Document:

exv4w3

 

Exhibit 4.3

Form of Subscription Agreement

SUBSCRIPTION AGREEMENT

                          , 2007

Gentlemen:

     The undersigned (the “Investor”) hereby confirms its agreement with you as follows:

     1. This Subscription Agreement (this “Agreement”) is made as of the date set forth below
between Polymedix, Inc., a Delaware corporation (the “Company”), and the Investor.

     2. The Company has authorized the sale and issuance to certain investors of up to an
aggregate of                      units (the “Units”), each consisting of (i)            shares (each a “Share” and
collectively, the “Shares”) of its common stock, par value $0.001 per share (the “Common Stock”), and (ii) warrants (“Warrant,”
collectively, the “Warrants”) to purchase      shares of Common Stock
(and the fractional amount being the “Warrant Ratio”), subject to adjustment by the Company’s Board
of Directors, or a committee thereof, for a purchase price of $           per Unit (the “Purchase
Price”). The Shares issuable upon exercise of the Warrants are referred to herein as “Warrant
Shares” and, together with the Units, the Shares and the Warrants, are collectively referred to
herein as the “Securities.”

     3. The offering and sale of the Units (the “Offering”) is being made pursuant to (1) an
effective Registration Statement on Form SB-2 (Registration No. 333-142787) (filed by the Company
with the Securities and Exchange Commission (the
“Commission”)) (the “Registration
Statement”), (2) if applicable, certain “free
writing prospectuses” (as that term is defined in Rule 405 under the
Securities Act of 1933, as amended), that have or will be filed with the Commission and delivered
to the Investor on or prior to the date hereof, (3) a preliminary prospectus dated May 30, 2007
(the “Preliminary Prospectus”), and (4) a final prospectus (together with the Preliminary
Prospectus, the “Prospectus”) containing certain supplemental information regarding the Units and
terms of the Offering that will be filed with the Commission and delivered to the Investor (or made
available to the Investor by the filing by the Company of an electronic version thereof with the
Commission) along with the Company’s counterpart to this Agreement.

     4. The Company and the Investor agree that the Investor will purchase from the Company and the
Company will issue and sell to the Investor the Units set forth below for the aggregate purchase
price set forth below. The Units shall be purchased pursuant to the Terms and Conditions for
Purchase of Units attached hereto as Annex I and incorporated herein by this reference as if fully
set forth herein. The Investor acknowledges that the Offering is not being underwritten by the
placement agent (the “Placement Agent”) named in the Prospectus Supplement and that there is no
minimum offering amount.

     5. The manner of settlement of the Shares included in the Units purchased by the Investor
shall be determined by such Investor as follows:

 

 

Delivery by electronic book-entry at The Depository Trust Company (“DTC”), registered in the
Investor’s name and address as set forth below, and released by The American Stock Transfer
& Trust Company, the Company’s transfer agent (the “Transfer Agent”) (attention:
                     (     )      -          ), to the Investor at the Closing (as defined in Section 3.1 of
Annex A hereto). NO LATER THAN TWO (2) BUSINESS DAYS AFTER THE EXECUTION OF THIS AGREEMENT
BY THE INVESTOR AND THE COMPANY, THE INVESTOR SHALL:

	 	(I)	 	DIRECT THE BROKER-DEALER AT WHICH THE ACCOUNT OR ACCOUNTS TO BE CREDITED WITH
THE SHARES ARE MAINTAINED TO SET UP A DEPOSIT/WITHDRAWAL AT CUSTODIAN (“DWAC”)
INSTRUCTING THE TRANSFER AGENT TO CREDIT SUCH ACCOUNT OR ACCOUNTS WITH THE SHARES, AND
	 
	 	(II)	 	REMIT BY WIRE TRANSFER THE AMOUNT OF FUNDS EQUAL TO THE AGGREGATE PURCHASE
PRICE FOR THE UNITS BEING PURCHASED BY THE INVESTOR TO THE FOLLOWING ACCOUNT:
	 
	 	 	 	[PYMX wire instructions here]

IT IS THE INVESTOR’S RESPONSIBILITY TO (A) MAKE THE NECESSARY WIRE TRANSFER OR CONFIRM THE PROPER
ACCOUNT BALANCE IN A TIMELY MANNER AND (B) ARRANGE FOR SETTLEMENT BY WAY OF DWAC IN A TIMELY
MANNER. IF THE INVESTOR DOES NOT DELIVER THE AGGREGATE PURCHASE PRICE FOR THE UNITS OR DOES NOT
MAKE PROPER ARRANGEMENTS FOR SETTLEMENT IN A TIMELY MANNER, THE UNITS MAY NOT BE DELIVERED AT
CLOSING TO THE INVESTOR OR THE INVESTOR MAY BE EXCLUDED FROM THE CLOSING ALTOGETHER.

     6. The executed Warrant shall be delivered in accordance with the terms set forth in Annex I
hereto.

     7. The Investor represents that, except as set forth below, (a) it has had no position, office
or other material relationship within the past three years with the Company or persons known to it
to be affiliates of the Company, (b) it is not a NASD member or an Associated Person (as such term
is defined under the NASD Membership and Registration Rules Section 1011) as of the Closing, and
(c) neither the Investor nor any group of Investors (as identified in a public filing made with the
Commission) of which the Investor is a part in connection with the Offering of the Units, acquired,
or obtained the right to acquire, 20% or more of the Common Stock (or securities convertible into
or exercisable for Common Stock) or the voting power of the Company on a post-transaction basis.
Exceptions: (If no exceptions, write “none.” If left blank, response will be deemed to be
“none.”)

     8. The Investor represents that it has received or can obtain on the SEC’s Edgar filing system
the Prospectus, which is part of the Company’s Registration Statement, the Preliminary Prospectus,
the documents incorporated by reference therein, and any free writing

2

 

prospectus (collectively, the “Disclosure Package”), prior to or in connection with the
receipt of this Agreement along with the Company’s counterpart to this Agreement.

     9. No offer by the Investor to buy Units will be accepted and no part of the Purchase Price
will be delivered to the Company until the Company has accepted such offer by countersigning a copy
of this Agreement, and any such offer may be withdrawn or revoked, without obligation or commitment
of any kind, at any time prior to the Company (or a Placement Agent on behalf of the Company)
sending (in writing, facsimile or by electronic mail) notice of its acceptance of such offer. An
indication of interest will involve no obligation or commitment of any kind until this Agreement is
accepted and countersigned by or on behalf of the Company.

          Number of Units:

          Purchase Price Per Unit: $

          Aggregate Purchase Price: $

3

 

     Please confirm that the foregoing correctly sets forth the agreement between us by signing in
the space provided below for that purpose.

	 	 	 	 	 
	 	 	Dated as of:                           , 2007
	 
	 	 	 	 
	 	 	 
	 

	 	INVESTOR	 	 
	 
	 	 	 	 
	 

	 	By:	 	 
	 

	 	 	 	 
	 
	 	 	 	 
	 

	 	Print Name:  	 	 
	 

	 	 	 	 
	 
	 	 	 	 
	 

	 	Title:	 	 
	 

	 	 	 	 
	 
	 	 	 	 
	 

	 	Address:	 	 
	 

	 	 	 	 
	 
	 	 	 	 
	 

	 	 	 	 

Agreed and Accepted this _____ day of _______________, 2007:

	 	 	 	 	 
	POLYMEDIX, INC.	 	 
	 
	 	 	 	 
	By:

	 	 	 	 
	 

	 	 	 	 
	 

	 	Title:
	 	 

4

 

ANNEX I

TERMS AND CONDITIONS FOR PURCHASE OF UNITS

     1. Authorization and Sale of the Units; Defined Terms.

          1.1 Subject to the terms and conditions of this Agreement, the Company has authorized the sale
of the Units.

          1.2 Capitalized terms used herein but not otherwise defined have the meanings ascribed to them
in the Agreement.

     2. Agreement to Sell and Purchase the Units; Placement Agent.

          2.1 At the Closing (as defined in Section 3.1), the Company will sell to the Investor, and the
Investor will purchase from the Company, upon the terms and conditions set forth herein, the number
of Units set forth on the last page of the Agreement to which these Terms and Conditions for
Purchase of Units are attached as Annex I (the “Signature Page”) for the aggregate purchase price
therefor set forth on the Signature Page.

          2.2 The Company proposes to enter into substantially this same form of Subscription Agreement
with certain other investors (the “Other Investors”) and expects to complete sales of Units to
them. The Investor and the Other Investors are hereinafter sometimes collectively referred to as
the “Investors,” and this Agreement and the Subscription Agreements executed by the Other Investors
are hereinafter sometimes collectively referred to as the “Agreements.”

          2.3 Investor acknowledges that the Company intends to pay Rodman & Renshaw, LLC (the
“Placement Agent”) a fee (the “Placement Fee”) in respect of the sale of Units to the Investor.

          2.4 The Company has entered into a Placement Agency Agreement, dated December      , 2007 (the
“Placement Agreement”), with the Placement Agent that contains certain representations, warranties,
covenants, and agreements of the Company that may be relied upon by the Investor, which shall be a
third party beneficiary thereof. A copy of the Placement Agreement is available upon request.

     3. Closings and Delivery of the Units and Funds.

          3.1 Closing. The completion of the purchase and sale of the Units (the “Closing”) shall occur
at a place and time (the “Closing Date”) to be specified by the Company and the Placement Agent,
and of which the Investors will be notified in advance by the Placement Agent, in accordance with
Rule 15c6-1 promulgated under the Securities Exchange Act of 1934, as amended (the “Exchange Act”).
At the Closing, (a) the Company shall cause the Transfer Agent to deliver to the Investor the
number of Shares set forth on the Signature Page registered in the name of the Investor or, if so
indicated on the Investor Questionnaire attached hereto as Schedule A, in the name of a nominee
designated by the Investor and as contemplated

Annex I- Page 1

 

by procedures set forth in the Agreement and the Placement Agreement, (b) the Company shall
cause to be delivered to the Investor a Warrant to purchase a number of whole Warrant Shares
determined by multiplying the number of Shares set forth on the signature page by the Warrant Ratio
and rounding down to the nearest whole number and (c) the aggregate purchase price for the Units
being purchased by the Investor will be delivered by or on behalf of the Investor to the Company.

          3.2 (a) Conditions to the Company’s Obligations. The Company’s obligation to issue and sell
the Units to the Investor shall be subject to: (i) the receipt by the Company of the purchase price
for the Units being purchased hereunder as set forth on the Signature Page and (ii) the accuracy of
the representations and warranties made by the Investor and the fulfillment of those undertakings
of the Investor to be fulfilled prior to the Closing Date.

               (b) Conditions to the Investor’s Obligations. The Investor’s obligation to purchase the Units
will be subject to the accuracy of the representations and warranties made by the Company contained
in the Placement Agreement and the fulfillment of those undertakings of the Company to be fulfilled
prior to the Closing Date those contained in the Placement Agreement and the Subscription
Agreement, and to the condition that the Placement Agent shall not have determined that the
conditions to the closing in the Placement Agreement have not been satisfied. The Investor’s
obligations are expressly not conditioned on the purchase by any or all of the Other Investors of
the Units that they have agreed to purchase from the Company or the issuance of any minimum amount
of Units by the Company.

          3.3 Delivery of Funds. No later than two (2) business days after the execution of this
Agreement by the Investor and the Company, the Investor shall remit by wire transfer the amount
of funds equal to the aggregate purchase price for the Units being purchased by the Investor to the
following account designated by the Company:

     [PYMX wire instructions here]

          3.4 Delivery of Shares by Electronic Book-Entry at The Depository Trust Company. No later
than two (2) business days after the execution of this Agreement by the Investor and the
Company, the Investor shall direct the broker-dealer at which the account or accounts to be
credited with the Shares being purchased by such Investor are maintained, which broker/dealer shall
be a DTC participant, to set up a Deposit/Withdrawal at Custodian (“DWAC”) instructing The American
Stock Transfer & Trust Company, the Company’s transfer agent, to credit such account or accounts
with the Shares by means of an electronic book-entry delivery. Such DWAC shall indicate the
settlement date for the deposit of the Shares, which date shall be provided to the Investor by the
Placement Agent. Simultaneously with the delivery to the Company by the Investor of the funds
pursuant to Section 3.3 above, the Company shall direct its transfer agent to credit the Investor’s
account or accounts with the Shares pursuant to the information contained in the DWAC.

     4. Representations, Warranties and Covenants of the Investor.

          4.1 The Investor represents and warrants to, and covenants with, the Company that (a) the
Investor has answered all questions on the Signature Page and the Investor

Annex I- Page 2

 

Questionnaire for use in preparation of the Prospectus Supplement and the answers thereto are
true and correct as of the date hereof and will be true and correct as of the Closing Date and (b)
the Investor, in connection with its decision to purchase the number of Units set forth on the
Signature Page, is relying only upon the Disclosure Package and the representations and warranties
of the Company contained herein and the Placement Agency Agreement.

          4.2 The Investor acknowledges, represents and agrees that no action has been or will be taken
in any jurisdiction outside the United States by the Company or the Placement Agent that would
permit an offering of the Units, or possession or distribution of offering materials in connection
with the issue of the Units in any jurisdiction outside the United States where action for that
purpose is required. Each Investor outside the United States will comply with all applicable laws
and regulations in each foreign jurisdiction in which it purchases, offers, sells or delivers Units
or has in its possession or distributes any offering material, in all cases at its own expense.
The Placement Agent is not authorized to make and have not made any representation or use of any
information in connection with the issue, placement, purchase and sale of the Units, except as set
forth or incorporated by reference in the Disclosure Package.

          4.3 The Investor further represents and warrants to, and covenants with, the Company that (a)
the Investor has full right, power, authority and capacity to enter into this Agreement and to
consummate the transactions contemplated hereby and has taken all necessary action to authorize the
execution, delivery and performance of this Agreement, and (b) this Agreement constitutes a valid
and binding obligation of the Investor enforceable against the Investor in accordance with its
terms, except as enforceability may be limited by applicable bankruptcy, insolvency,
reorganization, moratorium or similar laws affecting creditors’ and contracting parties’ rights
generally and except as enforceability may be subject to general principles of equity (regardless
of whether such enforceability is considered in a proceeding in equity or at law) and except as the
indemnification agreements of the Investors herein may be legally unenforceable.

          4.4 The Investor understands that nothing in this Agreement, the Prospectus or any other
materials presented to the Investor in connection with the purchase and sale of the Units
constitutes legal, tax or investment advice. The Investor has consulted such legal, tax and
investment advisors as it, in its sole discretion, has deemed necessary or appropriate in
connection with its purchase of Units.

          4.5 Each Investor represents, warrants and agrees that, since the earlier to occur of (i) the
date on which the Placement Agent first contacted such Investor about the Offering and (ii) the
date of this Agreement, it has not engaged in any transactions in the securities of the Company
(including, without limitation, any Short Sales involving the Company’s securities). Each Investor
covenants that it will not engage in any transactions in the securities of the Company (including
Short Sales) prior to the time that the transactions contemplated by this Agreement have been
consummated and are publicly disclosed. Each Investor agrees that it will not use any of the Units
acquired pursuant to this Agreement to cover any short position in the Common Stock if doing so
would be in violation of applicable securities laws. For purposes hereof, “Short Sales” include,
without limitation, all “short sales” as defined in Rule 200 promulgated under Regulation SHO under
the Exchange Act, whether or not against the box, and all types of direct and indirect stock
pledges, forward sales contracts, options, puts,

Annex I- Page 3

 

calls, short sales, swaps, “put equivalent positions” (as defined in Rule 16a-1(h) under the
Exchange Act) and similar arrangements (including on a total return basis), and sales and other
transactions through non-US broker dealers or foreign regulated brokers.

     5. Survival of Representations, Warranties and Agreements; Third Party Beneficiary.
Notwithstanding any investigation made by any party to this Agreement or by the Placement Agent,
all covenants, agreements, representations and warranties made by the Company and the Investor
herein will survive the execution of this Agreement, the delivery to the Investor of the Units
being purchased and the payment therefor. The Placement Agent shall be a third party beneficiaries
with respect to representations, warranties and agreements of the Investor in Section 4 hereof.

     6. Notices. All notices, requests, consents and other communications hereunder will be in
writing, will be mailed (a) if within the domestic United States by first-class registered or
certified airmail, or nationally recognized overnight express courier, postage prepaid, or by
facsimile or (b) if delivered from outside the United States, by International Federal Express or
facsimile, and will be deemed given (i) if delivered by first-class registered or certified mail
domestic, three business days after so mailed, (ii) if delivered by nationally recognized overnight
carrier, one business day after so mailed, (iii) if delivered by International Federal Express, two
business days after so mailed and (iv) if delivered by facsimile, upon electric confirmation of
receipt and will be delivered and addressed as follows:

(a)  if to the Company, to:

Polymedix, Inc.

170 N. Radnor-Chester Road

Suite 300

Radnor, Pennsylvania 19087

Facsimile: (484) 598-2333

Attention: Edward F. Smith, Chief Financial Officer

with copies to:

Pepper Hamilton, LLP

400 Berwyn Park

899 Cassatt Avenue

Berwyn, Pennsylvania 19312

Attention: Jeffrey P. Libson

Facsimile: (610) 640-7835

                    (b) if to the Investor, at its address on the Signature Page hereto, or at such other address
or addresses as may have been furnished to the Company in writing.

     7. Changes. This Agreement may not be modified or amended except pursuant to an instrument in
writing signed by the Company and the Investor.

Annex I- Page 4

 

     8. Headings. The headings of the various sections of this Agreement have been inserted for
convenience of reference only and will not be deemed to be part of this Agreement.

     9. Severability. In case any provision contained in this Agreement should be invalid, illegal
or unenforceable in any respect, the validity, legality and enforceability of the remaining
provisions contained herein will not in any way be affected or impaired thereby.

     10. Governing Law. This Agreement will be governed by, and construed in accordance with, the
internal laws of the State of New York, without giving effect to the principles of conflicts of law
that would require the application of the laws of any other jurisdiction.

     11. Counterparts. This Agreement may be executed in two or more counterparts, each of which
will constitute an original, but all of which, when taken together, will constitute but one
instrument, and will become effective when one or more counterparts have been signed by each party
hereto and delivered to the other parties. The Company and the Investor acknowledge and agree that
the Company shall deliver its counterpart to the Investor along with the Prospectus and the
Prospectus Supplement (or the filing by the Company of an electronic version thereof with the
Commission).

     12. Confirmation of Sale. The Investor acknowledges and agrees that such Investor’s receipt
of the Company’s counterpart to this Agreement, together with the Prospectus and the Prospectus
Supplement (or the filing by the Company of an electronic version thereof with the Commission),
shall constitute written confirmation of the Company’s sale of Units to such Investor.

     13. Termination. In the event that the Company decides to terminate Offering prior to
Closing, this Agreement shall terminate without any further action on the part of the parties
hereto and any monies remitted to the Escrow Agent will be promptly refunded by the Escrow Agent,
without interest, to the Investor.

Annex I- Page 5

 

SCHEDULE A TO ANNEX I

POLYMEDIX, INC.

INVESTOR QUESTIONNAIRE

Pursuant to Section 3 of Annex I to the Agreement, please provide us with the following
information:

	 	1.	 	The exact name that your Shares and Warrants are to be registered in. You may
use a nominee name if appropriate:
	 
	 	 	 	                                                                                
                    
	 
	 	 	 	                                                                                
                    
	 
	 	2.	 	The relationship between the Investor and the registered holder listed in
response to item 1 above:
	 
	 	 	 	                                                                                
                    
	 
	 	 	 	                                                                                
                    
	 
	 	3.	 	The mailing address of the registered holder listed in response to item 1
above:
	 
	 	 	 	                                                                                
                    
	 
	 	 	 	                                                                                
                    
	 
	 	 	 	                                                                                
                    
	 
	 	4.	 	The Social Security Number or Tax Identification Number of the registered
holder listed in the response to item 1 above:
	 
	 	 	 	                                                                                
                    
	 
	 	5.	 	Name of DTC Participant (broker-dealer at which the account or accounts to be
credited with the Shares are maintained); please include the name and telephone number
of the contract person at the broker-dealer:
	 
	 	 	 	                                                                                
                    
	 
	 	 	 	                                                                                
                    
	 
	 	 	 	                                                                                
                    
	 
	 	 	 	                                                                                
                    

Schedule A to Annex I- Page 1

 

	 	6.	 	DTC Participant Number:
	 
	 	 	 	                                                                                
                    
	 
	 	7.	 	Name of Account at DTC Participant being credited with the Shares:
	 
	 	 	 	                                                                                
                    
	 
	 	 	 	                                                                                
                    
	 
	 	8.	 	Account Number at DTC Participant being credited with the Shares:
	 
	 	 	 	                                                                                
                    

Schedule A to Annex I- Page 2exv4w4

 

Exhibit 4.4

POLYMEDIX, INC.

WARRANT TO PURCHASE COMMON STOCK

To Purchase [          ] Shares of Common Stock

Date of Issuance:                     , 2007

VOID AFTER [          ], 2012

     THIS CERTIFIES THAT, for value received, [                    ], or permitted registered assigns (the
“Holder”), is entitled to subscribe for and purchase at the Exercise Price (defined below) from
PolyMedix, Inc., a Delaware corporation (the “Company”), up to [                    ] shares of the common
stock of the Company, par value $0.001 per share (the “Common Stock”). This warrant is one of a
series of warrants issued by the Company as of the date hereof (individually a “Warrant”,
collectively, “Company Warrants”) pursuant to that certain subscription agreement between the
Company and the Holder, dated as of                     , 2007 (the “Subscription Agreement”).

     1. DEFINITIONS. Capitalized terms used herein but not otherwise defined herein shall
have their respective meanings as set forth in the Subscription Agreement. As used herein, the
following terms shall have the following respective meanings:

          (a) “Exercise Period” shall mean the period commencing with the date hereof and ending five
years from the date hereof, unless sooner terminated as provided below.

          (b) “Exercise Price” shall mean $                     per share, subject to adjustment pursuant to
Section 4 below.

          (c) “Exercise Shares” shall mean the shares of Common Stock issuable upon exercise of this
Warrant.

          (d) “Trading Day” shall mean (i) any day on which the Common Stock is listed or quoted on its
primary Trading Market, (ii) if the Common Stock is not then listed or quoted and traded on any
eligible market (meaning any of the New York Stock Exchange, American Stock Exchange (“AMEX”) or
The NASDAQ Global Market), then a day on which trading occurs on the OTC Bulletin Board (or any
successor thereto), or (iii) if trading does not occur on the OTC Bulletin Board (or any successor
thereto), any business day.

     2. EXERCISE OF WARRANT. The rights represented by this Warrant may, subject to
Section 6 below, be exercised in whole or in part at any time during the Exercise Period, by
delivery of the following to the Company at its address set forth on the signature page hereto (or
at such other address as it may designate by notice in writing to the Holder):

          (a) An executed Notice of Exercise in the form attached hereto; and

          (b) Payment of the Exercise Price either in cash or by check (subject to the limitations in
Section 2.2 below.

 

 

     Execution and delivery of the Notice of Exercise shall have the same effect as cancellation of
the original Warrant and issuance of a new Warrant evidencing the right to purchase the remaining
number of Exercise Shares, if any. If requested by the Company, Holder agrees to provide this
Warrant, or an affidavit of lost security, to the Company within a reasonable period after the
delivery of the Notice of Exercise.

     Certificates for shares purchased hereunder shall be transmitted by the transfer agent of the
Company to the Holder by crediting the account of the Holder’s prime broker with the Depository
Trust Company through its Deposits and Withdrawal at Custodian (DWAC) system if the Company is a
participant in such system, and otherwise by physical delivery to the address specified by the
Holder in the Notice of Exercise within three business days from the delivery to the Company of the
Notice of Exercise, surrender of this Warrant and payment of the aggregate Exercise Price as set
forth above. This Warrant shall be deemed to have been exercised on the date the Exercise Price is
received by the Company. The Exercise Shares shall be deemed to have been issued, and Holder or
any other person so designated to be named therein shall be deemed to have become a holder of
record of such shares for all purposes, as of the date this Warrant has been exercised by payment
to the Company of the Exercise Price. If by the close of the third Trading Day after delivery of a
Notice of Exercise, the Company fails to deliver to the Holder a certificate representing the
required number of Exercise Shares in the manner required pursuant to this Section 2, and
such failure to deliver the Exercise Shares is caused by the Company’s failure to use commercially
reasonable efforts to comply with this Section 2 and/or the covenants in Section
3.1 herein, and if after such third Trading Day and prior to the receipt of such Exercise
Shares, the Holder purchases (in an open market transaction or otherwise) shares of Common Stock to
deliver in satisfaction of a sale by the Holder of the Exercise Shares which the Holder anticipated
receiving upon such exercise (a “Buy-In”), then the Company shall, within three Trading Days after
the Holder’s request and in the Holder’s sole discretion, either (1) pay in cash to the Holder an
amount equal to the Holder’s total purchase price (including brokerage commissions, if any) for the
shares of Common Stock so purchased (the “Buy-In Price”), at which point the Company’s obligation
to deliver such certificate (and to issue such Exercise Shares) shall terminate or (ii) promptly
honor its obligation to deliver to the Holder a certificate or certificates representing such
Exercise Shares and pay cash to the Holder in an amount equal to the excess (if any) of the Buy-In
Price over the product of (a) such number of Exercise Shares, times (b) the closing bid price on
the date of the event giving rise to the Company’s obligation to deliver such certificate.

     The person in whose name any Exercise Shares are to be issued upon exercise of this Warrant
shall be deemed to have become the holder of record of such shares on the date on which this
Warrant was surrendered and payment of the Exercise Price was made, irrespective of the date of
delivery of such certificate or certificates, except that, if the date of such surrender and
payment is a date when the stock transfer books of the Company are closed, such person shall be
deemed to have become the holder of such shares at the close of business on the next succeeding
date on which the stock transfer books are open.

     To the extent permitted by law, the Company’s obligations to issue and deliver Exercise Shares
in accordance with the terms hereof are absolute and unconditional, irrespective of any action or
inaction by the Holder to enforce the same, any waiver or consent with respect to any provision
hereof, the recovery of any judgment against any person or entity or any action to

2

 

enforce the same, or any setoff, counterclaim, recoupment, limitation or termination, or any
breach or alleged breach by the Holder or any other person or entity of any obligation to the
Company or any violation or alleged violation of law by the Holder or any other person or entity,
and irrespective of any other circumstance which might otherwise limit such obligation of the
Company to the Holder in connection with the issuance of Exercise Shares. Nothing herein shall
limit a Holder’s right to pursue any other remedies available to it hereunder, at law or in equity
including, without limitation, a decree of specific performance and/or injunctive relief with
respect to the Company’s failure to timely deliver certificates representing shares of Common Stock
upon exercise of this Warrant as required pursuant to the terms hereof.

          2.2 ISSUANCE OF NEW WARRANTS. Upon any partial exercise of this Warrant, the Company,
at its expense, will forthwith and, in any event within five business days, issue and deliver to
the Holder a new warrant or warrants of like tenor, registered in the name of the Holder,
exercisable, in the aggregate, for the balance of the number of shares of Common Stock remaining
available for purchase under this Warrant.

          2.3 EXERCISE LIMITATIONS; HOLDER’S RESTRICTIONS. A Holder shall not have the right to
exercise any portion of this Warrant, pursuant to Section 2 or otherwise, to the extent
that after giving effect to such issuance after exercise, such Holder (together with such Holder’s
affiliates), as set forth on the applicable Notice of Exercise, would beneficially own in excess of
4.99% of the number of shares of the Common Stock outstanding immediately after giving effect to
such issuance. For purposes of the foregoing sentence, the number of shares of Common Stock
beneficially owned by such Holder and its affiliates shall include the number of shares of Common
Stock issuable upon exercise of this Warrant with respect to which the determination of such
sentence is being made, but shall exclude the number of shares of Common Stock which would be
issuable upon (a) exercise of the remaining, non-exercised portion of this Warrant beneficially
owned by such Holder or any of its affiliates and (b) exercise or conversion of the unexercised or
non-converted portion of any other securities of the Company (including, without limitation, any
other shares of Common Stock or Warrants) subject to a limitation on conversion or exercise
analogous to the limitation contained herein beneficially owned by such Holder or any of its
affiliates. Except as set forth in the preceding sentence, for purposes of this Section
2.4, beneficial ownership shall be calculated in accordance with Section 13(d) of the Exchange
Act, it being acknowledged by a Holder that the Company is not representing to such Holder that
such calculation is in compliance with Section 13(d) of the Exchange Act and such Holder is solely
responsible for any schedules required to be filed in accordance therewith. To the extent that the
limitation contained in this Section 2.4 applies, the determination of whether this Warrant
is exercisable (in relation to other securities owned by such Holder) and of which a portion of
this Warrant is exercisable shall be in the sole discretion of a Holder, and the submission of a
Notice of Exercise shall be deemed to be each Holder’s determination of whether this Warrant is
exercisable (in relation to other securities owned by such Holder) and of which portion of this
Warrant is exercisable, in each case subject to such aggregate percentage limitation, and the
Company shall have no obligation to verify or confirm the accuracy of such determination. For
purposes of this Section 2.4, in determining the number of outstanding shares of Common
Stock, a Holder may rely on the number of outstanding shares of Common Stock as reflected in (x) the Company’s most recent Form 10-Q or Form 10-K, as the case may be, (y) a more recent public
announcement by the Company or (z) any other notice by the Company or the Company’s Transfer Agent
setting forth the number of shares of

3

 

Common Stock outstanding. Upon the written or oral request of a Holder, the Company shall
within two Trading Days confirm orally and in writing to such Holder the number of shares of Common
Stock then outstanding. In any case, the number of outstanding shares of Common Stock shall be
determined after giving effect to the conversion or exercise of securities of the Company,
including this Warrant, by such Holder or its affiliates since the date as of which such number of
outstanding shares of Common Stock was reported. The provisions of this Section 2.4 may be
waived by such Holder, at the election of such Holder, upon not less than 61 days’ prior notice to
the Company to allow the Holder to become the beneficial owner of not more than 9.99% of the Common
Stock outstanding, and the provisions of this Section 2.4 shall continue to apply until
such 61st day (or such later date, as determined by such Holder, as may be specified in such notice
of waiver).

     3. COVENANTS OF THE COMPANY.

          3.1 COVENANTS AS TO EXERCISE SHARES. The Company covenants and agrees that all
Exercise Shares that may be issued upon the exercise of the rights represented by this Warrant
will, upon issuance, be validly issued and outstanding, fully paid and nonassessable, and free from
all taxes, liens and charges with respect to the issuance thereof. The Company further covenants
and agrees that the Company will at all times during the Exercise Period, have authorized and
reserved, free from preemptive rights, a sufficient number of shares of Common Stock to provide for
the exercise of the rights represented by this Warrant. If at any time during the Exercise Period
the number of authorized but unissued shares of Common Stock shall not be sufficient to permit
exercise of this Warrant, the Company will take such corporate action as may, in the opinion of its
counsel, be necessary to increase its authorized but unissued shares of Common Stock to such number
of shares as shall be sufficient for such purposes. The Company shall use commercially reasonable
efforts to keep a registration statement (a “Registration Statement”) with respect to the issuance
and sale of the Exercise Shares to the Holder, or such Holder’s valid assignee, in effect during
the Exercise Period or such shorter period that will terminate when this Warrant has been
exercised, and during such time period shall use commercially reasonable efforts to obtain the
prompt withdrawal of any stop order suspending the effectiveness of any such Registration
Statement. At any time during which the Exercise Shares are included in a then-effective
Registration Statement, the Company may suspend the ability of the Holder to exercise this Warrant
in any manner contemplated by this Warrant, for a reasonable period or periods (a “Black-out
Period”), in the event that (i)(a) an event occurs and is continuing as a result of which the
Registration Statement including the Exercise Shares, any related prospectus or any document
incorporated therein by reference as then amended or supplement would, in the Company’s good faith
judgment, contain an untrue statement of a material fact or omit to state a material fact necessary
in order to make the statements therein, in the light of the circumstances under which they were
made, not misleading, and (b) the Company determined in its good faith judgment that the disclosure
of such event at such time would be to the detriment of the business, operations or prospects of
the Company or the disclosure otherwise relates to a business transaction, operations or other
material event which has not yet been publicly disclosed, or (ii) the Registration Statement is no
longer effective and the holder is not permitted to sell Exercise Shares pursuant to any other
registration statement or an exemption to the registration requirements of the Securities Act of
1933, as amended (the “Securities Act”); provided, however, that in the event that a Black-out
Period occurs subsequent to the one year anniversary of the Date of Issuance,

4

 

this Warrant shall be exercised subject to the terms and conditions of Section 2.1.
Notwithstanding the foregoing provisions of this Section 3.1, (i) if a Holder is not able
to exercise this Warrant because the Company has implemented a Black-out Period, then the Exercise
Period shall be extended for the number of calendar days covered by such Black-out Period and (ii)
the Company will use commercially reasonable efforts to ensure that the aggregate number of days
covered by Black-out Periods shall not last for more than twenty (20) consecutive days or exceed
sixty (60) in a particular calendar year; provided, however, that the holder may not receive any
penalties, cash payments or any other liquidated damages for failure to deliver registered Exercise
Shares so long as the Company has used commercially reasonable efforts to deliver the Holder the
Exercise Shares as contemplated in Section 2 herein or otherwise complies with the covenants in
this Section 3.1, and (c) if the Black-out Period is required because the Registration
Statement is no longer effective and the Holder is not permitted to sell Exercise Shares pursuant
to any other registration statement or an exemption to the registration requirements of the
Securities Act of 1933, then the Exercise Period shall be extended until such Holder may sell such
Exercise Shares.

     4. CASHLESS EXERCISE. If at any time there is no effective Registration Statement
registering, or no current prospectus available for, the resale of the Exercise Shares by the
Holder, then this Warrant may also be exercised at such time by means of a “cashless exercise” in
which the Holder shall be entitled to receive a certificate for the number of Exercise Shares equal
to the quotient obtained by dividing [(A-B) (X)] by (A), where:

	 	 	 	 	 	 	 
	 

	 	(A)
	 	=
	 	the VWAP on the Trading Day immediately preceding the date of such election;
	 
	 	 	 	 	 	 
	 

	 	(B)
	 	=
	 	the Exercise Price of this Warrant, as adjusted; and
	 
	 	 	 	 	 	 
	 

	 	(X)
	 	=
	 	the number of Exercise Shares issuable upon exercise of this Warrant in accordance with the terms of this Warrant by means of a cash exercise rather than a cashless exercise.

“VWAP” means, for any date, the price determined by the first of the following clauses that
applies: (a) if the Common Stock is then listed or quoted on a Trading Market, the daily volume
weighted average price of the Common Stock for such date (or the nearest preceding date) on the
Trading Market on which the Common Stock is then listed or quoted for trading as reported by
Bloomberg L.P. (based on a Trading Day from 9:30 a.m. (New York City time) to 4:02 p.m. (New York
City time); (b) if the OTC Bulletin Board is not a Trading Market, the volume weighted average
price of the Common Stock for such date (or the nearest preceding date) on the OTC Bulletin Board;
(c) if the Common Stock is not then quoted for trading on the OTC Bulletin Board and if prices for
the Common Stock are then reported in the “Pink Sheets” published by Pink Sheets, LLC (or a similar
organization or agency succeeding to its functions of reporting prices), the most recent bid price
per share of the Common Stock so reported; or (d) in all other cases, the fair market value of a
share of Common Stock as determined by an independent appraiser selected in good faith by the
Purchasers of a majority in interest of the Shares then outstanding and reasonably acceptable to
the Company, the fees and expenses of which shall be paid by the Company.

5

 

     5. NO IMPAIRMENT. Except and to the extent as waived or consented to by each holder
of Company Warrants, the Company will not, by amendment of its Certificate of Incorporation 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 to be observed or performed hereunder by the Company, but will at all times in
good faith assist in the carrying out of all the provisions of this Warrant and in the taking of
all such action as may be necessary or appropriate in order to protect the exercise rights of the
Holder against impairment.

     6. ADJUSTMENT OF EXERCISE PRICE AND SHARES.

          (a) In the event of changes in the outstanding Common Stock of the Company by reason of stock
dividends, split-ups, recapitalizations, reclassifications, combinations or exchanges of shares,
separations, reorganizations, liquidations, consolidation, acquisition of the Company (whether
through merger or acquisition of substantially all the assets or stock of the Company), or the
like, the number, class and type of shares available under this Warrant in the aggregate and the
Exercise Price shall be correspondingly adjusted to give the Holder of this Warrant, on exercise
for the same aggregate Exercise Price, the total number, class, and type of shares or other
property as the Holder would have owned had this Warrant been exercised prior to the event and had
the Holder continued to hold such shares until the event requiring adjustment. The form of this
Warrant need not be changed because of any adjustment in the number of Exercise Shares subject to
this Warrant.

          (b) If at any time or from time to time the holders of Common Stock of the Company (or any
shares of stock or other securities at the time receivable upon the exercise of this Warrant) shall
have received or become entitled to receive, without payment therefor,

          (i) Common Stock or any shares of stock or other securities which are at any time
directly or indirectly convertible into or exchangeable for Common Stock, or any rights or
options to subscribe for, purchase or otherwise acquire any of the foregoing by way of
dividend or other distribution (other than a dividend or distribution covered in Section
4(a) above);

          (ii) any cash paid or payable otherwise than as a cash dividend; or

          (iii) Common Stock or additional stock or other securities or property (including cash)
by way of spinoff, split-up, reclassification, combination of shares or similar corporate
rearrangement (other than shares of Common Stock pursuant to Section 4(a) above),

then and in each such case, the Holder hereof will, upon the exercise of this Warrant, be entitled
to receive, in addition to the number of shares of Common Stock receivable thereupon, and without
payment of any additional consideration therefor, the amount of stock and other securities and
property, as applicable, (including cash in the cases referred to in clauses (ii) and (iii) above)
which such Holder would hold on the date of such exercise had such Holder been the holder of record
of such Common Stock as of the date on which holders of Common Stock

6

 

received or became entitled to receive such shares or all other additional stock and other
securities and property.

          (c) Upon the occurrence of each adjustment pursuant to this Section 4, the Company at
its expense will, at the written request of the Holder, promptly compute such adjustment in
accordance with the terms of this Warrant and prepare a certificate setting forth such adjustment,
including a statement of the adjusted Exercise Price and adjusted number or type of Exercise Shares
or other securities issuable upon exercise of this Warrant (as applicable), describing the
transactions giving rise to such adjustments and showing in detail the facts upon which such
adjustment is based. Upon written request, the Company will promptly deliver a copy of each such
certificate to the Holder and to the Company’s transfer agent.

     7. FRACTIONAL SHARES. No fractional shares shall be issued upon the exercise of this
Warrant as a consequence of any adjustment pursuant hereto. All Exercise Shares (including
fractions) issuable upon exercise of this Warrant may be aggregated for purposes of determining
whether the exercise would result in the issuance of any fractional share. If, after aggregation,
the exercise would result in the issuance of a fractional share, the Company shall, in lieu of
issuance of any fractional share, pay the Holder otherwise entitled to such fraction a sum in cash
equal to the product resulting from multiplying the then current Fair Market Value of an Exercise
Share by such fraction. “Fair Market Value” of one share of Common Stock shall mean (i) the
average of the closing sales prices for the shares of Common Stock on AMEX or other trading market
where such security is listed or traded as reported by Bloomberg Financial Markets (or a comparable
reporting service of national reputation selected by the Company and reasonably acceptable to the
Holder if Bloomberg Financial Markets is not then reporting sales prices of such security)
(collectively, “Bloomberg”) for the ten (10) consecutive trading days immediately preceding such
date, or (ii) if AMEX is not the principal trading market for the shares of Common Stock, the
average of the reported sales prices reported by Bloomberg on the principal trading market for the
Common Stock during the same period, or, if there is no sales price for such period, the last sales
price reported by Bloomberg for such period, or (iii) if neither of the foregoing applies, the last
sales price of such security in the over-the-counter market on the pink sheets or bulletin board
for such security as reported by Bloomberg, or if no sales price is so reported for such security,
the last bid price of such security as reported by Bloomberg or (iv) if Fair Market Value cannot be
calculated as of such date on any of the foregoing bases, the Fair Market Value shall be as
determined by the Board of Directors of the Company in the exercise of its good faith judgment.

     8. FUNDAMENTAL TRANSACTIONS. If, at any time while this Warrant is outstanding, (i) the Company effects any merger or consolidation of the Company with or into another entity, in
which the shareholders of the Company as of immediately prior to the transaction own less than a
majority of the outstanding stock of the surviving entity, (ii) the Company effects any sale of all
or substantially all of its assets in one or a series of related transactions, (iii) any tender
offer or exchange offer (whether by the Company or another person or entity) is completed pursuant
to which holders of Common Stock are permitted to tender or exchange their shares for other
securities, cash or property, or (iv) the Company effects any reclassification of the Common Stock
or any compulsory share exchange pursuant to which the Common Stock is effectively converted into
or exchanged for other securities, cash or property (other than as a result of a subdivision or
combination of shares of Common Stock covered by

7

 

Section 4 above) (each, a “Fundamental Transaction”), then the Holder shall have the
right thereafter to receive, upon exercise of this Warrant, the same amount and kind of securities,
cash or property, as applicable, as it would have been entitled to receive upon the occurrence of
such Fundamental Transaction if it had been, immediately prior to such Fundamental Transaction, the
holder of the number of Exercise Shares then issuable upon exercise in full of this Warrant (the
“Alternate Consideration”). Following any transaction contemplated by this Section 6, the
term Exercise Shares shall be deemed to refer to the shares for which this Warrant is thereafter
exercisable in accordance with the provisions hereof. In addition, if holders of Common Stock are
given a choice as to the securities, cash (which shall be treated in accordance with the preceding
paragraph) or property to be received in a Fundamental Transaction (including a right to elect to
receive any particular one or combination of more than one of the foregoing), then the Holder shall
be given the same choice of consideration upon any exercise of this Warrant following such
Fundamental Transaction, which choice of consideration can be made at the time of exercise at any
time prior to the expiration of the Exercise Period.

     9. NO STOCKHOLDER RIGHTS. Other than as provided in Section 3.3 or otherwise
herein, this Warrant in and of itself shall not entitle the Holder to any voting rights or other
rights as a stockholder of the Company.

     10. TRANSFER OF WARRANT. Subject to compliance with any applicable laws, this Warrant
and all rights hereunder are transferable, by the Holder in person or by duly authorized attorney,
upon delivery of this Warrant and the form of assignment attached hereto to any transferee
designated by the Holder. The transferee shall sign an investment letter in form and substance
reasonably satisfactory to the Company and its counsel.

     11. 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 impose (which shall, in the case of a mutilated Warrant, include the surrender thereof),
issue a new Warrant of like denomination and tenor as this Warrant so lost, stolen, mutilated or
destroyed. Any such new Warrant shall constitute an original contractual obligation of the
Company, whether or not the allegedly lost, stolen, mutilated or destroyed Warrant shall be at any
time enforceable by anyone.

     12. NOTICES, ETC. All notices required or permitted hereunder shall be in writing and
shall be deemed effectively given: (a) upon personal delivery to the party to be notified, (b)
when sent by confirmed telex, electronic transmission or facsimile if sent during normal business
hours of the recipient, if not, then on the next business day, (c) five days after having been sent
by registered or certified mail, return receipt requested, postage prepaid, or (d) one day after
deposit with a nationally recognized overnight courier, specifying next day delivery, with written
verification of receipt. All communications shall be sent to the Company at the address listed on
the signature page hereto and to the Holder at the applicable address set forth on the applicable
signature page to the Subscription Agreement or at such other address as the Company or the Holder
may designate by ten (10) days advance written notice to the other parties hereto.

     13. ACCEPTANCE. Receipt of this Warrant by the Holder shall constitute acceptance of
and agreement to all of the terms and conditions contained herein.

8

 

     14. GOVERNING LAW. This Warrant shall be governed by, and construed in accordance
with, the laws of the State of New York. The Holder hereby submits to the non-exclusive
jurisdiction of the Federal and state courts in the Borough of Manhattan in The City of New York in
any suit or proceeding arising out of or relating to this Agreement or the transactions
contemplated thereby. The Holder irrevocably and unconditionally waives any objection to the
laying of venue of any suit or proceeding arising out of or relating to this Warrant in Federal and
state courts in the Borough of Manhattan in The City of New York and irrevocably and
unconditionally waives and agrees not to plead or claim in any such court that any such suit or
proceeding in any such court has been brought in an inconvenient forum.

     15. AMENDMENT
OR WAIVER. Any term of this Warrant may be amended or waived (either generally
or in a particular instance and either retroactively or prospectively) with the written consent of
the Company and the holders of Company Warrants representing at least two-thirds of the number of
shares of Common Stock then subject to outstanding Company Warrants, except that the amendment or
waiver of any provision of Sections 4 or 8 shall require the written consent of the Company and the
holders of Company Warrants representing at least 90% of the number of shares of Common Stock then
subject to outstanding Company Warrants. Notwithstanding the foregoing, (a) this Warrant may be
amended and the observance of any term hereunder may be waived without the written consent of the
Holder only in a manner which applies to all Company Warrants in the same fashion and (b) the
number of Exercise Shares subject to this Warrant and the Exercise Price of this Warrant may not be
amended, and the right to exercise this Warrant may not be waived, without the written consent of
the Holder. The Company shall give prompt written notice to the Holder of any amendment hereof or
waiver hereunder that was effected without the Holder’s written consent. No waivers of any term,
condition or provision of this Warrant, in any one or more instances, shall be deemed to be, or
construed as, a further or continuing waiver of any such term, condition or provision.

[REMAINDER OF PAGE INTENTIONALLY LEFT BLANK]

9

 

     IN WITNESS WHEREOF, the Company has caused this Warrant to be executed by its duly authorized
officer as of ___, 2007.

	 	 	 	 	 
	 	POLYMEDIX, INC.

 	 
	 	By:  	 	 
	 	 	Name:  	 	 
	 	 	Title:  	 	 
	 

170 N. Radnor-Chester Road

Suite 300

Radnor, Pennsylvania 19087

10

 

NOTICE OF EXERCISE

TO: POLYMEDIX, INC.

     (1) The undersigned hereby elects to purchase [                    ] shares of the common stock, par
value $0.001 (the “Common Stock”), of POLYMEDIX, INC. (the “Company”) pursuant to the terms of the
attached Warrant, and tenders herewith payment of the exercise price in full, together with all
applicable transfer taxes, if any, subject to the limitations set forth in Section 2.1 of
the Warrant.

     (2) Please issue the certificate for shares of Common Stock in the name of, and pay any cash
for any fractional share to:

                                                                       
                             

Print or type name

                                                                       
                             

Social Security or other Identifying Number

                                                                       
                             

Street Address

   
                                                                    
                             

City, State, Zip Code

     (3) If such number of shares shall not be all the shares purchasable upon the exercise of the
Warrants evidenced by this Warrant, a new warrant certificate for the balance of such Warrants
remaining unexercised shall be registered in the name of and delivered to:

     Please insert Social Security or other identifying number:                                              
             

(Please print name and address)

	 	 	 	 	 	 	 
	Dated:
	 	 	 	 	 	 
	 

	 	 
	 	 	 	 
	 

	 	(Date)
	 	 
	 	(Signature)
	 
	 	 	 	 	 	 
	 

	 	 	 	 	 	 
	 

	 	 	 	 	 	(Print Name)

11

 

ASSIGNMENT FORM

     (To assign the foregoing Warrant, execute this form and supply required information. Do not
use this form to purchase shares.)

     FOR VALUE RECEIVED, the foregoing Warrant and all rights evidenced thereby are hereby assigned to

	 	 	 	 	 	 	 
	 

	 	Name:
	 	 	 	 
	 

	 	 	 	 	 	 
	 

	 	 	 	 	 	(Please Print)
	 
	 	 	 	 	 	 
	 

	 	Address:	 	 	 	 
	 

	 	 	 	 	 	 
	 

	 	 	 	 	 	(Please Print)
	 
	 	 	 	 	 	 
	 

	 	Dated:
	 	 	 	                                                            , 2007
	 
	 	 	 	 	 	 
	 

	 	Holder’s Signature:	 	 	 	 
	 

	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 

	 	Holder’s Address:	 	 	 	 
	 

	 	 	 	 	 	 

NOTE: The signature to this Assignment Form must correspond with the name as it appears on the
face of the Warrant, without alteration or enlargement or any change whatever. Officers of
corporations and those acting in a fiduciary or other representative capacity should file proper
evidence of authority to assign the foregoing Warrant.

12

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