EX-10.1



 Exhibit 10.1 

AMENDMENT NO. 1 TO 

SECURITIES PURCHASE AGREEMENT 

AND SERIES D WARRANTS 

This Amendment No. 1 to Securities Purchase Agreement and Series D Warrants (this “Amendment”) is made and entered into
as of September 29, 2014, and amends (i) that certain Securities Purchase Agreement, dated as of February 13, 2009, (the “Agreement”), by and among Cleveland Biolabs, Inc., a Delaware corporation (the
“Company”), and the parties (each individually a “Purchaser,” and collectively the “Purchasers”) named on the purchaser signature pages attached thereto, and (ii) those certain Common Stock
Purchase Warrants issued to the Purchasers pursuant to the Agreement. Capitalized terms not otherwise defined herein shall have the meaning given to them in the Agreement. 

WHEREAS, the Company and the undersigned Purchasers desire to amend the Agreement to remove any and all restrictions on the Company’s
ability to effect an issuance involving a Variable Rate Transaction and to amend each of the Warrants to extend the exercise price and provide anti-dilution protection for Variable Rate Transactions; 

WHEREAS, Article 5.5 of the Agreement provides that the terms and provisions of the Agreement may be amended with the written consent of the
Company and the Purchasers holding at least 67% of the outstanding Preferred Stock and Section 5(l) of the Warrants provides that the Warrants may be amended with the written consent of the Company and Holders holding Warrants at least equal to
67% of the Warrant Shares issuable upon exercise of all then outstanding Warrants (collectively, the “Required Purchasers”); and 

WHEREAS, the undersigned are the former holders (or their transferees) of the Preferred Stock issued under the Agreement and together the
undersigned constitute the Required Purchasers. 
 NOW, THEREFORE, IN CONSIDERATION of the foregoing recitals and the mutual covenants
contained in this Amendment, and for other good and valuable consideration, the receipt and adequacy of which are hereby acknowledged, the parties agree as follows: 

ARTICLE 1 
 AMENDMENT TO
AGREEMENT 
 1.1 Amendment to Section 1.1 of the Agreement. The definition of Variable Rate Transaction is hereby
deleted in its entirety from Section 1.1 of the Agreement. 
 1.2 Amendment to Section 4.13(b) of the Agreement.
Section 4.13(b) of the Agreement is hereby deleted in its entirety from the Agreement. 
 1.3 Amendment to
Section 4.13(d) of the Agreement. Section 4.13(d) of the Agreement is hereby amended and restated in its entirety to read as follow: 

“(c) Notwithstanding the foregoing, this Section 4.13 shall not apply in respect of an Exempt Issuance.” 

  
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 ARTICLE 2 

AMENDMENT TO WARRANTS 

2.1 Amendment to First Paragraph of the Warrants. The “Termination Date” of each of the Warrants (as defined in
the first paragraph of the Warrants) is hereby amended to be “March 30, 2018.” 
 2.2 Amendment to Section 3(b) of
the Warrants. The following sentence is hereby inserted at the end of Section 3(b) in each of the Warrants: 
 “Notwithstanding
anything to the contrary, if the Company, at any time while this Warrant is outstanding, shall issue any Common Stock or Common Stock Equivalents to entitle any Person to acquire shares of Common Stock in a Variable Rate Transaction (as defined
below), then for every five million shares sold in a Variable Rate Transaction (i.e. at five million shares sold; ten million shares sold, etc.), the weighted average share price of the last five million shares shall be calculated and that share
price shall then become the Exercise Price of the Warrant if such price is lower than the Exercise Price then in effect on the date of sale of the 5,000,000 (five millionth) share used in the calculation. A “Variable Rate
Transaction” means a transaction in which the Company (i) issues or sells any debt or equity securities that are convertible into, exchangeable or exercisable for, or include the right to receive, additional shares of Common Stock at a
conversion price, exercise price or exchange rate or other price that is based upon, and/or varies with, the trading prices of, or quotations for, the shares of Common Stock at any time after the initial issuance of such debt or equity securities or
(ii) enters into any agreement, including, but not limited to, an equity line of credit, whereby the Company may sell securities at a future determined price.” 

ARTICLE 3 

MISCELLANEOUS 
 3.1
Severability. In the event one or more of the provisions of this Amendment should, for any reason, be held to be invalid, illegal or unenforceable in any respect, such invalidity, illegality or unenforceability shall not affect any other
provisions of this Amendment, and this Amendment shall be construed as if such invalid, illegal or unenforceable provision had never been contained herein. 

3.2 Counterparts. This Amendment may be executed in counterparts, each of which shall be deemed an original, but all of which
together shall constitute one and the same Amendment. 
 3.3 Conflicts. In the event of any inconsistencies between this
Amendment and the Agreement or Warrants, the terms of this Amendment shall govern. Except as provided for herein, all other terms and conditions of the Agreement and Warrants shall remain unchanged 

  
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and the parties hereto reaffirm the terms and conditions of such Agreement and Warrants. This Amendment may only be amended by a document, in writing, of even or subsequent date hereof, executed
by the Company and the Required Purchasers. 
 3.4 Successors and Assigns. The provisions hereof shall inure to the benefit
of, and be binding upon, the parties hereto and their respective successors, assigns, heirs, executors and administrators and other legal representatives. 

3.5 Governing Law. All questions concerning the construction, validity, enforcement and interpretation of this Amendment 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. 

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 IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the
date set forth in the first paragraph hereof. 
  

			
	COMPANY:
	
	CLEVELAND BIOLABS, INC.
		
	By:	 	 /s/ Yakov Kogan

	Name:	 	Yakov Kogan
	Title:	 	Chief Executive Officer


 Signature Page to First Amendment to Securities Purchase Agreement and Series D Warrants








 IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the
date set forth in the first paragraph hereof. 
  

			
	REQUIRED PURCHASERS:
	
	Individual: Walter Schenker IRA / Principal Trust Company
	
	 /s/ Walter Schenker

	Name:	 	Walter Schenker
		
	Date:	 	 9/26/14

	
	Entity:
		
	Name:	 	  

		
	By:	 	  

	Name:	 	  

	Title:	 	  

		
	Date:	 	  




  
 Signature Page
to First Amendment to Securities Purchase Agreement and Series D Warrants 








 IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the
date set forth in the first paragraph hereof. 
  

			
	REQUIRED PURCHASERS:
	
	Individual:
	
	 /s/ William F. Quirk, Jr.

	Name:	 	William F. Quirk, Jr.
		
	Date:	 	 11 September 2014

	
	Entity:
		
	Name:	 	  

		
	By:	 	  

	Name:	 	  

	Title:	 	  

		
	Date:	 	  




  
 Signature Page
to First Amendment to Securities Purchase Agreement and Series D Warrants 








 IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the
date set forth in the first paragraph hereof. 
  

			
	REQUIRED PURCHASERS:
	
	Individual:
	
	  

	Name:	 	
		
	Date:	 	  

	
	Entity:
		
	Name:	 	 J.S.A. Investments

		
	By:	 	 /s/ Joelle A. Meyerson

	Name:	 	 Joelle A. Meyerson

	Title:	 	 Manager

		
	Date:	 	  




  
 Signature Page
to First Amendment to Securities Purchase Agreement and Series D Warrants 








 IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the
date set forth in the first paragraph hereof. 
  

			
	REQUIRED PURCHASERS:
	
	Individual: Martin H. Meyerson, Trust
	
	 /s/ Martin H. Meyerson

	Name:	 	Martin H. Meyerson
		
	Date:	 	  

	
	Entity:
		
	Name:	 	  

		
	By:	 	  

	Name:	 	  

	Title:	 	  

		
	Date:	 	  




  
 Signature Page
to First Amendment to Securities Purchase Agreement and Series D Warrants 








 IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the
date set forth in the first paragraph hereof. 
  

			
	REQUIRED PURCHASERS:
	
	Individual:
	
	  

	Name:	 	
		
	Date:	 	  

	
	Entity:
		
	Name:	 	 MAZ Partners, LP.

	1130 Route 46, Suite 22
	Parsippany, NJ 07054
		
	By:	 	 /s/ Walter Schenker

	Name:	 	 Walter Schenker

	Title:	 	 Principal

		
	Date:	 	 Sept. 22, 2014




  
 Signature Page
to First Amendment to Securities Purchase Agreement and Series D Warrants 








 IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the
date set forth in the first paragraph hereof. 
  

			
	REQUIRED PURCHASERS:
	
	Individual:
	
	 /s/ Walter Schenker

	Name:	 	Walter Schenker
		
	Date:	 	 September 22, 2014

	
	Entity:
		
	Name:	 	  

		
	By:	 	  

	Name:	 	  

	Title:	 	  

		
	Date:	 	  




  
 Signature Page
to First Amendment to Securities Purchase Agreement and Series D Warrants 








 IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the
date set forth in the first paragraph hereof. 
  

			
	REQUIRED PURCHASERS:
	
	Individual:
	
	 /s/ James W. Harpel

	Name:	 	James W. Harpel
		
	Date:	 	 9/22/14

	
	Entity:
		
	Name:	 	  

		
	By:	 	  

	Name:	 	  

	Title:	 	  

		
	Date:	 	  




  
 Signature Page
to First Amendment to Securities Purchase Agreement and Series D Warrants 








 IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the
date set forth in the first paragraph hereof. 
  

			
	REQUIRED PURCHASERS:
	
	Individual:
	
	 /s/ Paul P. Tanico

	Name:	 	Paul P. Tanico
		
	Date:	 	 September 18, 2014

	
	Entity:
		
	Name:	 	  

		
	By:	 	  

	Name:	 	  

	Title:	 	  

		
	Date:	 	  




  
 Signature Page
to First Amendment to Securities Purchase Agreement and Series D Warrants 








 IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the
date set forth in the first paragraph hereof. 
  

			
	REQUIRED PURCHASERS:
	
	Individual:
	
	 /s/ Robert J. Brous

	Name:	 	Robert J. Brous
		
	Date:	 	 9/18/14

	
	Entity:
		
	Name:	 	  

		
	By:	 	  

	Name:	 	  

	Title:	 	  

		
	Date:	 	  




  
 Signature Page
to First Amendment to Securities Purchase Agreement and Series D Warrants 








 IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the
date set forth in the first paragraph hereof. 
  

			
	REQUIRED PURCHASERS:
	
	Individual:
	
	  

	Name:	 	
		
	Date:	 	  

	
	Entity:
		
	Name:	 	 Berdon Ventures, LLC

		 	F. Berdon Co. LLC
		
	By:	 	 /s/ J. Berdon

	Name:	 	  

	Title:	 	  

		
	Date:	 	 9/18/14




  
 Signature Page
to First Amendment to Securities Purchase Agreement and Series D Warrants 








 IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the
date set forth in the first paragraph hereof. 
  

			
	REQUIRED PURCHASERS:
	
	Individual:
	
	 /s/ Arline McGowan

	Name:	 	Arline McGowan
		
	Date:	 	 9/10/14

	
	 /s/ Richard S. McGowan

	Name:	 	Richard S. McGowan
		
	Date:	 	 9/10/14

	
	Entity:
		
	Name:	 	  

		
	By:	 	  

	Name:	 	  

	Title:	 	  

		
	Date:	 	  




  
 Signature Page
to First Amendment to Securities Purchase Agreement and Series D Warrants 








 IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the
date set forth in the first paragraph hereof. 
  

			
	REQUIRED PURCHASERS:
	
	Individual:
	
	 /s/ Ellen Adams

	Name:	 	Ellen Adams
		
	Date:	 	 9/10/14

	
	Entity:
		
	Name:	 	  

		
	By:	 	  

	Name:	 	  

	Title:	 	  

		
	Date:	 	  




  
 Signature Page
to First Amendment to Securities Purchase Agreement and Series D Warrants 








 IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the
date set forth in the first paragraph hereof. 
  

			
	REQUIRED PURCHASERS:
	
	Individual:
	
	  

	Name:	 	
		
	Date:	 	
	  

	
	Entity:
		
	Name:	 	 Ellen Adams Trust

		
	By:	 	 /s/ Ellen Adams

	Name:	 	 Ellen Adams

	Title:	 	  

		
	Date:	 	 9/10/14




  
 Signature Page
to First Amendment to Securities Purchase Agreement and Series D Warrants 








 IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the
date set forth in the first paragraph hereof. 
  

			
	REQUIRED PURCHASERS:
	
	Individual:
	
	  

	Name:	 	
		
	Date:	 	
	  

	
	Entity:
		
	Name:	 	 James W. Harpel Trust 40

		
	By:	 	 /s/ Leo A. Guthart

	Name:	 	 Leo A. Guthart

	Title:	 	 Trustee

		
	Date:	 	 September 23, 2014




  
 Signature Page
to First Amendment to Securities Purchase Agreement and Series D Warrants 








 IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the
date set forth in the first paragraph hereof. 
  

			
	REQUIRED PURCHASERS:
	
	Individual:
	
	  

	Name:	 	
		
	Date:	 	
	  

		
	Entity:	 	
		
	Name:	 	 Anthony Harpel Trust 40

		
	By:	 	 /s/ Leo A. Guthart

	Name:	 	 Leo A. Guthart

	Title:	 	 Trustee

		
	Date:	 	 9/23/14




  
 Signature Page
to First Amendment to Securities Purchase Agreement and Series D Warrants 








 IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the
date set forth in the first paragraph hereof. 
  

			
	REQUIRED PURCHASERS:
	
	Individual:
	
	 /s/ Susan Schenker

	Name:	 	Susan Schenker
		
	Date:	 	 9/23/14

	
	Entity:
		
	Name:	 	  

		
	By:	 	  

	Name:	 	  

	Title:	 	  

		
	Date:	 	  




  
 Signature Page
to First Amendment to Securities Purchase Agreement and Series D Warrants 








 IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the
date set forth in the first paragraph hereof. 
  

			
	REQUIRED PURCHASERS:
	
	Individual:
	
	 /s/ Michael N. Emmerman

	Name:	 	Michael N. Emmerman
		
	Date:	 	 16 September 2014

	
	Entity:
		
	Name:	 	  

		
	By:	 	  

	Name:	 	  

	Title:	 	  

		
	Date:	 	  




  
 Signature Page
to First Amendment to Securities Purchase Agreement and Series D Warrants