<PAGE>
                                                                     EXHIBIT 4.6


THIS WARRANT AND THE SHARES OF COMMON STOCK ISSUABLE UPON EXERCISE OF THIS
WARRANT HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED,
AND MAY NOT BE OFFERED, SOLD OR OTHERWISE TRANSFERRED, PLEDGED OR HYPOTHECATED
OR EXERCISED UNLESS AND UNTIL SUCH WARRANT AND/OR SHARES OF COMMON STOCK IS
REGISTERED UNDER SUCH ACT OR AN OPINION OF COUNSEL SATISFACTORY TO THE COMPANY
IS OBTAINED TO THE EFFECT THAT SUCH REGISTRATION IS NOT REQUIRED. THIS WARRANT
AND THE SHARES OF COMMON STOCK ISSUABLE UPON EXERCISE OF THIS WARRANT ARE
SUBJECT TO THE RESTRICTIONS ON TRANSFER SET FORTH IN SECTIONS 4 AND 10 OF THIS
WARRANT.

Warrant No. 1                                         Number of Shares: 100,000
                                                        (subject to adjustment)
Date of Issuance: September 30, 2002


                               Cell Pathways, Inc.

                          Common Stock Purchase Warrant

                             (Void after five years)

Cell Pathways, Inc., a Delaware corporation (the "Company"), for value received,
hereby certifies that Coalianz, LLC, or its registered assigns (the "Registered
Holder"), is entitled, subject to the terms and conditions set forth below, to
purchase from the Company, at any time or from time to time on or before 5:00
p.m. (Eastern time) on September 30, 2007 One Hundred Thousand (100,000) shares
of Common Stock, of the Company at a purchase price of $1.00 (One dollar) per
share. The shares purchasable upon exercise of this Warrant, and the purchase
price per share, each as adjusted from time to time pursuant to the provisions
of this Warrant, are hereinafter referred to as the "Warrant Shares" and the
"Purchase Price," respectively.

1.  EXERCISE.

         (a) This Warrant may be exercised by the Registered Holder, in whole or
in part, by surrendering this Warrant, with the purchase form appended hereto as
Exhibit I duly executed by the Registered Holder or by the Registered 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, in lawful money of the United States, of the Purchase Price payable in
respect of the number of Warrant Shares purchased upon such exercise.

<PAGE>


         (b) The Registered Holder may, at its option, elect to pay some or all
of the Purchase Price payable upon an exercise of this Warrant by canceling all
or a portion of this Warrant. If the Registered Holder wishes to exercise this
Warrant by this method, the number of Warrant Shares purchaseable (which shall
in no event exceed the total number of Warrant Shares purchasable under this
Warrant as set forth above), subject to adjustment under Section 2 of this
Warrant) shall be determined as follows:

              X=Y[(A-B)/A]; where

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

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

A= the Fair Market Value of one share of Common Stock.

B= the Purchase Price of one share of Common Stock.

           The Fair Market Value per share of Common Stock shall be determined
as follows:

                  (i) If the Common Stock is listed on a national securities
         exchange, the Nasdaq National Market or another nationally recognized
         trading system (including, without limitation, the OTC Bulletin Board
         or any successor and, if the average daily trading volume for the
         preceding 10 days has been at least 100,000 shares, the Pink Sheets) as
         of the Exercise Date, the Fair Market Value per share of Common Stock
         shall be deemed to be the average of the high and low reported sale
         prices per share of Common Stock thereon on the trading day immediately
         preceding the Exercise Date (provided that if no such price is reported
         on such day, the Fair Market Value per share of Common Stock shall be
         determined pursuant to clause (ii)).

                  (ii) If the Common Stock is not listed on a national
         securities exchange, the Nasdaq National Market or another nationally
         recognized trading system as of the Exercise Date, the Fair Market
         Value per share of Common Stock shall be deemed to be the amount most
         recently determined by the Board of Directors to represent the fair
         market value per share of the Common Stock (including without
         limitation a determination for purposes of granting Common Stock
         options or issuing Common Stock under an employee benefit plan of the
         Company); and, upon request of the Registered Holder, the Board of
         Directors (or a representative thereof) shall promptly notify the
         Registered Holder of the Fair Market Value per share of Common Stock.
         Notwithstanding the foregoing, if the Board of Directors has not made
         such a determination within the three-month period prior to the
         Exercise Date, then (A) the Board of Directors shall make a
         determination of the Fair Market Value per share of the Common Stock
         within 15 days of a request by the Registered

                                       2

<PAGE>

         Holder that it do so, and (B) the exercise of this Warrant pursuant to
         this subsection 1(b) shall be delayed until such determination is made.

         (c) Each 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 subsection 1(a) above
accompanied by payment in full of the Purchase Price (the "Exercise Date"). At
such time, the person or persons in whose name or names any certificates for
Warrant Shares shall be issuable upon such exercise as provided in subsection
1(d) below shall be deemed to have become the holder or holders of record of the
Warrant Shares represented by such certificates.

         (d) As soon as practicable after the exercise of this Warrant in full
or in part, and in any event within 5 business days thereafter, the Company, at
its expense, will cause to be issued in the name of, and delivered to, the
Registered Holder, or as such Holder (upon payment by such Holder of any
applicable transfer taxes) may direct:

                  (i) a certificate or certificates for the number of full
         Warrant Shares to which the Registered Holder shall be entitled upon
         such exercise plus, in lieu of any fractional share to which the
         Registered Holder would otherwise be entitled, cash in an amount
         determined pursuant to Section 3 hereof; and

                  (ii) in case such 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 remaining
         Warrant Shares.

2.  ADJUSTMENTS.

         (a) Adjustment for Stock Splits and Combinations. If the Company shall
at any time or from time to time after the date on which this Warrant was first
issued (the "Original Issue Date") effect a subdivision of the outstanding
Common Stock, the Purchase Price then in effect immediately before that
subdivision shall be proportionately decreased. If the Company shall at any time
or from time to time after the Original Issue Date combine the outstanding
shares of Common Stock, the Purchase Price then in effect immediately before the
combination shall be proportionately increased. Any adjustment under this
paragraph shall become effective at the close of business on the date the
subdivision or combination becomes effective.

         (b) Adjustment for Certain Dividends and Distributions. In the event
the Company at any time, or from time to time after the Original Issue Date
shall make or issue, or fix a record date for the determination of holders of
Common Stock entitled to receive, a dividend or other distribution payable in
additional shares of Common Stock, then and in each such event the Purchase
Price then in effect immediately before such event shall be decreased as of the
time of such issuance or, in the event such a record date shall have been fixed,
as of the


                                       3
<PAGE>


close of business on such record date, by multiplying the Purchase Price then in
effect by a fraction:

         (1)  the numerator of which shall be the total number of shares of
              Common Stock issued and outstanding immediately prior to the time
              of such issuance or the close of business on such record date, and

         (2)  the denominator of which shall be the total number of shares of
              Common Stock issued and outstanding immediately prior to the time
              of such issuance or the close of business on such record date plus
              the number of shares of Common Stock issuable in payment of such
              dividend or distribution;

provided, however, if such record date shall have been fixed and such dividend
is not fully paid or if such distribution is not fully made on the date fixed
therefor, the Purchase Price shall be recomputed accordingly as of the close of
business on such record date and thereafter the Purchase Price shall be adjusted
pursuant to this paragraph as of the time of actual payment of such dividends or
distributions.

         (c) Adjustment in Number of Warrant Shares. When any adjustment is
required to be made in the Purchase Price pursuant to subsections 2(a) or 2(b),
the number of Warrant Shares purchasable upon the exercise of this Warrant shall
be changed to the number determined by dividing (i) an amount equal to the
number of shares issuable upon the exercise of this Warrant immediately prior to
such adjustment, multiplied by the Purchase Price in effect immediately prior to
such adjustment, by (ii) the Purchase Price in effect immediately after such
adjustment.

         (d) Adjustments for Other Dividends and Distributions. In the event the
Company at any time or from time to time after the Original Issue Date shall
make or issue, or fix a record date for the determination of holders of Common
Stock entitled to receive, a dividend or other distribution payable in
securities of the Company (other than shares of Common Stock) or in cash or
other property (other than cash out of earnings or earned surplus, determined in
accordance with generally accepted accounting principles), then and in each such
event provision shall be made so that the Registered Holder shall receive upon
exercise hereof, in addition to the number of shares of Common Stock issuable
hereunder, the kind and amount of securities of the Company and/or cash and
other property which the Registered Holder would have been entitled to receive
had this Warrant been exercised into Common Stock on the date of such event and
had the Registered Holder thereafter, during the period from the date of such
event to and including the Exercise Date, retained any such securities
receivable, giving application to all adjustments called for during such period
under this Section 2 with respect to the rights of the Registered Holder.

         (e) Adjustment for Mergers or Reorganizations, etc. If there shall
occur any reorganization, recapitalization, consolidation or merger involving
the Company in which the Common Stock is converted into or exchanged for
securities, cash or other property (other than a transaction covered by

                                       4
<PAGE>


subsections 2(a), 2(b) or 2(d)), then, following any such reorganization,
recapitalization, consolidation or merger, the Registered Holder shall receive
upon exercise hereof the kind and amount of securities, cash or other property
which the Registered Holder would have been entitled to receive if, immediately
prior to such reorganization, recapitalization, consolidation or merger, the
Registered Holder had held the number of shares of Common Stock subject to this
Warrant. Notwithstanding the foregoing sentence, if (x) there shall occur any
reorganization, recapitalization, consolidation or merger involving the Company
in which the Common Stock is converted into or exchanged for anything other than
solely equity securities, and (y) the common stock of the acquiring or surviving
company is publicly traded, then, as part of any such reorganization,
recapitalization, consolidation or merger, (i) the Registered Holder shall have
the right thereafter to receive upon the exercise hereof such number of shares
of common stock of the acquiring or surviving company as is determined by
multiplying (A) the number of shares of Common Stock then subject to this
Warrant by (B) a fraction, the numerator of which is the Fair Market Value per
share of Common Stock as of the effective date of such transaction, as
determined pursuant to subsection 1(b), and the denominator of which is the fair
market value per share of common stock of the acquiring or surviving company as
of the effective date of such transaction, as determined in good faith by the
Board of Directors of the Company (using the principles set forth in subsection
1(b) to the extent applicable), and (ii) the exercise price per share of common
stock of the acquiring or surviving company shall be the Purchase Price divided
by the fraction referred to in clause (B) above. In any such case, appropriate
adjustment (as determined in good faith by the Board of Directors of the
Company) shall be made in the application of the provisions set forth herein
with respect to the rights and interests thereafter of the Registered Holder, to
the end that the provisions set forth in this Section 2 (including provisions
with respect to changes in and other adjustments of the Purchase Price) shall
thereafter be applicable, as nearly as reasonably may be, in relation to any
securities, cash or other property thereafter deliverable upon the exercise of
this Warrant.

         (e) Certificate as to Adjustments. Upon the occurrence of each
adjustment or readjustment of the Purchase Price pursuant to this Section 2, the
Company at its expense shall promptly compute such adjustment or readjustment in
accordance with the terms hereof and furnish to the Registered Holder a
certificate setting forth such adjustment or readjustment (including the kind
and amount of securities, cash or other property for which this Warrant shall be
exercisable and the Purchase Price) and showing in detail the facts upon which
such adjustment or readjustment is based. The Company shall, upon the written
request at any time of the Registered Holder, furnish or cause to be furnished
to the Registered Holder a certificate setting forth (i) the Purchase Price then
in effect and (ii) the number of shares of Common Stock and the amount, if any,
of other securities, cash or property which then would be received upon the
exercise of this Warrant.

3. FRACTIONAL SHARES. The Company shall not be required upon the exercise of
this Warrant to issue any fractional shares, but shall make an adjustment
therefor

                                       5
<PAGE>

in cash on the basis of the Fair Market Value per share of Common Stock, as
determined pursuant to subsection 1(b) above.

4.  REQUIREMENTS FOR TRANSFER.

         (a) This Warrant and the Warrant Shares shall not be sold or
transferred unless either (i) they first shall have been registered under the
Securities Act of 1933, as amended (the "Act"), or (ii) the Company first shall
have been furnished with an opinion of legal counsel, reasonably satisfactory to
the Company, to the effect that such sale or transfer is exempt from the
registration requirements of the Act.

         (b) Notwithstanding the foregoing, no registration or opinion of
counsel shall be required for a transfer by a Registered Holder which is a
corporation to a wholly owned subsidiary of such corporation, a transfer by a
Registered Holder which is a partnership, in connection with the liquidation of
such partnership, to a partner of such partnership or a retired partner of such
partnership or to the estate of any such partner or retired partner, a transfer
by a Registered Holder which is a limited liability company, in connection with
the liquidation of such limited liability company, to a member of such limited
liability company or a retired member or to the estate of any such member or
retired member, or a transfer by a Registered Holder which is a member of the
National Association of Securities Dealers (the "NASD") to an officer or
employee of the Registered Holder as permitted by NASD rules, provided that the
transferee in each case agrees in writing to be subject to the terms of this
Section 4.

         (c) Each certificate representing Warrant Shares shall bear a legend
substantially in the following form:

         "The securities represented by this certificate have not been
         registered under the Securities Act of 1933, as amended, and may not be
         offered, sold or otherwise transferred, pledged or hypothecated unless
         and until such securities are registered under such Act or an opinion
         of counsel satisfactory to the Company is obtained to the effect that
         such registration is not required."

The foregoing legend shall be removed from the certificates representing any
Warrant Shares, at the request of the holder thereof, at such time as they
become eligible for resale pursuant to Rule 144(k).

5. NO IMPAIRMENT. The Company will not, by amendment of its charter or through
any 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 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 holder of this Warrant against impairment.

6.  NOTICES OF RECORD DATE, ETC.  In the event:


                                       6
<PAGE>

         (a) the Company shall take a record of the holders of its Common Stock
(or other stock or securities at the time deliverable upon the exercise of this
Warrant) for the purpose of entitling or enabling them to receive any dividend
or other distribution, or to receive any right to subscribe for or purchase any
shares of stock of any class or any other securities, or to receive any other
right; or of any capital reorganization of the Company, any reclassification of
the Common Stock of the Company, any consolidation or merger of the Company with
or into another corporation (other than a consolidation or merger in which the
Company is the surviving entity and its Common Stock is not converted into or
exchanged for any other securities or property), or any transfer of all or
substantially all of the assets of the Company; or

         (b) of the voluntary or involuntary dissolution, liquidation or
winding-up of the Company,

then, and in each such case, the Company will mail or cause to be mailed to the
Registered Holder a notice specifying, as the case may be, (i) the record date
for such dividend, distribution or right, and the amount and character of such
dividend, distribution or right, or (ii) the effective date on which such
reorganization, reclassification, consolidation, merger, transfer, dissolution,
liquidation or winding-up is to take place, and the time, if any is to be fixed,
as of which the holders of record of Common Stock (or such other stock or
securities at the time deliverable upon the exercise of this Warrant) shall be
entitled to exchange their shares of Common Stock (or such other stock or
securities) for securities or other property deliverable upon such
reorganization, reclassification, consolidation, merger, transfer, dissolution,
liquidation or winding-up. Such notice shall be mailed at least ten days prior
to the record date or effective date for the event specified in such notice.

7. RESERVATION OF STOCK. The Company will at all times reserve and keep
available, solely for issuance and delivery upon the exercise of this Warrant,
such number of Warrant Shares and other securities, cash and/or property, as
from time to time shall be issuable upon the exercise of this Warrant.

8. EXCHANGE OF WARRANTS. Upon the surrender by the Registered Holder, properly
endorsed, to the Company at the principal office of the Company, the Company
will, subject to the provisions of Section 4 hereof, issue and deliver to or
upon the order of such Holder, at the Company's expense, a new Warrant or
Warrants of like tenor, in the name of the Registered Holder or as the
Registered Holder (upon payment by the Registered Holder of any applicable
transfer taxes) may direct, calling in the aggregate on the face or faces
thereof for the number of shares of Common Stock (or other securities, cash
and/or property) then issuable upon exercise of this Warrant.

9. REPLACEMENT OF WARRANTS. Upon 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) upon delivery of an indemnity
agreement (with surety if reasonably required) in an amount reasonably
satisfactory to the

                                       7
<PAGE>

Company, or (in the case of mutilation) upon surrender and cancellation of this
Warrant, the Company will issue, in lieu thereof, a new Warrant of like tenor.


10.  TRANSFERS, ETC.

         (a) The Company will maintain a register containing the name and
address of the Registered Holder of this Warrant. The Registered Holder may
change its or his address as shown on the warrant register by written notice to
the Company requesting such change.

         (b) Subject to the provisions of Section 4 hereof, this Warrant and all
rights hereunder are transferable, in whole or in part, upon surrender of this
Warrant with a properly executed assignment (in the form of Exhibit II hereto)
at the principal office of the Company.

         (c) Until any transfer of this Warrant is made in the warrant register,
the Company may treat the Registered Holder as the absolute owner hereof for all
purposes; provided, however, that if and when this Warrant is properly assigned
in blank, the Company may (but shall not be obligated to) treat the bearer
hereof as the absolute owner hereof for all purposes, notwithstanding any notice
to the contrary.

11.  REPRESENTATIONS OF THE REGISTERED HOLDER.  The Registered Holder of this
Warrant represents and warrants to the Company as follows:

         (a) Investment. The Registered Holder is acquiring this Warrant and the
Warrant Shares issuable upon the exercise of this Warrant, for its own account
for investment and not with a view to, or for sale in connection with, any
distribution thereof, nor with any present intention of distributing or selling
the same, except as otherwise may be permitted under applicable securities laws.

         (b) Authority. The Registered Holder has full power and authority to
enter into and to perform this Warrant in accordance with its terms. The
Registered Holder has not been organized specifically for the purpose of
investing in the Company.

         (c) Accredited Investor.  The Registered Holder is an Accredited
Investor within the definition set forth in Rule 501(a) promulgated under the
Securities Act.

12. MAILING OF NOTICES, ETC. All notices and other communications from the
Company to the Registered Holder shall be mailed by first-class certified or
registered mail, postage prepaid, to the address last furnished to the Company
in writing by the Registered Holder. All notices and other communications from
the Registered Holder or in connection herewith to the Company shall be mailed
by first-class certified or registered mail, postage prepaid, to the Company at
its principal office set forth below. If the Company should at any time change
the location of its principal office to a place other than as set forth below,
it shall give prompt written notice to the Registered Holder and thereafter all
references in

                                       8
<PAGE>

this Warrant to the location of its principal office at the particular time
shall be as so specified in such notice.

13. NO RIGHTS AS STOCKHOLDER. Until the exercise of this Warrant, the Registered
Holder shall not have or exercise any rights by virtue hereof as a stockholder
of the Company. Notwithstanding the foregoing, in the event (i) the Company
effects a split of the Common Stock by means of a stock dividend and the
Purchase Price of and the number of Warrant Shares are adjusted as of the date
of the distribution of the dividend (rather than as of the record date for such
dividend), and (ii) the Registered Holder exercises this Warrant between the
record date and the distribution date for such stock dividend, the Registered
Holder shall be entitled to receive, on the distribution date, the stock
dividend with respect to the shares of Common Stock acquired upon such exercise,
notwithstanding the fact that such shares were not outstanding as of the close
of business on the record date for such stock dividend.

14. CHANGE OR WAIVER. Any term of this Warrant may be changed or waived only by
an instrument in writing signed by the party against which enforcement of the
change or waiver is sought.

15. SECTION HEADINGS. The section headings in this Warrant are for the
convenience of the parties and in no way alter, modify, amend, limit or restrict
the contractual obligations of the parties.

16. GOVERNING LAW. This Warrant will be governed by and construed in accordance
with the internal laws of the State of New York (without reference to the
conflicts of law provisions thereof).

         EXECUTED as of the Date of Issuance indicated above.

                                          Cell Pathways, Inc.

                                          By: /s/ Robert J. Towarnicki
                                             ---------------------------
                                          Title: Chief Executive Officer
                                                ------------------------
ATTEST:

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

                                       9

<PAGE>


EXHIBIT I

PURCHASE FORM

To:_________________                                        Dated:____________


The undersigned, pursuant to the provisions set forth in the attached Warrant
(No. ___), hereby irrevocably elects to purchase (check applicable box):

         o   _____ shares of the Common Stock covered by such Warrant; or

         o   the maximum number of shares of Common Stock covered by such
             Warrant pursuant to the cashless exercise procedure set forth
             in Section 1(b).

The undersigned herewith makes payment of the full purchase price for such
shares at the price per share provided for in such Warrant, which is $________.
Such payment takes the form of (check applicable box or boxes):

         o   $______ in lawful money of the United States; and/or

         o   the cancellation of such portion of the attached Warrant as is
             exercisable for a total of _____ Warrant Shares (using a Fair
             Market Value of $_____ per share for purposes of this
             calculation); and/or

         o   the cancellation of such number of Warrant Shares as is
             necessary, in accordance with the formula set forth in Section
             1(b), to exercise this Warrant with respect to the maximum
             number of Warrant Shares purchasable pursuant to the cashless
             exercise procedure set forth in Section 1(b).

                                         Signature:
                                                   ---------------------------

                                         Address:
                                                   ---------------------------

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

                                       10

<PAGE>


EXHIBIT II

ASSIGNMENT FORM

FOR VALUE RECEIVED, ________________________________________ hereby sells,
assigns and transfers all of the rights of the undersigned under the attached
Warrant (No. ____) with respect to the number of shares of Common Stock covered
thereby set forth below, unto:
<TABLE>
<CAPTION>
Name of Assignee                         Address                                No. of Shares
----------------                         -------                                -------------
<S>                                     <C>                                    <C>




</TABLE>

Dated:_____________________

Signature:________________________________

Signature Guaranteed:

By: _______________________


The signature should be guaranteed by an eligible guarantor institution (banks,
stockbrokers, savings and loan associations and credit unions with membership in
an approved signature guarantee medallion program) pursuant to Rule 17Ad-15
under the Securities Exchange Act of 1934.


                                       11