EX-10.1



 Exhibit 10.1 

AMENDMENT NO. 1 TO AT-THE-MARKET ISSUANCE SALES AGREEMENT 

September 16, 2016 
 Ladies and Gentlemen:

 MediciNova, Inc. (the “Company”), and MLV & Co. LLC (“MLV”) , are parties to that certain
At-the-Market Issuance Sales Agreement dated May 22, 2015 (the “Original Agreement”). All capitalized terms not defined herein shall have the meanings ascribed to them in the Original Agreement. The parties, together with FBR
Capital Markets & Co. (“FBR” and together with MLV, the “Agent”), intending to be legally bound, hereby amend the Original Agreement as follows (to be effective as set forth in paragraph 6 below): 

1. Section 1 of the Original Agreement is hereby amended to replace 

“The Company has filed, in accordance with the provisions of the Securities Act of 1933, as amended, and the rules and
regulations thereunder (the “Securities Act”), with the Securities and Exchange Commission (the “Commission”), a registration statement on Form S-3 (File No. 333-185022), including a base prospectus, relating
to certain securities, including the Placement Shares to be issued from time to time by the Company, and which incorporates by reference documents that the Company has filed or will file in accordance with the provisions of the Securities Exchange
Act of 1934, as amended, and the rules and regulations thereunder (the “Exchange Act”). 
 With, 

“The Company has filed, in accordance with the provisions of the Securities Act of 1933, as amended, and the rules and
regulations thereunder (the “Securities Act”), with the Securities and Exchange Commission (the “Commission”), a registration statement on Form S-3 (File No. 333-208274), including a base prospectus, relating
to certain securities, including the Placement Shares to be issued from time to time by the Company, and which incorporates by reference documents that the Company has filed or will file in accordance with the provisions of the Securities Exchange
Act of 1934, as amended, and the rules and regulations thereunder (the “Exchange Act”). 
 2. All references to
“MLV & Co. LLC” and “MLV” set forth in the Original Agreement are revised to read “MLV & Co. LLC and FBR Capital Markets & Co.” and “the Agent,” respectively. 

3. All references to “May 22, 2015” set forth in Schedule I and Exhibit 7(l) of the Original Agreement are revised to read
“May 22, 2015 (as amended by Amendment No. 1 to At-the-Market Issuance Sales Agreement, dated September 16, 2016)”. 

4. Section 14 of the Original Agreement is hereby amended to replace 

“MLV & Co. LLC 

1301 Avenue of the Americas, 

43rd Floor 
 New York, New York
10019 
 Attention: Legal Department 

Telephone: (212) 542-5880 

Email: mlvlegal@mlvco.com 







 with a copy (which shall not constitute notice) to: 

K&L Gates LLP 
 1 Park Plaza,
Twelfth Floor 
 Irvine, CA 92614 

Attention: Michael Hedge 

Telephone: (949) 623-3519 

Email: michael.hedge@klgates.com 

and if to the Company, shall be delivered to: 

MediciNova, Inc. 
 4275 Executive
Square, Suite 650 
 La Jolla, CA 92037 

Attention: Yuichi Iwaki, M.D., Ph.D. 

Telephone: (858) 246-8671 

Email: iwaki@medicinova.com 

with a copy to: 
 Pillsbury
Winthrop Shaw Pittman LLP 
 501 W. Broadway, Suite 1100 

San Diego, CA 92101-3575 

Attention: David R. Snyder 

Telephone: (619) 544-3369 

Email: dave.snyder@pillsburylaw.com” 

With, 
 “FBR Capital
Markets & Co. 
 1300 North 17th Street, Suite 1400 

Arlington, VA 22209 
 Attention:
Legal Department 
 E-mail: atmadmin@fbr.com 

And 
 MLV & Co. LLC 

299 Park Avenue, 7th Floor 
 New
York, NY 10171 
 Attention: Legal Department 

Facsimile: (212) 542-5880 
 Email:
mlvlegal@mlvco.com 
 with a copy (which shall not constitute notice) to: 

Duane Morris LLP 
 One Riverfront
Plaza 
 1037 Raymond Boulevard, Suite 1800 

Newark, NJ 07102 
 Attention:
James T. Seery 
 Email: JTSeery@duanemorris.com 

  
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 and if to the Company, shall be delivered to: 

MediciNova, Inc. 
 4275 Executive
Square, Suite 650 
 La Jolla, CA 92037 

Attention: Yuichi Iwaki, M.D., Ph.D. 

Telephone: (858) 246-8671 

Email: iwaki@medicinova.com 

with a copy (which shall not constitute notice) to: 

Gunderson Dettmer Stough Villeneuve Franklin & Hachigian, LLP 

3570 Carmel Mountain Road, Suite 200 

San Diego, CA 92130 
 Attention:
Kirt W. Shuldberg 
 Telephone: (858) 436-8060 

Email: kshuldberg@gunder.com” 

5. Schedule 3 is hereby amended to replace 

“The Company 
  

			
	 Yuichi Iwaki, M.D., Ph.D.
	  	iwaki@medicinova.com
	 Esther van den Boom
	  	esther@medicinova.com
	 Kazuko Matsuda, M.D., Ph.D., MPH
	  	matsuda@medicinova.com
	 Masatsune Okajima
	  	okajima@medicinova.com
	 Geoffrey O’Brien, JD, MBA
	  	obrien@medicinova.com
	 John O’Neil
	  	oneil@medicinova.com
	 Kiyomi Suzue
	  	suzue@medicinova.com

 MLV 
  

			
	 Randy Billhardt
	  	rbillhardt@mlvco.com
	 Ryan Loforte
	  	rloforte@mlvco.com
	 Patrice McNicoll
	  	pmcnicoll@mlvco.com
	 Miranda Toledano
	  	mtoledano@mlvco.com

 With a copy to mlvatmdesk@mlvco.com” 

With, 
 “The Company

  

			
	 Yuichi Iwaki, M.D., Ph.D.
	  	iwaki@medicinova.com
	 Ryan Selhorn
	  	rselhorn@medicinova.com
	 Kazuko Matsuda, M.D., Ph.D., MPH
	  	matsuda@medicinova.com


  
 3 









			
	 Masatsune Okajima
	  	okajima@medicinova.com
	 Geoffrey O’Brien, JD, MBA
	  	obrien@medicinova.com
	 Olamide Esan
	  	oesan@medicinova.com
	 Kiyomi Suzue
	  	suzue@medicinova.com

 MLV and FBR 
  

			
	 Patrice McNicoll
	  	pmcnicoll@fbr.com
	 Matthew Feinberg
	  	mfeinberg@fbr.com
	 Ryan Loforte
	  	rloforte@fbr.com

 With a copy to atmadmin@fbr.com.” 

6. Except as specifically set forth herein, all other provisions of the Original Agreement shall remain in full force and effect. 

7. Entire Agreement; Amendment; Severability. This Amendment No. 1 to Sales Agreement together with the Original Agreement
(including all schedules and exhibits attached hereto and thereto and Placement Notices issued pursuant hereto and thereto) constitutes the entire agreement and supersedes all other prior and contemporaneous agreements and undertakings, both written
and oral, among the parties hereto with regard to the subject matter hereof. All references in the Original Agreement to the “Agreement” shall mean the Original Agreement as amended by this Amendment No. 1; provided, however,
that all references to “date of this Agreement” in the Original Agreement shall continue to refer to the date of the Original Agreement, and the reference to “time of execution of this Agreement” set forth in Section 13(a)
shall continue to refer to the time of execution of the Original Agreement. 
 8. Applicable Law; Consent to Jurisdiction. This
amendment shall be governed by, and construed in accordance with, the internal laws of the State of New York without regard to the principles of conflicts of laws. Each party hereby irrevocably submits to the non-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 with any transaction contemplated hereby, 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 brought in an inconvenient forum or that the venue of such suit, action or proceeding is improper. 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 (certified or registered mail, return receipt requested) to such party at the address
in effect for notices to it under this amendment 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
manner permitted by law. 
 9. Waiver of Jury Trial. The Company, MLV and FBR each hereby irrevocably waives any right it may have to
a trial by jury in respect of any claim based upon or arising out of this amendment or any transaction contemplated hereby. 
 10.
Counterparts. This amendment may be executed in two or more counterparts, each of which shall be deemed an original, but all of which together shall constitute one and the same instrument. Delivery of an executed amendment by one party to the
other may be made by facsimile transmission. 

  
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 If the foregoing correctly sets forth the understanding among the Company, MLV and FBR, please so
indicate in the space provided below for that purpose, whereupon this letter shall constitute a binding amendment to the Agreement between the Company, MLV and FBR. 

 

			
	Very truly yours,


  

			
	MEDICINOVA, INC.
		
	By:	 	/s/ Yuichi Iwaki
	Name: Yuichi Iwaki, M.D., Ph.D.
	Title: President and Chief Executive Officer


  

			
	MLV & CO. LLC
		
	By:	 	/s/ Patrice McNicoll
	Name: Patrice McNicoll
	Title: Chief Executive Officer


  

			
	FBR CAPITAL MARKETS & CO.
		
	By:	 	/s/ Patrice McNicoll
	Name: Patrice McNicoll
	Title: Co-Head of Capital Markets