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

 

2

--------------------------------------------------------------------------------

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.

 

4

--------------------------------------------------------------------------------

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