EX-4.6



 Exhibit 4.6 

THIS WARRANT AND THE SHARES ISSUABLE HEREUNDER HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED, AND MAY NOT BE SOLD, PLEDGED OR
OTHERWISE TRANSFERRED EXCEPT IN ACCORDANCE WITH APPLICABLE LAW. 
 WARRANT TO PURCHASE STOCK 

 

			
	Corporation:	  	EVELO BIOSCIENCES, INC.
	Number of Shares:	  	See Section 1.7
	Class of Stock:	  	Series A-3 Preferred Stock
	Initial Exercise Price:	  	$1.20 per share
	Issue Date:	  	August 15, 2016
	Expiration Date:	  	August 15, 2026

 THIS WARRANT CERTIFIES THAT, for good and
valuable consideration, the receipt of which is hereby acknowledged, PACIFIC WESTERN BANK or its permitted assignee (“Holder”) is entitled to purchase the
number of fully paid and nonassessable shares of the class of securities (the “Shares”) of EVELO BIOSCIENCES, INC. (the “Company”) at the initial
exercise price per Share (the “Warrant Price”) all as set forth above and as adjusted pursuant to Article 2 of this warrant, subject to the provisions and upon the terms and conditions set forth in this warrant. 

ARTICLE 1 
 EXERCISE

 1.1    Method of Exercise. Holder may exercise this warrant by delivering this warrant and a duly
executed Notice of Exercise in substantially the form attached as Appendix 1 to the principal office of the Company. Unless Holder is exercising the conversion right set forth in Section 1.2, Holder shall also deliver to the Company a check for
the aggregate Warrant Price for the Shares being purchased. 
 1.2    Conversion Right. In lieu of
exercising this warrant as specified in Section 1.1, Holder may from time to time convert this warrant, in whole or in part, into a number of Shares determined by dividing (a) the aggregate fair market value of the Shares or other
securities otherwise issuable upon exercise of this warrant minus the aggregate Warrant Price of such Shares by (b) the fair market value of one Share. The fair market value of the Shares shall be determined pursuant to Section 1.3. In
connection with each such conversion, or other exercise of this Warrant pursuant to Section 1.1, Holder shall be deemed to have restated each of the representations and warranties in Section 3.5 of this Warrant as of the date thereof. 

1.3    Fair Market Value. If the Shares are traded regularly in a public market, the fair market value of
the Shares shall be the closing price of the Shares (or the closing price of the Company’s stock into which the Shares are convertible) reported for the business day immediately before Holder delivers its Notice of Exercise to the Company. If
the Shares are not regularly traded in a public market, the Board of Directors of the Company shall determine fair market value in its reasonable good faith judgment. 







 1.4    Delivery of Certificate and New Warrant. Promptly after
Holder exercises or converts this warrant, the Company shall deliver to Holder certificates for the Shares acquired and, if this warrant has not been fully exercised or converted and has not expired, a new warrant representing the Shares not so
acquired. 
 1.5    Replacement of Warrants. On receipt of evidence reasonably satisfactory to the Company
of the loss, theft, destruction or mutilation of this warrant and, in the case of loss, theft or destruction, on delivery of an indemnity agreement reasonably satisfactory in form and amount to the Company or, in the case of mutilation, on surrender
and cancellation of this warrant, the Company at its expense shall execute and deliver, in lieu of this warrant, a new warrant of like tenor. 

1.6    Treatment of Warrant Upon Acquisition of the Company. 

1.6.1    “Acquisition.” For the purpose of this warrant, “Acquisition”
means (a) any sale, exclusive license, or other disposition of all or substantially all of the assets (including intellectual property) of the Company, or (b) any reorganization, consolidation, merger or sale of the voting securities of
the Company (other than a merger or consolidation effective exclusively to change the Company’s domicile) or other transaction, in each case, where the holders of the Company’s securities before the transaction beneficially own less than
50% of the outstanding voting securities of the surviving entity after the transaction. 
 1.6.2    Exercise
Upon Acquisition. Upon the closing of any Acquisition in which the consideration to be received by the Company’s stockholders consists of cash, marketable securities, or a combination of both cash and marketable securities, this warrant
shall be deemed to have been automatically converted pursuant to Section 1.2 immediately prior to such Acquisition, and thereafter Holder shall participate in the Acquisition on the same terms as other holders of the same class of securities of
the Company, provided, however, that if the fair market value of the Shares, as determined pursuant to Section 1.3, in connection with such Acquisition is less than the aggregate Warrant Price, then this warrant shall terminate without exercise
or conversion immediately prior, and subject, to the closing of such Acquisition. 
 1.6.3    Assumption of
Warrant. Upon the closing of any Acquisition not referred to in Section 1.6.2, the successor entity shall assume the obligations of this warrant, and this warrant shall thereafter be exercisable for the same securities and/or other property
as would have been paid for the Shares issuable upon exercise of the unexercised portion of this warrant as if such Shares were outstanding on and as of the closing of such Acquisition, subject to further adjustment from time to time in accordance
with the provisions of this warrant. 
 1.7    Number of Shares. The Number of Shares for which this
Warrant shall be exercisable shall be equal to the lesser of (I) (a) one and one quarter of one percent (1.25%) of the principal amount of all Tranche A Term Loans (as defined in that certain Loan and Security Agreement by and among the Company
and Pacific Western Bank dated as of the date hereof) made by Pacific Western Bank to the Company in excess of $7,000,000 (which amount shall not exceed $3,000,000) divided by (b) the Warrant Price (subject to adjustment as set forth in
Section 2) or (II) 31,248 shares. 

  
 2. 








 ARTICLE 2 

ADJUSTMENTS TO THE SHARES 

2.1    Stock Dividends, Splits, Etc. If the Company declares or pays a dividend on its common stock payable
in common stock, or other securities, or subdivides the outstanding common stock into a greater amount of common stock, then upon exercise of this warrant, for each Share acquired, Holder shall receive, without cost to Holder, the total number and
kind of securities to which Holder would have been entitled had Holder owned the Shares of record as of the date the dividend or subdivision occurred. 

2.2    Reclassification, Exchange or Substitution. Upon any reclassification, exchange, substitution, or
other event that results in a change of the number and/or class of the securities issuable upon exercise or conversion of this warrant, Holder shall be entitled to receive, upon exercise or conversion of this warrant, the number and kind of
securities and property that Holder would have received for the Shares if this warrant had been exercised immediately before such reclassification, exchange, substitution, or other event. Such an event shall include any automatic conversion of the
outstanding or issuable securities of the Company of the same class or series as the Shares to common stock pursuant to the terms of the Company’s Amended and Restated Certificate of Incorporation upon the closing of a registered public
offering of the Company’s common stock. The Company or its successor shall promptly issue to Holder a new warrant for such new securities or other property. The new warrant shall provide for adjustments which shall be as nearly equivalent as
may be practicable to the adjustments provided for in this Article 2 including, without limitation, adjustments to the Warrant Price and to the number of securities or property issuable upon exercise of the new warrant. The provisions of this
Section 2.2 shall similarly apply to successive reclassifications, exchanges, substitutions, or other events. 

2.3    Adjustments for Combinations, Etc. If the outstanding Shares are combined or consolidated, by
reclassification or otherwise, into a lesser number of shares, the Warrant Price shall be proportionately increased. If the outstanding Shares are combined or consolidated, by reclassification or otherwise, into a greater number of shares, the
Warrant Price shall be proportionately decreased. 
 2.4    Adjustments for Diluting Issuances. In the
event of the issuance (a “Diluting Issuance”) by the Company after the Issue Date of securities at a price per share less than the Warrant Price, then the number of shares of common stock issuable upon conversion of the
Shares shall be adjusted in accordance with those provisions of the Company’s Articles (Certificate) of Incorporation that apply to Diluting Issuances. 

2.5    Certificate as to Adjustments. Upon each adjustment of the Warrant Price, the Company at its expense
shall promptly compute such adjustment, and furnish Holder with a certificate of its Chief Financial Officer setting forth such adjustment and the facts upon which such adjustment is based. The Company shall, upon written request, furnish Holder a
certificate setting forth the Warrant Price in effect upon the date thereof and the series of adjustments leading to such Warrant Price. 

  
 3. 








 2.6    Fractional Shares. No fractional Shares shall be
issuable upon exercise or conversion of the Warrant and the Number of Shares to be issued shall be rounded down to the nearest whole Share. If a fractional share interest arises upon any exercise or conversion of the Warrant, the Company shall
eliminate such fractional share interest by paying Holder the amount computed by multiplying the fractional interest by the fair market value of a full Share. 

ARTICLE 3 

REPRESENTATIONS AND COVENANTS OF THE COMPANY AND OF THE HOLDER 

3.1    Representations and Warranties of the Company. The Company hereby represents and warrants to the
Holder as follows: 
 (a)    The initial Warrant Price referenced on the first page of this warrant is not
greater than the fair market value of the Shares as of the date of this warrant. 
 (b)    All Shares which may
be issued upon the exercise of the purchase right represented by this Warrant in accordance with this Warrant, and all securities, if any, issuable upon conversion of the Shares in accordance with the Company’s Amended and Restated Certificate
of Incorporation, shall, upon issuance, be duly authorized, validly issued, fully paid and nonassessable, and free of any liens and encumbrances except for restrictions on transfer provided for herein or under applicable federal and state securities
laws. 
 (c)    The Company’s capitalization table attached to this warrant is true and complete as of the
Issue Date. 
 3.2    Notice of Certain Events. The Company shall provide Holder with not less than 10
days prior written notice of, including a description of the material facts surrounding, any of the following events: (a) declaration of any dividend or distribution upon its common stock, whether in cash, property, stock, or other securities
and whether or not a regular cash dividend; (b) offering for subscription pro rata to the holders of any class or series of its stock any additional shares of stock of any class or series or other rights; (c) effecting any reclassification
or recapitalization of common stock; or (d) the merger or consolidation with or into any other corporation, or sale, lease, license, or conveyance of all or substantially all of its assets, or liquidation, dissolution or winding up. 

3.3    Information Rights. Prior to an initial public offering of the Company’s common stock and
provided Holder holds this warrant and/or any of the Shares, the Company shall deliver to the Holder the financial information required to be delivered to Major Investors (as defined in the IRA) under Section 3.1(a) and 3.1(b) pursuant to that
certain Investors Rights Agreement dated as of June 16, 2016 by and among the Company and the investors named therein (the “IRA”). 

3.4    Registration Under Securities Act of 1933, as amended. The Company agrees that the Shares or, if the
Shares are convertible into common stock of the Company, such common stock, shall be “Registrable Securities”, and Holder shall be a “Holder” under the IRA. 

  
 4. 








 3.5    Holder Investment Representations. Holder makes the
representations to the Company set forth in Exhibit A hereof in connection with the issuance of this warrant and the Shares (collectively, the “Securities”). 

3.6    Market Stand Off. Holder agrees that it shall be subject to the Market Standoff provisions in
Section 2.11 of the IRA. 
 3.7    Company Agreements. If upon exercise of this warrant (other than
in connection with an Acquisition or an initial public offering of the Company’s common stock) Holder continues to hold the Shares, upon the request of the Company, Holder shall execute a counterpart signature page to the investor and
stockholder agreements governing the rights and obligations in respect to the Company’s Series A-3 Preferred Stock. 

ARTICLE 4 

MISCELLANEOUS 

4.1    Term: Exercise Upon Expiration. This warrant is exercisable in whole or in part, at any time and from
time to time on or before the Expiration Date set forth above. If this warrant has not been exercised prior to the Expiration Date, this warrant shall be deemed to have been automatically exercised on the Expiration Date by “cashless”
conversion pursuant to Section 1.2. 
 4.2    Legends. This warrant and the Shares (and the
securities issuable, directly or indirectly, upon conversion of the Shares, if any) shall be imprinted with a legend in substantially the following form: 

THIS SECURITY HAS NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED, AND MAY NOT BE SOLD, PLEDGED OR OTHERWISE TRANSFERRED EXCEPT IN ACCORDANCE
WITH APPLICABLE LAW. 
 4.3    Compliance with Securities Laws on Transfer. This warrant and the Shares
issuable upon exercise of this warrant (and the securities issuable, directly or indirectly, upon conversion of the Shares, if any) may not be transferred or assigned in whole or in part without compliance with applicable federal and state
securities laws by the transferor and the transferee. The Company shall not require Holder to provide an opinion of counsel if the transfer is to an affiliate of Holder or if there is no material question as to the availability of current
information as referenced in Rule 144(c), Holder represents that it has complied with Rule 144 (d) and (e) in reasonable detail, the selling broker represents that it has complied with Rule 144(f), and the Company is provided with a copy of
Holder’s notice of proposed sale. 
 4.4    Transfer Procedure. Subject to the provisions of
Section 4.3, Holder may transfer all or part of this warrant or the Shares issuable upon exercise of this warrant (or the securities issuable, directly or indirectly, upon conversion of the Shares, if any) by giving the Company notice of the
portion of the warrant being transferred setting forth the name, address and taxpayer identification number of the transferee and surrendering this warrant to the Company for reissuance to the transferee(s) (and Holder, if applicable). No surrender
or reissuance shall be required for a transfer to an affiliate of Holder. 

  
 5. 








 4.5    Notices. All notices and other communications from the
Company to the Holder, or vice versa, shall be deemed delivered and effective when given personally or mailed by first-class registered or certified mail, postage prepaid, at such address as may have been furnished to the Company or the Holder, as
the case may be, in writing by the Company or such Holder from time to time. All notices to the Holder shall be addressed as follows: 

Pacific Western Bank 
 Attn:
Warrant Administrator 
 406 Blackwell Street, Suite 240 

Durham, NC 27701 
 All notices to
the Company shall be addressed as follows: 
 EVELO BIOSCIENCES, INC. 

620 Memorial Drive, Suite 208 

Cambridge, MA 02139 
 Attn: Chief
Executive Officer 
 FAX:
                                         

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

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

4.8    Governing Law. This warrant shall be governed by and construed in accordance with the laws of the
State of Delaware, without giving effect to its principles regarding conflicts of law that would result in the application of the laws of any other jurisdiction. 

[Signature Page Follows] 

  
 6. 








 IN WITNESS WHEREOF, the undersigned has executed this Warrant to Purchase Stock as of the date set forth above.

  

			
	EVELO BIOSCIENCES, INC.
		
	By:	 	 /s/ Jennifer
Glennon                                        


	Name:	 	Jennifer Glennon
	Title:	 	Assistant Secretary


  

			
	Acknowledged and agreed:
	
	PACIFIC WESTERN BANK
		
	By:	 	 /s/ John
Orlando                                        


	Name:	 	John Orlando
	Title:	 	Vice President








 [Signature Page to Warrant to Purchase Stock] 

  
 2. 








 APPENDIX 1 

NOTICE OF EXERCISE 

1.    The undersigned hereby elects to purchase
                 shares of the                      stock of EVELO
BIOSCIENCES, INC. pursuant to the terms of the attached warrant, and tenders herewith payment of the purchase price of such shares in full. 

1.    The undersigned hereby elects to convert the attached warrant into shares in the manner specified in the
warrant. This conversion is exercised with respect to                  of the shares covered by the warrant. 

[Strike paragraph that does not apply.] 

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

	
	  

(Holder’s Name)

	
	  

	
	  
 (Address)


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

	
	PACIFIC WESTERN BANK or Registered Assignee
	
	  
 (Signature)

	
	  
 (Date)









 EXHIBIT A 

INVESTMENT REPRESENTATIONS 

(a)    Holder is aware of the Company’s business affairs and financial condition, and has acquired sufficient information about the
Company to reach an informed and knowledgeable decision to acquire the Securities. Holder is purchasing the Securities for its own account for investment purposes only, not as a nominee or agent, and not with a view towards, or for resale in
connection with, any “distribution” thereof for purposes of the Securities Act of 1933, as amended (the “Securities Act”). Holder has such knowledge and experience in financial business matters and Holder is capable of evaluating
the merits and risks of the purchase of the Securities and of protecting its interests in connection therewith. 
 (b)    Holder
understands that the Securities have not been registered under the Securities Act in reliance upon a specific exemption therefrom, which exemption depends upon, among other things, the bona fide nature of Holder’s investment intent as expressed
herein. 
 (c)    Holder further understands that the Securities must be held indefinitely, and Holder must therefore bear the economic
risk therewith, unless the Securities are subsequently registered under the Securities Act or unless an exemption from registration is otherwise available. In addition, Holder understands that the certificate evidencing the Securities will be
imprinted with a legend which prohibits the transfer of the Securities unless they are registered or such registration is not required. 

(d)    Holder is familiar with the provisions of Rule 144, promulgated pursuant to the Securities Act, which, in substance, permits
limited public resale of “restricted securities” acquired, directly or indirectly, from the issuer thereof, in a non-public offering subject to the satisfaction of certain conditions. 

(e)    The Securities may be resold in certain limited circumstances subject to the provisions of Rule 144, which requires, among other
things, the existence of a public market for the Securities, the availability of certain current public information about the Company, the resale occurring not less than one year after a party has purchased and paid for the security to be sold, the
sales being effected through a “broker’s transaction” or in transactions directly with a “market maker” and the number of securities being sold during any three-month period not exceeding specified limitations. 

(f)    Holder further understands that in the event that all of the applicable requirements of Rule 144 are not satisfied, registration
under the Securities Act, compliance with Regulation A, or some other registration exemption will be required. 
 (g)    Holder is an
“accredited investor” as defined in Rule 501(a) of Regulation D promulgated under the Securities Act.