Exhibit 4.1



 Exhibit 4.1 

THIS WARRANT AND THE UNDERLYING SECURITIES HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE “SECURITIES
ACT”), OR UNDER THE SECURITIES LAWS OF ANY STATE. THESE SECURITIES MAY NOT BE OFFERED, SOLD OR OTHERWISE TRANSFERRED, PLEDGED OR HYPOTHECATED EXCEPT AS PERMITTED UNDER THE ACT AND APPLICABLE STATE SECURITIES LAWS IN ACCORDANCE WITH
APPLICABLE REGISTRATION REQUIREMENTS OR AN EXEMPTION THEREFROM. THE ISSUER OF THESE SECURITIES MAY REQUIRE AN OPINION OF COUNSEL REASONABLY SATISFACTORY TO THE ISSUER THAT SUCH OFFER, SALE, TRANSFER, PLEDGE OR HYPOTHECATION OTHERWISE COMPLIES WITH
THE ACT AND ANY APPLICABLE STATE SECURITIES LAWS. THIS WARRANT MUST BE SURRENDERED TO THE COMPANY OR ITS TRANSFER AGENT AS A CONDITION PRECEDENT TO THE SALE, TRANSFER, PLEDGE OR HYPOTHECATION OF ANY INTEREST IN ANY OF THE SECURITIES REPRESENTED
HEREBY, EXCEPT AS PROVIDED HEREIN. THE SHARES OF COMMON STOCK UNDERLYING THIS WARRANT ARE SUBJECT TO THE REGISTRATION RIGHTS AGREEMENT, DATED             , 2015, AMONG THE COMPANY,
BROOKLINE GROUP, LLC AND THE PURCHASERS IDENTIFIED THEREIN. 
 WARRANT TO PURCHASE SHARES OF COMMON STOCK 

of 
 CONTRAFECT
CORPORATION 
 Dated as of             , 2015 

Void after the date specified in Section 8 

Warrant No. 
 THIS CERTIFIES THAT, for value received,
                    , or its registered assigns (the “Holder”), is entitled, subject to the provisions and upon the terms and
conditions set forth herein, to purchase from ContraFect Corporation, a Delaware corporation (the “Company”), Shares (as defined below), in the amounts, at such times and at the price per share set forth in Section 1. The term
“Warrant” as used herein shall include this Warrant and any warrants delivered in substitution or exchange therefor as provided herein. 

The following is a statement of the rights of the Holder and the conditions to which this Warrant is subject, and to which Holder, by acceptance of this
Warrant, agrees: 
 1. Number and Price of Shares; Exercise Period. 

(a) Definition of Shares. “Shares” shall mean shares of the
Company’s common stock, par value $0.0001 per share (“Common Stock”). 

(b) Number of Shares. Subject to any previous exercise of the Warrant, the Holder shall have the right to purchase
                 Shares. 
 (c)
Exercise Price. The exercise price per Share shall be equal to $8.00 (the “Exercise Price”). The Exercise Price shall be subject to adjustment pursuant to Section 6 hereof.

 (d) Exercise Period. This Warrant shall be exercisable, in whole or in part, prior to (or in
connection with) the expiration of this Warrant as set forth in Section 8. 
 2. Exercise of the Warrant. 

(a) Exercise. The purchase rights represented by this Warrant may be exercised at the election of the Holder, in
whole or in part, in accordance with Section 1, by: 
 (i) the tender to the Company at its principal office (or such
other office or agency as the Company may designate) of a notice of exercise in the form of Exhibit A (the “Notice of Exercise”), duly completed and executed by or on behalf of the Holder, together with the surrender of this
Warrant; and 
 (ii) the payment to the Company of an amount equal to (x) the Exercise Price multiplied by (y) the number of
Shares being purchased, by wire transfer or certified, cashier’s or other check acceptable to the Company and payable to the order of the Company. 







 (b) Stock Certificates. The rights under this Warrant shall be deemed to have been
exercised and the Shares issuable upon such exercise shall be deemed to have been issued immediately prior to the close of business on the date this Warrant is exercised in accordance with its terms, and the person entitled to receive the Shares
issuable upon such exercise shall be treated for all purposes as the holder of record of such Shares as of the close of business on such date. As promptly as reasonably practicable on or after such date, the Company shall issue and deliver to the
person or persons entitled to receive the same a certificate or certificates for that number of shares issuable upon such exercise. In the event that the rights under this Warrant are exercised in part and have not expired, the Company shall execute
and deliver a new Warrant reflecting the number of Shares that remain subject to this Warrant. 
 (c) No Fractional Shares or
Scrip. No fractional shares or scrip representing fractional shares shall be issued upon the exercise of the rights under this Warrant. In lieu of such fractional share to which the Holder would otherwise be entitled, the Company shall make
a cash payment equal to the Exercise Price multiplied by such fraction. 
 (d) Conditional Exercise. The Holder may exercise
this Warrant conditioned upon (and effective immediately prior to) consummation of any transaction that would cause the expiration of this Warrant pursuant to Section 8 by so indicating in the notice of exercise. 

(e) Reservation of Stock. The Company agrees during the term the rights under this Warrant are exercisable to take all
reasonable action to reserve and keep available from its authorized and unissued Shares (or any such other class or series of stock then issuable upon exercise of this Warrant) for the purpose of effecting the exercise of this Warrant such number of
Shares (or any shares of stock to be issued on conversion of such Shares) as shall from time to time be sufficient to effect the exercise of the rights under this Warrant; and if at any time the number of authorized but unissued Shares (or any such
other class or series of stock then issuable upon exercise of this Warrant) shall not be sufficient for purposes of the exercise of this Warrant in accordance with its terms and the conversion of the Shares, without limitation of such other remedies
as may be available to the Holder, the Company will use all reasonable efforts to take such corporate action as may be necessary to increase its authorized and unissued Shares (and any shares of stock to be issued on conversion of such Shares) to a
number of Shares as shall be sufficient for such purposes. 
 3. Replacement of the Warrant. Subject to the receipt of evidence reasonably
satisfactory to the Company of the loss, theft, destruction or mutilation of this Warrant and, in the case of loss, theft or destruction, on delivery of an indemnity agreement reasonably satisfactory in form and substance to the Company or, in the
case of mutilation, on surrender and cancellation of this Warrant, the Company at the expense of the Holder shall execute and deliver, in lieu of this Warrant, a new warrant of like tenor and amount. 

4. Transfer of the Warrant. 
 (a)
Warrant Register. The Company shall maintain a register (the “Warrant Register”) containing the name and address of the Holder. Until this Warrant is transferred on the Warrant Register in accordance herewith, the
Company may treat the Holder as shown on the Warrant Register as the absolute owner of this Warrant for all purposes, notwithstanding any notice to the contrary. Any Holder of this Warrant (or of any portion of this Warrant) may change its address
as shown on the Warrant Register by written notice to the Company requesting a change. 

  
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 (b) Warrant Agent. The Company may appoint an agent for the purpose
of maintaining the Warrant Register referred to in Section 4(a), issuing the Shares or other securities then issuable upon the exercise of the rights under this Warrant, exchanging this Warrant, replacing this Warrant or conducting related
activities. 
 (c) Transferability of the Warrant. Subject to the provisions of this Warrant with
respect to compliance with the Securities Act and limitations on assignments and transfers, including without limitation compliance with the restrictions on transfer set forth in Section 5, title to this Warrant may be transferred by
endorsement (by the transferor and the transferee executing the assignment form attached as Exhibit B (the “Assignment Form”)) and delivery in the same manner as a negotiable instrument transferable by
endorsement and delivery. 
 (d) Exchange of the Warrant upon a Transfer. On surrender of this
Warrant (and a properly endorsed Assignment Form) for exchange, subject to the provisions of this Warrant with respect to compliance with the Securities Act and limitations on assignments and transfers, the Company shall issue to or on the order of
the Holder a new warrant or warrants of like tenor, in the name of the Holder or as the Holder (on payment by the Holder of any applicable transfer taxes) may direct, for the number of shares issuable upon exercise hereof, and the Company shall
register any such transfer upon the Warrant Register. This Warrant (and the securities issuable upon exercise of the rights under this Warrant) must be surrendered to the Company or its warrant or transfer agent, as applicable, as a condition
precedent to the sale, pledge, hypothecation or other transfer of any interest in any of the securities represented hereby, except as provided in Section 5(b). 

(e) Taxes. In no event shall the Company be required to pay any tax which may be payable in respect of any
transfer involved in the issue and delivery of any certificate in a name other than that of the Holder, and the Company shall not be required to issue or deliver any such certificate unless and until the person or persons requesting the issue
thereof shall have paid to the Company the amount of such tax or shall have established to the satisfaction of the Company that such tax has been paid or is not payable. 

5. Restrictions on Transfer of the Warrant and Shares; Compliance with Securities Laws. By acceptance of this Warrant, the Holder agrees to comply with
the following: 
 (a) Restrictions on Transfers. Except as provided in Section 5(b), this Warrant may not
be transferred or assigned in whole or in part without the Company’s prior written consent (which shall not be unreasonably withheld), and any attempt by Holder to transfer or assign any rights, duties or obligations that arise under this
Warrant without such permission shall be void. Any transfer of this Warrant or the Shares issuable upon conversion of this Warrant (the “Securities”) must be in compliance with all applicable federal and
state securities laws. The Holder agrees not to make any sale, assignment, transfer, pledge or other disposition of all or any portion of the Securities, or any beneficial interest therein, unless and until the transferee thereof has agreed in
writing for the benefit of the Company to take and hold such Securities subject to, and to be bound by, the terms and conditions set forth in this Warrant to the same extent as if the transferee were the original Holder hereunder, and 

 (i) there is then in effect a registration statement under the Securities Act covering such proposed disposition and such
disposition is made in accordance with such registration statement, or 
 (ii) (A) such Holder shall have given prior written notice to the
Company of such Holder’s intention to make such disposition and shall have furnished the Company with a detailed description of the manner and circumstances of the proposed disposition, (B) the transferee shall have confirmed to the
satisfaction of the Company in writing, substantially in the form of Exhibit A-1, that the Securities are being acquired (i) solely for the transferee’s own account and not as a nominee for any other party, (ii) for investment and
(iii) not with a view toward distribution or resale, and shall have confirmed such other matters related thereto as may be reasonably requested by the Company, including that the transferee is in compliance with all applicable laws and
(C) such Holder shall have furnished the Company with (i) an opinion of counsel, reasonably satisfactory to the Company, to the effect that such disposition will not require registration of such Securities under the Securities Act or
(ii) a “no action” letter from the Securities and Exchange Commission to the effect that the transfer of such Securities without registration will not result in a recommendation by the staff of the Securities and Exchange Commission
that action be taken with respect thereto, whereupon such Holder shall be entitled to transfer such Securities in accordance with the terms of the notice delivered by the Holder to the Company. 

  
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 (b) Permitted Transfers. Permitted transfers include (i) a
transfer not involving a change in beneficial ownership, (ii) transactions involving the distribution without consideration of Securities by any Holder to (x) a parent, subsidiary or other affiliate of a Holder that is a corporation,
(y) any of the Holder’s partners, members or other equity owners, or retired partners or members, or to the estate of any of its partners, members or other equity owners or retired partners or members, or (z) a venture capital fund
that is controlled by or under common control with one or more general partners or managing members of, or shares the same management company with, the Holder or (iii) transfers to “accredited investors” within the meaning of
Regulation D under the Securities Act; provided, in each of (i)-(iii) above, that the Holder shall give written notice to the Company of the Holder’s intention to
effect such disposition and shall have furnished the Company with a detailed description of the manner and circumstances of the proposed disposition at least five (5) business days prior to the intended transfer, and, in (iii) above, that
(A) the transferee shall have confirmed to the Company in writing, substantially in the form of Exhibit A-1, that the Securities are being acquired (1) solely for the transferee’s own account and not as a nominee for any other
party, (2) for investment and (3) not with a view toward distribution or resale, and shall have confirmed such other matters related thereto as may be reasonably requested by the Company, including that the transferee is in compliance with
all applicable laws and (B) such Holder shall have furnished the Company with (1) an opinion of counsel, reasonably satisfactory to the Company, to the effect that such disposition will not require registration of such Securities under the
Securities Act or (2) a “no action” letter from the Securities and Exchange Commission to the effect that the transfer of such Securities without registration will not result in a recommendation by the staff of the Securities and
Exchange Commission that action be taken with respect thereto, whereupon such Holder shall be entitled to transfer such Securities in accordance with the terms of the notice delivered by the Holder to the Company. 

(c) Investment Representation Statement. Unless the rights under this Warrant are exercised pursuant to an
effective registration statement under the Securities Act that includes the Shares with respect to which the Warrant was exercised, it shall be a condition to any exercise of the rights under this Warrant that the Holder shall have confirmed to the
satisfaction of the Company in writing, substantially in the form of Exhibit A-1, that the Shares so purchased are being acquired solely for the Holder’s own account and not as a nominee for any other
party, for investment and not with a view toward distribution or resale and that the Holder shall have confirmed such other matters related thereto as may be reasonably requested by the Company. 

(d) Securities Law Legend. The Securities shall (unless otherwise permitted by the provisions of this Warrant) be
stamped or imprinted with a legend substantially similar to the following (in addition to any legend required by state securities laws): 

THE SECURITIES REPRESENTED BY THIS CERTIFICATE AND THE SECURITIES INTO WHICH THESE SECURITIES ARE CONVERTIBLE HAVE NOT BEEN REGISTERED UNDER THE SECURITIES
ACT OF 1933, AS AMENDED (THE “ACT”), OR UNDER THE SECURITIES LAWS OF ANY STATES. THESE SECURITIES ARE SUBJECT TO RESTRICTIONS ON TRANSFERABILITY AND RESALE AND MAY NOT BE OFFERED FOR SALE, SOLD, TRANSFERRED OR RESOLD EXCEPT AS PERMITTED
UNDER THE ACT AND APPLICABLE STATE SECURITIES LAWS, PURSUANT TO REGISTRATION OR AN EXEMPTION THEREFROM. HOLDERS SHOULD BE AWARE THAT THEY MAY BE REQUIRED TO BEAR THE FINANCIAL RISKS OF THIS INVESTMENT FOR AN INDEFINITE PERIOD OF TIME. THE ISSUER OF
THESE SECURITIES MAY REQUIRE AN OPINION OF COUNSEL IN FORM AND SUBSTANCE SATISFACTORY TO THE COMPANY TO THE EFFECT THAT ANY PROPOSED TRANSFER OR RESALE IS IN COMPLIANCE WITH THE ACT AND APPLICABLE STATE SECURITIES LAWS. ANY TRANSFEREE OF THIS
CERTIFICATE SHOULD CAREFULLY REVIEW THE TERMS OF THIS SECURITY. THE PRINCIPAL AMOUNT REPRESENTED BY THIS CERTIFICATE AND THE SECURITIES ISSUABLE UPON CONVERSION HEREOF MAY BE LESS THAN THE AMOUNT SET FORTH ON THE FACE HEREOF PURSUANT TO SECTION 2(b)
OF THIS SECURITY. 
 (e) Instructions Regarding Transfer Restrictions. The Holder consents to the Company making
a notation on its records and giving instructions to any transfer agent in order to implement the restrictions on transfer established in this Section 5. 

  
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 (f) Registration Rights Agreement. The Shares issuable upon
conversion of this Warrant are entitled to the benefits of the Registration Rights Agreement, dated June [     ], 2015, among the Company, Brookline Group, LLC and the purchasers identified therein. 

(g) Removal of Legend. The legend referring to federal and state securities laws identified in Section 5(d)
stamped on a certificate evidencing a Warrant or the Shares issuable upon conversion of a Warrant and the stock transfer instructions and record notations with respect to such securities shall be removed and the Company shall issue a certificate
without such legend to the holder of such securities if (i) such securities are registered under the Securities Act, or (ii) such holder provides the Company with an opinion of counsel reasonably acceptable to the Company to the effect
that a sale or transfer of such securities may be made without registration or qualification. 
 6. Adjustments. Subject to the
expiration of this Warrant pursuant to Section 8, the number of Shares purchasable hereunder and the Exercise Price therefor are subject to adjustment from time to time, as follows: 

(a) Merger or Reorganization. If at any time there shall be a Fundamental Transaction (as defined below) involving
the Company (other than as otherwise provided for herein or as would cause the expiration of this Warrant under Section 8) in which shares of the Company’s Common Stock are converted into or exchanged for securities, cash or other
property, then, as a part of such Fundamental Transaction, lawful provision shall be made so that the Holder shall thereafter be entitled to receive upon exercise of this Warrant, the kind and amount of securities, cash or other property of the
successor corporation resulting from such Fundamental Transaction, equivalent in value to that which a holder of the Shares deliverable upon exercise of this Warrant would have been entitled in such Fundamental Transaction if the right to purchase
the Shares hereunder had been exercised immediately prior to such Fundamental Transaction. In any such case, appropriate adjustment (as determined in good faith by the Board of Directors of the successor corporation) shall be made in the application
of the provisions of this Warrant with respect to the rights and interests of the Holder after such Fundamental Transaction to the end that the provisions of this Warrant shall be applicable after the event, as near as reasonably may be, in relation
to any shares or other securities deliverable after that event upon the exercise of this Warrant. For purposes hereof, “Fundamental Transaction” means that (i) the Company, directly or indirectly, in
one or more related transactions effects any merger or consolidation of the Company with or into another person, (ii) the Company, directly or indirectly, effects any sale, lease, license, assignment, transfer, conveyance or other disposition
of all or substantially all of its assets in one or a series of related transactions, (iii) any, direct or indirect, purchase offer, tender offer or exchange offer (whether by the Company or another person) is completed pursuant to which
holders of Common Stock are permitted to sell, tender or exchange their shares for other securities, cash or property and has been accepted by the holders of 50% or more of the outstanding shares of Common Stock, (iv) the Company, directly or
indirectly, in one or more related transactions effects any reclassification, reorganization or recapitalization 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, or (v) the Company, directly or indirectly, in one or more related transactions consummates a stock or share purchase agreement or other business combination (including, without limitation, a reorganization,
recapitalization, spin-off or scheme of arrangement) with another person or group of persons whereby such other person or group acquires more than 50% of the outstanding shares of Common Stock (not including any shares of Common Stock held by the
other person or other persons making or party to, or associated or affiliated with the other persons making or party to, such stock or share purchase agreement or other business combination). 

(b) Reclassification of Shares. If the securities issuable upon exercise of this Warrant are changed into the same
or a different number of securities of any other class or classes by reclassification, capital reorganization, conversion of all outstanding shares of the relevant class or series (other than as would cause the expiration of this Warrant pursuant to
Section 8) or otherwise (other than as otherwise provided for herein) (a “Reclassification”), then, in any such event, in lieu of the number of Shares which the Holder would otherwise have been
entitled to receive, the Holder shall have the right thereafter to exercise this Warrant for a number of shares of such other class or classes of stock that a holder of the number of securities deliverable upon exercise of this Warrant immediately
before that change would have been entitled to receive in such Reclassification, all subject to further adjustment as provided herein with respect to such other shares. 

  
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 (c) Subdivisions and Combinations. In the event that the outstanding
shares of the securities issuable upon exercise of this Warrant are subdivided (by stock split, by payment of a stock dividend or otherwise) into a greater number of shares of such securities, the number of Shares issuable upon exercise of the
rights under this Warrant immediately prior to such subdivision shall, concurrently with the effectiveness of such subdivision, be proportionately increased, and the Exercise Price shall be proportionately decreased, and in the event that the
outstanding shares of the securities issuable upon exercise of this Warrant are combined (by reclassification or otherwise) into a lesser number of shares of such securities, the number of Shares issuable upon exercise of the rights under this
Warrant immediately prior to such combination shall, concurrently with the effectiveness of such combination, be proportionately decreased, and the Exercise Price shall be proportionately increased. 

(d) Redemption. In the event that all of the outstanding shares of the securities issuable upon exercise of this
Warrant are redeemed in accordance with the Company’s certificate of incorporation, this Warrant shall thereafter be exercisable for a number of shares of the Company’s common stock equal to the number of shares of common stock that would
have been received if this Warrant had been exercised in full immediately prior to such redemption and any securities received thereupon had been simultaneously converted into common stock. 

(e) Notice of Adjustments. Upon any adjustment in accordance with this Section 6, the Company shall give
notice thereof to the Holder, which notice shall state the event giving rise to the adjustment, the Exercise Price as adjusted and the number of securities or other property purchasable upon the exercise of the rights under this Warrant, setting
forth in reasonable detail the method of calculation of each. The Company shall, upon the written request of any Holder, furnish or cause to be furnished to such Holder a certificate setting forth (i) such adjustments, (ii) the Exercise
Price at the time in effect and (iii) the number of securities and the amount, if any, of other property that at the time would be received upon exercise of this Warrant. 

7. Notification of Certain Events. Prior to the expiration of this Warrant pursuant to Section 8, in the event that the Company shall authorize:

 (a) the issuance of any dividend or other distribution on the capital stock of the Company (other than (i) dividends or
distributions otherwise provided for in Section 6, (ii) repurchases of common stock issued to or held by employees, officers, directors or consultants of the Company or its subsidiaries upon termination of their employment or services
pursuant to agreements providing for the right of said repurchase; or (iii) repurchases of common stock issued to or held by employees, officers, directors or consultants of the Company or its subsidiaries pursuant to rights of first refusal or
first offer contained in agreements providing for such rights), whether in cash, property, stock or other securities; 
 (b) the voluntary
liquidation, dissolution or winding up of the Company; or 
 (c) any transaction resulting in the expiration of this Warrant pursuant to
Section 8(b) 
 the Company shall send to the Holder of this Warrant at least 10 business days prior written notice of the date on which a record shall
be taken for any such dividend or distribution specified in clause (a) or the expected effective date of any such other event specified in clause (b) or (c), as applicable. The notice provisions set forth in this section may be shortened
or waived prospectively or retrospectively by the consent of the holders of a majority of the Shares issuable upon exercise of the rights under the Warrants. 

8. Expiration of the Warrant. This Warrant shall expire and shall no longer be exercisable as of the earlier of: 

(a) 5:00 p.m., Eastern time, on the date that is three years from the date of this Warrant; 

(b) the acquisition of the Company by another entity by means of any transaction or series of related transactions to which the Company is a
party (including, without limitation, any stock acquisition, reorganization, merger or consolidation, but excluding any sale of stock for capital raising purposes and any transaction effected primarily for purposes of changing the Company’s
jurisdiction of incorporation) other than a transaction or series of related transactions in which the holders of the voting securities of the Company outstanding immediately prior to 

  
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such transaction or series of related transactions retain, immediately after such transaction or series of transactions, as a result of shares in the Company held by such holders prior to such
transaction or series of transactions, at least a majority of the total voting power represented by the outstanding voting securities of the Company or such other surviving or resulting entity (or if the Company or such other surviving or resulting
entity is a wholly-owned subsidiary immediately following such acquisition); or 
 (c) a sale, lease or other disposition of all or
substantially all of the assets of the Company taken as a whole by means of any transaction or series of related transactions, except where such sale, lease or other disposition is to a wholly-owned subsidiary of the Company. 

9. No Rights as a Stockholder. Nothing contained herein shall entitle the Holder to any rights as a stockholder of the Company or to be deemed the
holder of any securities that may at any time be issuable on the exercise of the rights hereunder for any purpose nor shall anything contained herein be construed to confer upon the Holder, as such, any right to vote for the election of directors or
upon any matter submitted to stockholders at any meeting thereof, or to give or withhold consent to any corporate action (whether upon any recapitalization, issuance of stock, reclassification of stock, change of par value or change of stock to no
par value, consolidation, merger, conveyance or otherwise) or to receive notice of meetings, or to receive dividends or subscription rights or any other rights of a stockholder of the Company until the rights under the Warrant shall have been
exercised and the Shares purchasable upon exercise of the rights hereunder shall have become deliverable as provided herein. 
 10. Representations and
Warranties of the Holder. By acceptance of this Warrant, the Holder represents and warrants to the Company as follows: 

(a) No Registration. The Holder understands that the Securities have not been, and will not be, registered under
the Securities Act by reason of a specific exemption from the registration provisions of the Securities Act, the availability of which depends upon, among other things, the bona fide nature of the investment intent
and the accuracy of the Holder’s representations as expressed herein or otherwise made pursuant hereto. 

(b) Investment Intent. The Holder is acquiring the Securities for investment for its own account, not as a nominee
or agent, and not with a view to, or for resale in connection with, any distribution thereof. The Holder has no present intention of selling, granting any participation in, or otherwise distributing the Securities, nor does it have any contract,
undertaking, agreement or arrangement for the same. 
 (c) Investment Experience. The Holder has
substantial experience in evaluating and investing in private placement transactions of securities in companies similar to the Company, and has such knowledge and experience in financial or business matters so that it is capable of evaluating the
merits and risks of its investment in the Company and protecting its own interests. 
 (d) Speculative
Nature of Investment. The Holder understands and acknowledges that the Company has a limited financial and operating history and that its investment in the Company is highly speculative and involves substantial risks. The Holder can bear the
economic risk of its investment and is able, without impairing its financial condition, to hold the Securities for an indefinite period of time and to suffer a complete loss of its investment. 

(e) Access to Data. The Holder has had an opportunity to ask questions of officers of the Company, which questions
were answered to its satisfaction. The Holder believes that it has received all the information that it considers necessary or appropriate for deciding whether to acquire the Securities. The Holder understands that any such discussions, as well as
any information issued by the Company, were intended to describe certain aspects of the Company’s business and prospects, but were not necessarily a thorough or exhaustive description. The Holder acknowledges that any business plans prepared by
the Company have been, and continue to be, subject to change and that any projections included in such business plans or otherwise are necessarily speculative in nature, and it can be expected that some or all of the assumptions underlying the
projections will not materialize or will vary significantly from actual results. 

  
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 (f) Accredited Investor. The Holder represents that it is an
“accredited investor” within the meaning of Regulation D under the Securities Act and agrees to submit to the Company further assurances of such status as may be reasonably requested by the Company. 

(g) Residency. The residency of Holder (or, in the case of a partnership or corporation, such entity’s
principal place of business) is correctly set forth on the signature page hereto. 
 (h) Restrictions on
Resales. The Holder acknowledges that the Securities must be held indefinitely unless subsequently registered under the Securities Act or an exemption from such registration is available. The Holder is aware of the provisions of Rule 144
promulgated under the Securities Act, which permit resale of shares purchased in a private placement subject to the satisfaction of certain conditions, which may include, among other things, the availability of certain current public information
about the Company; the resale occurring not less than a specified period after a party has purchased and paid for the security to be sold; the number of shares being sold during any three-month period not exceeding specified limitations; the sale
being effected through a “broker’s transaction,” a transaction directly with a “market maker” or a “riskless principal transaction” (as those terms are defined in the Securities Act or the Securities Exchange Act
of 1934, as amended, and the rules and regulations promulgated thereunder); and the filing of a Form 144 notice, if applicable. The Holder acknowledges and understands that the Company may not be satisfying the current public information requirement
of Rule 144 at the time the Holder wishes to sell the Securities and that, in such event, the Holder may be precluded from selling the Securities under Rule 144 even if the other applicable requirements of Rule 144 have been satisfied. The Holder
acknowledges that, in the event the applicable requirements of Rule 144 are not met, registration under the Securities Act or an exemption from registration will be required for any disposition of the Securities. The Holder understands that,
although Rule 144 is not exclusive, the Securities and Exchange Commission has expressed its opinion that persons proposing to sell restricted securities received in a private offering other than in a registered offering or pursuant to Rule 144 will
have a substantial burden of proof in establishing that an exemption from registration is available for such offers or sales and that such persons and the brokers who participate in the transactions do so at their own risk. 

(i) Brokers and Finders. The Holder has not engaged any brokers, finders or agents in connection with the
Securities, and the Company has not incurred nor will incur, directly or indirectly, as a result of any action taken by the Holder, any liability for brokerage or finders’ fees or agents’ commissions or any similar charges in connection
with the Securities. 
 (j) Legal Counsel. The Holder has had the opportunity to review this
Warrant, the exhibits and schedules attached hereto and the transactions contemplated by this Warrant with its own legal counsel. The Holder is not relying on any statements or representations of the Company or its agents for legal advice with
respect to this investment or the transactions contemplated by this Warrant. 
 (k) Tax Advisors.
The Holder has reviewed with its own tax advisors the U.S. federal, state and local and non-U.S. tax consequences of this investment and the transactions contemplated by this Warrant. With respect to such matters, the Holder relies solely on
any such advisors and not on any statements or representations of the Company or any of its agents, written or oral. The Holder understands that it (and not the Company) shall be responsible for its own tax liability that may arise as a result of
this investment and the transactions contemplated by this Warrant. 
 11. Miscellaneous. 

(a) Amendments. Except as expressly provided herein, neither this Warrant nor any term hereof may be amended,
waived, discharged or terminated other than by a written instrument referencing this Warrant and signed by the Company and the Holder. 

(b) Waivers. No waiver of any single breach or default shall be deemed a waiver of any other breach or default
theretofore or thereafter occurring. 

  
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 (c) Notices. All notices and other communications required or
permitted hereunder shall be in writing and shall be mailed by registered or certified mail, postage prepaid, sent by facsimile or electronic mail (if to the Holder) or otherwise delivered by hand, messenger or courier service addressed:

 (i) if to the Holder, to the Holder at the Holder’s address, facsimile number or electronic mail address as shown in the
Company’s records, as may be updated in accordance with the provisions hereof, or until any such Holder so furnishes an address, facsimile number or electronic mail address to the Company, then to and at the address, facsimile number or
electronic mail address of the last holder of this Warrant for which the Company has contact information in its records; or 
 (ii) if to
the Company, to the attention of the Chief Executive Officer of the Company at the Company’s address as shown on the signature page hereto, or at such other current address as the Company shall have furnished to the Holder, with a copy to
Natalie Bogdanos, General Counsel & Corporate Secretary, at the same address. 
 Each such notice or other communication shall for all purposes of
this Warrant be treated as effective or having been given (i) if delivered by hand, messenger or courier service, when delivered (or if sent via a nationally-recognized overnight courier service, freight prepaid, specifying next-business-day
delivery, one business day after deposit with the courier), or (ii) if sent by mail, at the earlier of its receipt or five days after the same has been deposited in a regularly maintained receptacle for the deposit of the United States mail,
addressed and mailed as aforesaid, or (iii) if sent via facsimile, upon confirmation of facsimile transfer or, if sent via electronic mail, upon confirmation of delivery when directed to the relevant electronic mail address, if sent during
normal business hours of the recipient, or if not sent during normal business hours of the recipient, then on the recipient’s next business day. In the event of any conflict between the Company’s books and records and this Warrant or any
notice delivered hereunder, the Company’s books and records will control absent fraud or error. 
 (d) Governing
Law. This Warrant and all actions arising out of or in connection with this Warrant shall be governed by and construed in accordance with the laws of the State of Delaware, without regard to the conflicts of law provisions of the State of
Delaware, or of any other state. 
 (e) Jurisdiction and Venue. Each of the Holder and the Company
irrevocably consents to the exclusive jurisdiction of, and venue in, the state courts in the State of Delaware (or in the event of exclusive federal jurisdiction, the federal district courts in the State of Delaware), in connection with any matter
based upon or arising out of this Warrant or the matters contemplated herein, and agrees that process may be served upon them in any manner authorized by the laws of the State of Delaware for such persons. 

(f) Titles and Subtitles. The titles and subtitles used in this Warrant are used for convenience only and are not
to be considered in construing or interpreting this Warrant. All references in this Warrant to sections, paragraphs and exhibits shall, unless otherwise provided, refer to sections and paragraphs hereof and exhibits attached hereto.

 (g) Severability. If any provision of this Warrant becomes or is declared by a court of competent
jurisdiction to be illegal, unenforceable or void, portions of such provision, or such provision in its entirety, to the extent necessary, shall be severed from this Warrant, and such illegal, unenforceable or void provision shall be replaced with a
valid and enforceable provision that will achieve, to the extent possible, the same economic, business and other purposes of the illegal, unenforceable or void provision. The balance of this Warrant shall be enforceable in accordance with its
terms. 
 (h) Waiver of Jury Trial; Judicial Reference. EACH OF THE HOLDER AND THE COMPANY
WAIVES, TO THE FULLEST EXTENT PERMITTED BY LAW, ANY AND ALL RIGHT TO TRIAL BY JURY IN ANY LEGAL PROCEEDING (WHETHER BASED ON CONTRACT, TORT OR OTHERWISE) ARISING OUT OF OR RELATED TO THIS WARRANT. This paragraph shall not restrict the Holder or
the Company from exercising remedies under the Uniform Commercial Code or from exercising pre-judgment remedies under applicable law. 

  
 9 








 (i) Saturdays, Sundays and Holidays. If the last or appointed day for
the taking of any action or the expiration of any right required or granted herein shall be a Saturday, Sunday or U.S. federal holiday, then such action may be taken or such right may be exercised on the next succeeding day that is not a Saturday,
Sunday or U.S. federal holiday. 
 (j) Rights and Obligations Survive Exercise of the Warrant.
Except as otherwise provided herein, the rights and obligations of the Company and the Holder under this Warrant shall survive exercise of this Warrant. 

(k) Entire Agreement. Except as expressly set forth herein, this Warrant (including the exhibits attached hereto),
together with the Securities Purchase Agreement and Registration Rights Agreement, each as defined in the Placement Agency Agreement, by and among the Company, Brookline Group, LLC and M.M. Dillon & Co. Group LLC, dated June
[    ], 2015, constitutes the entire agreement and understanding of the Company and the Holder with respect to the subject matter hereof and supersede all prior agreements and understandings relating to the subject matter
hereof. 
 (signature page follows) 

  
 10 








 The Company and the Holder sign this Warrant as of the date stated on the first page. 

 

			
	CONTRAFECT CORPORATION
		
	By:		  

		
	Name:		
		
	Title:		
		
	Address:		


  

			
	AGREED AND ACKNOWLEDGED,
	
	[                    ]
		
	By:		  

		
	Name:		  

		
	Title:		  

		
	Address:		
		
	Fax number:		
		
	Email address:		

 [Signature Page to Investor Warrant] 







 EXHIBIT A 

NOTICE OF EXERCISE 
  

	TO:	CONTRAFECT CORPORATION (the “Company”) 

 Attention: Chief Executive
Officer 
  

	(1)	Exercise. The undersigned elects to purchase the following pursuant to the terms of the attached warrant: 

  

			
	Number of shares:		  

		
	Type of security:		  


  

	(2)	Method of Exercise. The undersigned elects to exercise the attached warrant pursuant to: 

  

			
	 ̈		A cash payment, and tenders herewith payment of the purchase price for such shares in full, together with all applicable transfer taxes, if any.


  

	(3)	Conditional Exercise. Is this a conditional exercise pursuant to Section 2(d): 

  

							
	 ̈		Yes		 ̈		No


 If “Yes,” indicate the applicable condition: 

 
  
  

 

	(4)	Stock Certificate. Please issue a certificate or certificates representing the shares in the name of: 

  

							
	 ̈				The undersigned		
				
	 ̈				Other—Name:		  

				
					Address:		  


  

	(5)	Unexercised Portion of the Warrant. Please issue a new warrant for the unexercised portion of the attached warrant in the name of: 


 

							
	 ̈				Not applicable		
				
	 ̈				The undersigned		
				
	 ̈				Other—Name:		  

				
					Address:		  


  

	(6)	Investment Intent. The undersigned represents and warrants that the aforesaid shares are being acquired for investment for its own account, not as a nominee or agent, and not with a view to, or for resale in
connection with, the distribution thereof, and that the undersigned has no present intention of selling, granting any participation in, or otherwise distributing the shares, nor does it have any contract, undertaking, agreement or arrangement for
the same, and all representations and warranties of the undersigned set forth in Section 12 of the attached warrant are true and correct as of the date hereof. 


 

	(7)	Investment Representation Statement and Market Stand-Off Agreement. The undersigned has executed, and delivers herewith, and is in substantive agreement with all applicable provisions of an Investment
Representation Statement in a form substantially similar to the form attached to the warrant as Exhibit A-1. 


  
 1 









	(8)	Consent to Receipt of Electronic Notice. Subject to the limitations set forth in Delaware General Corporation Law §232(e), the undersigned consents to the delivery of any notice to stockholders given by the
Company under the Delaware General Corporation Law or the Company’s certificate of incorporation or bylaws by (i) facsimile telecommunication to the facsimile number provided below (or to any other facsimile number for the undersigned in
the Company’s records), (ii) electronic mail to the electronic mail address provided below (or to any other electronic mail address for the undersigned in the Company’s records), (iii) posting on an electronic network together
with separate notice to the undersigned of such specific posting or (iv) any other form of electronic transmission (as defined in the Delaware General Corporation Law) directed to the undersigned. This consent may be revoked by the undersigned
by written notice to the Company and may be deemed revoked in the circumstances specified in Delaware General Corporation Law §232. 

  

	
	  

	(Print name of the warrant holder)
	
	  

	(Signature)
	
	  

	(Name and title of signatory, if applicable)
	
	  

	(Date)
	
	  

	(Fax number)
	
	  

	(Email address)









 EXHIBIT A-1 

INVESTMENT REPRESENTATION STATEMENT 
  

			
	INVESTOR:		AS IDENTIFIED ON THE SIGNATURE PAGE HERETO
		
	COMPANY:		CONTRAFECT CORPORATION
		
	SECURITIES:		THE WARRANT ISSUED ON JUNE [    ], 2015 (THE “WARRANT”) AND THE SECURITIES ISSUED OR ISSUABLE UPON EXERCISE THEREOF
		
	DATE:		  


 In connection with the purchase or acquisition of the above-listed Securities, the undersigned investor (the
“Investor”) represents and warrants to, and agrees with, the Company as follows: 
 1. No Registration. The Investor understands that the
Securities have not been, and will not be, registered under the Securities Act of 1933, as amended (the “Securities Act”), by reason of a specific exemption from the registration provisions of the Securities Act, the
availability of which depends upon, among other things, the bona fide nature of the investment intent and the accuracy of the Investor’s representations as expressed herein or otherwise made pursuant hereto. 

2. Investment Intent. The Investor is acquiring the Securities for investment for its own account, not as a nominee or agent, and not with a view to,
or for resale in connection with, any distribution thereof. The Investor has no present intention of selling, granting any participation in, or otherwise distributing the Securities, nor does it have any contract, undertaking, agreement or
arrangement for the same. 
 3. Investment Experience. The Investor has substantial experience in evaluating and investing in private placement
transactions of securities in companies similar to the Company, and has such knowledge and experience in financial or business matters so that it is capable of evaluating the merits and risks of its investment in the Company and protecting its own
interests. 
 4. Speculative Nature of Investment. The Investor understands and acknowledges that the Company has a limited financial and operating
history and that its investment in the Company is highly speculative and involves substantial risks. The Investor can bear the economic risk of its investment and is able, without impairing its financial condition, to hold the Securities for an
indefinite period of time and to suffer a complete loss of its investment. 
 5. Access to Data. The Investor has had an opportunity to ask questions
of officers of the Company, which questions were answered to its satisfaction. The Investor believes that it has received all the information that it considers necessary or appropriate for deciding whether to acquire the Securities. The Investor
understands that any such discussions, as well as any information issued by the Company, were intended to describe certain aspects of the Company’s business and prospects, but were not necessarily a thorough or exhaustive description. The
Investor acknowledges that any business plans prepared by the Company have been, and continue to be, subject to change and that any projections included in such business plans or otherwise are necessarily speculative in nature, and it can be
expected that some or all of the assumptions underlying the projections will not materialize or will vary significantly from actual results. 
 6.
Accredited Investor. The Investor represents that it is an “accredited investor” within the meaning of Regulation D under the Securities Act and agrees to submit to the Company further assurances of such status as may be reasonably
requested by the Company. 
 7. Residency. The residency of the Investor (or, in the case of a partnership or corporation, such entity’s
principal place of business) is correctly set forth on the signature page hereto. 

  
 1 








 8. Restrictions on Resales. The Investor acknowledges that the Securities must be held indefinitely unless
subsequently registered under the Securities Act or an exemption from such registration is available. The Investor is aware of the provisions of Rule 144 promulgated under the Securities Act, which permit resale of shares purchased in a private
placement subject to the satisfaction of certain conditions, which may include, among other things, the availability of certain current public information about the Company; the resale occurring not less than a specified period after a party has
purchased and paid for the security to be sold; the number of shares being sold during any three-month period not exceeding specified limitations; the sale being effected through a “broker’s transaction,” a transaction directly with a
“market maker” or a “riskless principal transaction” (as those terms are defined in the Securities Act or the Securities Exchange Act of 1934, as amended, and the rules and regulations promulgated thereunder); and the filing of a
Form 144 notice, if applicable. The Investor acknowledges and understands that the Company may not be satisfying the current public information requirement of Rule 144 at the time the Investor wishes to sell the Securities and that, in such event,
the Investor may be precluded from selling the Securities under Rule 144 even if the other applicable requirements of Rule 144 have been satisfied. The Investor understands and acknowledges that, in the event the applicable requirements of Rule 144
are not met, registration under the Securities Act or an exemption from registration will be required for any disposition of the Securities. The Investor understands that, although Rule 144 is not exclusive, the Securities and Exchange Commission
has expressed its opinion that persons proposing to sell restricted securities received in a private offering other than in a registered offering or pursuant to Rule 144 will have a substantial burden of proof in establishing that an exemption from
registration is available for those offers or sales and that those persons and the brokers who participate in the transactions do so at their own risk. 

9. Brokers and Finders. The Investor has not engaged any brokers, finders or agents in connection with the Securities, and the Company has not incurred
nor will incur, directly or indirectly, as a result of any action taken by the Investor, any liability for brokerage or finders’ fees or agents’ commissions or any similar charges in connection with the Securities. 

10. Legal Counsel. The Investor has had the opportunity to review the Warrant, the exhibits and schedules attached thereto and the transactions
contemplated by the Warrant with its own legal counsel. The Investor is not relying on any statements or representations of the Company or its agents for legal advice with respect to this investment or the transactions contemplated by the Warrant.

 11. Tax Advisors. The Investor has reviewed with its own tax advisors the U.S. federal, state and local and non-U.S. tax consequences of this
investment and the transactions contemplated by the Warrant. With respect to such matters, the Investor relies solely on such advisors and not on any statements or representations of the Company or any of its agents, written or oral. The Investor
understands that it (and not the Company) shall be responsible for its own tax liability that may arise as a result of this investment or the transactions contemplated by the Warrant. 

(signature page follows) 







 The Investor is signing this Investment Representation Statement on the date first written above. 

 

	
	INVESTOR
	
	  

	(Print name of the investor)
	
	  

	(Signature)
	
	  

	(Name and title of signatory, if applicable)
	
	  

	(Street address)
	
	  

	(City, state and ZIP)


 [Signature Page to Investment Representation Statement] 







 EXHIBIT B 

ASSIGNMENT FORM 
  

					
	ASSIGNOR:		AS IDENTIFIED ON THE SIGNATURE PAGE HERETO
		
	COMPANY:		CONTRAFECT CORPORATION
		
	WARRANT:		THE WARRANT TO PURCHASE SHARES OF COMMON STOCK ISSUED ON JUNE [    ], 2015 (THE “WARRANT”)
			
	DATE:		  
		

  

	(1)	Assignment. The undersigned registered holder of the Warrant (“Assignor”) assigns and transfers to the assignee named below (“Assignee”) all of the rights of
Assignor under the Warrant, with respect to the number of shares set forth below: 

  

					
	Name of Assignee:		  
		
			
	Address of Assignee:		  
		
			
			  
		
			
	Number of Shares Assigned:		  
		

 and does irrevocably constitute and appoint
[                    ] as attorney to make such transfer on the books of ContraFect Corporation, maintained for the purpose, with full power of
substitution in the premises. 
  

	(2)	Obligations of Assignee. Assignee agrees to take and hold the Warrant and any shares of stock to be issued upon exercise of the rights thereunder (and any shares issuable upon conversion thereof) (the
“Securities”) subject to, and to be bound by, the terms and conditions set forth in the Warrant to the same extent as if Assignee were the original holder thereof. 


 

	(3)	Investment Intent. Assignee represents and warrants that the Securities are being acquired for investment for its own account, not as a nominee or agent, and not with a view to, or for resale in connection
with, the distribution thereof, and that Assignee has no present intention of selling, granting any participation in, or otherwise distributing the shares, nor does it have any contract, undertaking, agreement or arrangement for the same, and all
representations and warranties set forth in Section 10 of the Warrant are true and correct as to Assignee as of the date hereof. 

  

	(4)	Investment Representation Statement. Assignee has executed, and delivers herewith, and is in substantive agreement with all applicable provisions of, an Investment Representation Statement in a form
substantially similar to the form attached to the Warrant as Exhibit A-1. 








 Assignor and Assignee are signing this Assignment Form on the date first set forth above. 

 

					
	ASSIGNOR				ASSIGNEE
			
	  
				  

	(Print name of Assignor)				(Print name of Assignee)
			
	  
				  

	(Signature of Assignor)				(Signature of Assignee)
			
	  
				  

	(Print name of signatory, if applicable)				(Print name of signatory, if applicable)
			
	  
				  

	(Print title of signatory, if applicable)				(Print title of signatory, if applicable)
			
	Address:				Address: