Document:

EX-10.3

 Exhibit 10.3 

RIGHTS AGREEMENT 
 This
Rights Agreement (this “Agreement”) is made this 17th day of June, 2014, by and between Cleveland BioLabs, Inc., a Delaware corporation (“CBLI”), Mikhail Mogutov, an individual (“Mogutov”), and
certain other purchasers (the “Additional Purchasers” and, together with Mogutov, the “Purchasers”). 
 WHEREAS,
the parties entered into a Securities Purchase Agreement, dated as of June 17, 2014 (the “Securities Purchase Agreement”), with respect to the purchase and sale of the Company’s common stock, par value $0.005 (the
“Common Stock”) and warrants; and 
 WHEREAS, the parties have agreed that the Purchasers shall have certain rights with
respect to its Common Stock of the Company. 
 NOW, THEREFORE, in consideration of the foregoing and the mutual agreements and covenants
hereinafter set forth, and for other good and valuable consideration, the receipt and sufficiency of which are hereby acknowledged, CBLI and the Purchasers agree as follows: 
  

	1.	Definitions. For purposes of this Agreement: 

 1.1 “2015 Annual
Meeting” means the Company’s 2015 annual meeting of stockholders. 
 1.2 “Affiliate” means any Person
that, directly or indirectly through one or more intermediaries, controls or is controlled by or is under common control with a Person, as such terms are used in and construed under Rule 405 under the Securities Act. 

1.3 “Mogutov Director” shall mean any director designated by Mogutov in accordance with Section 2.1. 

1.4 “Board” means the Company’s Board of Directors. 

1.5 “Common Stock” shall have the meaning assigned to such term in the recitals. 

1.6 “Closing” shall have the meaning set forth in the Securities Purchase Agreement. 

1.7 “Securities Act” means the Securities Act of 1933, as amended, and the rules and regulations promulgated
thereunder. 
 1.8 “Securities Purchase Agreement” shall have the meaning assigned to such term in the recitals.

 1.9 “Termination Date” shall have the meaning assigned to such term in Section 3.1. 

1.10 “Transfer” shall mean to directly or indirectly assign, sell, offer to sell, gift, pledge, mortgage, hypothecate,
encumber, dispose or in any other manner transfer or encumber, whether voluntarily, involuntarily, or by operation of law. 

	2.	Board Representation. 

 2.1 Board Designee. Effective immediately after
the Closing until the Termination Date, in addition to any other rights Mogutov may have as a stockholder of the Company, Mogutov shall have the right, following consultation with the Company, to designate one (1) director (the “Mogutov
Director”) for nomination for election to the Company’s Board. Subject to applicable law, the Company’s bylaws and the fiduciary duties of the Board, the Company agrees to use its reasonable best efforts (i) to cause the
appointment of the Mogutov Director to the Board as soon as practicably possible upon receipt of a designation notice from Mogutov to fill a vacancy on the Board and, if no vacancy exists, to increase the size of the Board to create such a vacancy,
and (ii) to cause the election of the Mogutov Director to the Board at its 2015 Annual Meeting and each annual or special meeting at which directors are elected until the Termination Date, including by (x) nominating and recommending such
individual to be elected as a director of the Company, (y) including such nomination and other required information regarding such individual in the Company’s proxy statement, and (z) soliciting proxies in connection with the election
of such individual as a director of the Company. 
 2.2 Vacancies. For so long as Mogutov has the right to designate the
Mogutov Director for nomination for election to the Board pursuant to Section 2.1, in the event that a vacancy is created at any time by (i) the death, disability, retirement, resignation or removal (with or without cause) of the Mogutov
Director or (ii) the failure of the Company’s stockholders at any annual or special meeting of the Company’s stockholders to elect the Mogutov Director resulting in a vacancy, Mogutov shall have the right to designate a replacement to
fill such vacancy, and the Company, subject to applicable law, the bylaws and the fiduciary duties of the Board, shall use its reasonable best efforts to take all necessary or desirable actions as may be required under applicable law to cause the
individual designated by Mogutov to be appointed or elected without delay. 
 2.3 Removal. For so long as Mogutov has the
right to designate the Mogutov Director for nomination for the election to the Board pursuant to this Agreement, the Company shall not take any action to cause the removal of the Mogutov Director without cause. If the Company is directed by Mogutov
to remove the Mogutov Director, the Company shall use its reasonable best efforts to take all necessary or desirable actions to effect such removal and to elect a replacement without delay as designated by Mogutov in accordance with Section 2.1
or Section 2.2, as applicable. 
 2.4 Exclusion. The Company may exclude the Mogutov Director from meetings of the Board
or its committees if (i) attendance would violate any applicable securities laws or listing requirements or (ii) the Board reasonably determines that such exclusion is necessary with respect to any matter in which such director holds any
interest adverse to the Company or its subsidiaries. 
 2.5 Adherence to Company Policy and Board Fees. Mogutov hereby agrees
to cause any director designated by it to be bound by and comply with the Company’s confidentiality, trading windows and blackout policies applicable to directors, as in effect from time to time. 

 2.6 Additional Board Designees. (i) If at any time and only during such time
when the total number of directors appointed to the Company’s Board exceeds ten (10) members, provided that and for so long as Mogutov and his Affiliates hold in the aggregate more than ten percent (10%) of the issued and outstanding
Common Stock of the Company, Mogutov shall have the right to designate one (1) additional director, or, (ii) if at any time and only during such time when the total number of directors appointed to the Company’s Board exceeds
twenty-one (21) members, provided that and for so long as Mogutov and his Affiliates hold in the aggregate more than twenty percent (20%) of the issued and outstanding Common Stock of the Company, Mogutov shall have the right to designate
two (2) additional directors (collectively, the “Additional Mogutov Directors”) and the provisions of this Agreement shall be applicable, mutatis mutandis, to the Additional Mogutov Directors. Notwithstanding the
foregoing, Mogutov shall not have the right to designate Additional Directors if such designation would violate the rules and regulations of the NASDAQ Stock Market. 
  

	3.	Miscellaneous. 

 3.1 Termination. This Agreement shall terminate at such
time when Mogutov and his Affiliates no longer hold in the aggregate more than three percent (3%) of the issued and outstanding Common Stock of the Company, provided, however that Section 3.2 herein shall survive the termination
(i) as to Mogutov, for so long as Mogutov and his Affiliates hold any securities of the Company and (ii) as to the Additional Purchasers, for so long as the Additional Purchasers and their Affiliates hold any securities of the Company.

 3.2 Information Rights. Upon three (3) business days prior request of a Purchaser, the Company shall permit a
representative of the Purchaser (the “Auditor”) to visit and inspect any of the Company’s property, corporate books, and financial records, to examine and make copies of the Company’s books of accounts and other financial
records, and to discuss the Company’s affairs, finances, and accounts with, and to be advised as to the same by, its managers, officers, employees and independent public accountants (and by this provision the Company hereby authorizes such
Auditor to discuss with such accountants the finances and affairs of the Company). In addition, upon request, the Company shall provide the Purchaser with a status update of any material development in any litigations or any administrative or
arbitration proceeding, if any. Any document provided by the Company under this Section may be provided by electronic means. Prior to providing any information to the Auditor that the Company believes is or may be material non-public information,
the Company shall so inform the Auditor and allow the Auditor to decline to see any such information. If the Auditor does not decline, prior to delivering such information to the Purchaser, the Company and such Purchaser shall have entered into a
customary written agreement with the Company regarding the confidentiality and use of such information. 
 3.3 Amendments;
Waivers. No provision of this Agreement may be waived, modified, supplemented or amended except in a written instrument signed, in the case of an amendment, by the Company and the Purchasers, provided that the consent of a Purchaser shall not be
required for any amendment or waiver if such amendment or waiver is not directly applicable to the rights of such Purchaser hereunder. No waiver of any default with respect to any provision, condition or requirement of this Agreement shall be deemed
to be a continuing 

 
waiver in the future or a waiver of any subsequent default or a waiver of any other provision, condition or requirement hereof, nor shall any delay or omission of any party to exercise any right
hereunder in any manner impair the exercise of any such right. 
 3.4 Headings. The headings herein are for convenience only,
do not constitute a part of this Agreement and shall not be deemed to limit or affect any of the provisions hereof. 
 3.5
Successors and Assigns. This Agreement shall be binding upon and inure to the benefit of the parties and their successors and permitted assigns. Neither the Company nor the Purchasers may assign this Agreement or any rights or obligations
hereunder without the prior written consent of each non-assigning party. 
 3.6 Third-Party Beneficiaries. This Agreement is
intended for the benefit of the parties hereto and their respective successors and permitted assigns and is not for the benefit of, nor may any provision hereof be enforced by, any other person. 

3.7 Governing Law. All questions concerning the construction, validity, enforcement and interpretation of this Agreement shall
be governed by and construed and enforced in accordance with the internal laws of the State of New York, without regard to the principles of conflicts of law thereof. Each party agrees that all legal proceedings concerning the interpretations,
enforcement and defense of the transactions contemplated by this Agreement (whether brought against a party hereto or its respective affiliates, directors, officers, shareholders, partners, members, employees or agents) shall be commenced
exclusively in the state and federal courts sitting in the City of New York. Each party hereby irrevocably submits to the exclusive jurisdiction of the state and federal courts sitting in the City of New York, Borough of Manhattan for the
adjudication of any dispute hereunder or in connection herewith or with any transaction contemplated hereby or discussed herein, and hereby irrevocably waives, and agrees not to assert in any suit, action or proceeding, any claim that it is not
personally subject to the jurisdiction of any such court, that such suit, action or proceeding is improper or is an inconvenient venue for such proceeding. Each party hereby irrevocably waives personal service of process and consents to process
being served in any such suit, action or proceeding by mailing a copy thereof via registered or certified mail or overnight delivery (with evidence of delivery) to such party at the address in effect for notices to it under this Agreement and agrees
that such service shall constitute good and sufficient service of process and notice thereof. Nothing contained herein shall be deemed to limit in any way any right to serve process in any other manner permitted by law. If either party shall
commence an action, suit or proceeding to enforce any provisions of this Agreement, then the prevailing party in such action, suit or proceeding shall be reimbursed by the other party for its reasonable attorneys’ fees and other costs and
expenses incurred with the investigation, preparation and prosecution of such action or proceeding. 
 3.8 Execution. This
Agreement may be executed in two or more counterparts, all of which when taken together shall be considered one and the same agreement and shall become effective when counterparts have been signed by each party and delivered to each other party, it
being understood that the parties need not sign the same counterpart. In the event that any signature is delivered by facsimile transmission or by e-mail delivery of a “.pdf” format data file, such signature shall create a valid and
binding obligation of the party executing (or on whose behalf such signature is executed) with the same force and effect as if such facsimile or “.pdf” signature page were an original thereof. 

 3.9 Severability. If any term, provision, covenant or restriction of this Agreement
is held by a court of competent jurisdiction to be invalid, illegal, void or unenforceable, the remainder of the terms, provisions, covenants and restrictions set forth herein shall remain in full force and effect and shall in no way be affected,
impaired or invalidated, and the parties hereto shall use their commercially reasonable efforts to find and employ an alternative means to achieve the same or substantially the same result as that contemplated by such term, provision, covenant or
restriction. It is hereby stipulated and declared to be the intention of the parties that they would have executed the remaining terms, provisions, covenants and restrictions without including any of such that may be hereafter declared invalid,
illegal, void or unenforceable. 
 3.10 Notices. All communications shall be sent to the respective parties at their addresses
as set forth in the Securities Purchase Agreement, or to such address as subsequently modified by written notice given in accordance with this Section 3.10. If notice is given to the Company, a copy shall also be sent to Cooley LLP, Attn: Marc
Recht, Esq., 500 Boylston Street, Boston, Massachusetts 02116. If notice is given to Mogutov, a copy shall also be sent to Mintz, Levin, Cohn, Ferris, Glovsky and Popeo, P.C., Attn: William C. Hicks, Esq., One Financial Center,
Boston, MA 02111. 
 3.11 Construction. The parties agree that each of them and/or their respective counsel have
reviewed and had an opportunity to revise this Agreement and, therefore, the normal rule of construction to the effect that any ambiguities are to be resolved against the drafting party shall not be employed in the interpretation of this Agreement.

 3.12 WAIVER OF JURY TRIAL. IN ANY ACTION, SUIT, OR PROCEEDING IN ANY JURISDICTION BROUGHT BY ANY PARTY AGAINST ANY OTHER
PARTY, THE PARTIES EACH KNOWINGLY AND INTENTIONALLY, TO THE GREATEST EXTENT PERMITTED BY APPLICABLE LAW, HEREBY ABSOLUTELY, UNCONDITIONALLY, IRREVOCABLY AND EXPRESSLY WAIVES FOREVER TRIAL BY JURY. 

3.13 English Language Controls. This Agreement has been made in Russian and English language. In the event of a conflict or
inconsistency between the English and Russian versions of this Agreement, the English version shall prevail. 
 [Signature Page Follows]

 IN WITNESS WHEREOF, the parties have executed this Rights Agreement as of the date first written
above. 
  

			
	CLEVELAND BIOLABS, INC.
		
	By:	 	/s/ Yakov Kogan
		
	Name:	 	Yakov Kogan, Ph.D., MBA
		
	Title:	 	Chief Executive Officer
	
	MIKHAIL MOGUTOV, PH.D.
		
	By:	 	/s/ Mikhail Mogutov

 [SIGNATURE PAGE OF ADDITIONAL PURCHASERS FOLLOWS] 

 [SIGNATURE PAGE OF ADDITIONAL PURCHASERS] 

Name of Additional Purchaser:
                                         
                                         
                                

Signature of Authorized Signatory of Additional Purchaser:
                                         
                                         
                       
 Name of
Authorized Signatory:
                                         
                                         
                                         
                           

Title of Authorized Signatory:
                                         
                                         
                                         
                            
  

 Name of Additional Purchaser:
                                         
                                         
                                         
                           

Signature of Authorized Signatory of Additional Purchaser:
                                         
                                         
                       
 Name of
Authorized Signatory:
                                         
                                         
                                         
                           

Title of Authorized Signatory:EX-10.4

 Exhibit 10.4 

FIRST AMENDMENT TO LOAN AND SECURITY AGREEMENT 

This FIRST AMENDMENT TO LOAN AND SECURITY AGREEMENT (this “Amendment”), dated as of June 18, 2014 (the
“Effective Date”), is by and among (a) (i) CLEVELAND BIOLABS, INC., a Delaware corporation (“Inc”) and (ii) BIOLAB 612, LLC, a limited liability company formed in the Russian Federation
(“LLC”) (Inc and LLC hereinafter individually and collectively referred to as the “Borrower”), and (b) HERCULES TECHNOLOGY II, L.P., a Delaware limited partnership (“Lender”). 

WHEREAS, Borrower and Lender are parties to a certain Loan and Security Agreement, dated as of September 30, 2013 (as the same may
from time to time be amended, modified or supplemented in accordance with its terms, the “Loan Agreement”); and 

WHEREAS, in accordance with Section 11.4 of the Loan Agreement, Borrower and Lender desire to amend the Loan Agreement as provided
herein. 
 NOW THEREFORE, in consideration of the mutual agreements contained in the Loan Agreement and herein and for other good and
valuable consideration, the receipt and sufficiency of which are hereby acknowledged, the parties hereto hereby agree as follows: 
 1.
Defined Terms. Terms not otherwise defined herein which are defined in the Loan Agreement shall have the same respective meanings herein as therein. 

2. Amendments to Loan Agreement. Subject to the satisfaction of the conditions set forth in Section 4 of this Amendment,
the Loan Agreement is hereby amended as follows: 
 (a) The Loan Agreement shall be amended by inserting the following new
definitions to appear alphabetically in Section 1.1 thereof: 
 “First Amendment” means that certain
First Amendment to the Loan and Security Agreement dated of June 18, 2014. 
 (b) Notwithstanding Section 2.4 of
the Loan Agreement, Lender hereby agrees to waive the Prepayment Charge owed by Borrower to Lender solely as a result of Borrower’s prepayment of the Paydown Amount (as defined in the First Amendment). 

3. Termination of Stock Pledge Agreement (Incuron). Reference is made to that certain Stock Pledge Agreement (Incuron)
dated as of November 22, 2013, pursuant to which Inc granted Lender a security interest in and pledged to the Lender one hundred percent (100.0%) of Inc’s ownership interest in Limited Liability Company “Incuron”
(“Incuron”) to further secure the Borrower’s obligations under the Loan Agreement. In connection with this Amendment, subject to Section 4 below, Lender hereby releases all security interests and liens granted to Lender in
all collateral granted by Inc in Incuron pursuant to the Loan Agreement and the Pledge Agreement, and such release shall automatically be effective without further action required by any party. 

4. Conditions to Effectiveness. Lender and Borrower agree that this Amendment shall become effective upon the
satisfaction of the following conditions precedent, each in form and substance satisfactory to Lender: 
 (a) Lender shall
have received a fully-executed counterpart of this Amendment signed by Borrower; 
 (b) Lender shall have received certified
resolutions of Borrower’s board of directors evidencing approval of this Amendment; 

  
 1 

 (c) Borrower shall have paid to Lender, Four Million Dollars ($4,000,000.00) (the
“Paydown Amount”) to be applied on account of the outstanding Secured Obligations of Borrower to Lender; and 

(d) Lender shall have received payment for all reasonable and documented out-of-pocket fees and expenses incurred by Lender in
connection with this Amendment, including, but not limited to, all legal fees and expenses, payable pursuant to Section 11.12 of the Loan Agreement. 

5. Representations and Warranties. The Borrower hereby represents and warrants to Lender as follows: 

(a) Representations and Warranties in the Agreement. The representations and warranties of Borrower set forth in
Section 5 of the Loan Agreement are true and correct in all material respects on and as of the Effective Date with the same effect as though made on and as of such date, except to the extent such representations and warranties expressly relate
to an earlier date. 
 (b) Authority, Etc. The execution and delivery by Borrower of this Amendment and the
performance by Borrower of all of its agreements and obligations under the Loan Agreement and the other Loan Documents, as amended hereby, are within the corporate authority of Borrower and have been duly authorized by all necessary corporate action
on the part of Borrower. With respect to Borrower, the execution and delivery by Borrower of this Amendment does not and will not require any registration with, consent or approval of, or notice to any Person (including any governmental authority).

 (c) Enforceability of Obligations. This Amendment, the Loan Agreement and the other Loan Documents, as amended
hereby, constitute the legal, valid and binding obligations of Borrower enforceable against Borrower in accordance with their terms, except as enforceability is limited by bankruptcy, insolvency, reorganization, moratorium, general equitable
principles or other laws relating to or affecting generally the enforcement of, creditors’ rights and except to the extent that availability of the remedy of specific performance or injunctive relief is subject to the discretion of the court
before which any proceeding therefor may be brought. 
 (d) No Default. Before and after giving effect to this
Amendment (i) no fact or condition exists that would (or would, with the passage of time, the giving of notice, or both) constitute an Event of Default, and (ii) no event that has had or could reasonably be expected to have a Material
Adverse Effect has occurred and is continuing. 
 (e) Event of Default. By its signature below, Borrower hereby agrees
that it shall constitute an Event of Default if any representation or warranty made herein should be false or misleading in any material respect when made. 

6. Reaffirmations. Except as expressly provided in this Amendment, all of the terms and conditions of the Loan Agreement and the
other Loan Documents remain in full force and effect. Nothing contained in this Amendment shall in any way prejudice, impair or effect any rights or remedies of Lender under the Loan Agreement and the other Loan Documents. Except as specifically
amended hereby, Borrower hereby ratifies, confirms, and reaffirms all covenants contained in the Loan Agreement and the other Loan Documents. The Loan Agreement, together with this Amendment, shall be read and construed as a single agreement. All
references in the Loan Documents to the Loan Agreement or any other Loan Document shall hereafter refer to the Loan Agreement or any other Loan Document as amended hereby. 

7. Execution in Counterparts. This Amendment may be executed in any number of counterparts, each of which shall be deemed an
original, but which together shall constitute one instrument. 

  
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 8. Miscellaneous.  

(a) THIS AMENDMENT SHALL BE GOVERNED BY, AND CONSTRUED AND ENFORCED IN ACCORDANCE WITH, THE LAWS OF THE STATE OF CALIFORNIA,
EXCLUDING CONFLICT OF LAWS PRINCIPLES THAT WOULD CAUSE THE APPLICATION OF LAWS OF ANY OTHER JURISDICTION. 
 (b) The captions
in this Amendment are for convenience of reference only and shall not define or limit the provisions hereof. 
 (c) This
Amendment expresses the entire understanding of the parties with respect to the transactions contemplated hereby. No prior negotiations or discussions shall limit, modify, or otherwise affect the provisions hereof. 

(d) Any determination that any provision of this Amendment or any application hereof is invalid, illegal or unenforceable in
any respect and in any instance shall not effect the validity, legality, or enforceability of such provision in any other instance, or the validity, legality or enforceability of any other provisions of this Amendment. 

[Remainder of this page intentionally left blank] 

  
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 IN WITNESS WHEREOF, Borrower and Lender have duly executed and delivered this Amendment as of the day and
year first above written. 
  

			
	BORROWER:
	
	CLEVELAND BIOLABS, INC.
		
	Signature:	 	 /s/ Yakov Kogan

	Print Name:	 	Yakov Kogan
	Title:	 	Chief Executive Officer
	
	BIOLAB 612, LLC
		
	Signature:	 	 /s/ Askar Kuchumov

	Print Name:	 	Askar Kuchumov, Ph.D.
	Title:	 	General Director

 Accepted in Palo Alto, California: 

 

			
	LENDER:
	
	HERCULES TECHNOLOGY GROWTH
CAPITAL, INC.
		
	Signature:	 	 /s/ Ben Bang

	Print Name:	 	Ben Bang
	Title:	 	Senior Counsel

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