutics, Inc.
                                    Two Chestnut Street
                                    Grafton, MA 01519
                                    508-856-5920 (Fax)
                                    Attention:  President

                                       7
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With a copy to:                     Mintz, Levin, Cohn, Ferris, Glovsky and
                                    Popeo, P.C.
                                    One Financial Center
                                    Boston, MA 02111
                                    617-542-6000
                                    617-542-2241 (Fax)
                                    Attention:  Jeffrey M. Wiesen, Esq.

      All such notices and communications shall be deemed to have been duly
given (i) five (5) business days after being deposited in the mail, postage
prepaid if mailed, (ii) one (1) business day after being sent by overnight
courier, (iii) when receipt acknowledged if telecopied and (iv) upon receipt if
delivered by hand.

      16.4. Headings. The headings in this Warrant are for convenience of
reference only and shall not limit or otherwise affect the terms hereof.

      16.5. Remedies. The Company stipulates that the remedies at law of the
holder of this Warrant in the event of any default or threatened default by the
Company in the performance of or compliance with any of the terms of this
Warrant are not and will not be adequate, and that such terms may be
specifically enforced by a decree for the specific performance of any agreement
contained herein or by an injunction against a violation of any of the terms
hereof or otherwise.

      16.6. Closing of Books. The Company will at no time close its transfer
books against the transfer of any Warrant or of any Shares issued or issuable
upon the exercise of the Warrant in a manner which interferes with the timely
exercise of this Warrant.

      16.7. No Rights or Liabilities as a Stockholder. This Warrant shall not
entitle the Warrant Holder to any voting rights or other rights as a stockholder
of the Company prior to the exercise or conversion of the Warrant, provided that
nothing herein shall be construed to limit or impair other rights that the
Warrant Holder may have under this Warrant or otherwise. No provision of this
Warrant, in the absence of affirmative action by the Warrant Holder to purchase
the Shares, and no mere enumeration herein of the rights or privileges of the
Warrant Holder, shall give rise to any liability of such Warrant Holder for the
Exercise Price or as a stockholder of the Company, whether such liability is
asserted by the Company or by creditors of the Company.

                                       8
<PAGE>

      IN WITNESS WHEREOF, the undersigned has caused this Warrant to be executed
as an instrument under seal.

                                   PTC THERAPEUTICS, INC.

                                   By: /s/ Stuart Peltz
                                       ________________________________
                                   Name:    Stuart W. Peltz, Ph.D.
                                   Title:   President

AGREED AND ACKNOWLEDGED:

THREE CROWNS CAPITAL (BERMUDA) LTD.


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<PAGE>

                                    EXHIBIT A

                    NOTICE OF EXERCISE OR NET ISSUE EXERCISE

                                                Date:
                                                      __________________________

PTC Therapeutics, Inc.
100 Corporate Court
Middlesex Business Center
South Plainfield, NJ 07080
Attention:  President

Gentlemen:

      The undersigned hereby elects to exercise or Net Issue Exercise the
enclosed Warrant issued to it by PTC Therapeutics, Inc. (the "Company") and
dated as of _______, 20__.

      The undersigned elects to:

      [ ]   Exercise the Warrant and to purchase thereunder ______ shares of the
            Series D Preferred Stock of the Company (the "Shares") at an
            exercise price of ______ per Share for an aggregate purchase price
            of Dollars ($_______) (the "Purchase Price"). Pursuant to the terms
            of the Warrant, the undersigned has delivered the Purchase Price
            herewith in full.

      [ ]   Net Issue Exercise ____% of the value of the Warrant at the current
            Exercise Price (as defined in the Warrant) of $_______ per Share.

                                                Very truly yours,

                                                ________________________________

Receipt Acknowledged:

PTC Therapeutics, Inc.

By
   ________________________________
on
   ________________________________

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