13D Filing: James E. Flynn and Proteon Therapeutics Inc (PRTO)

SECURITIES
AND EXCHANGE COMMISSION

Washington,
D.C. 20549

SCHEDULE
13D

[Rule 13d-101]

INFORMATION TO BE INCLUDED IN STATEMENTS FILED PURSUANT TO §
24.13d-1(a) AND AMENDMENTS THERETO FILED PURSUANT TO § 240.13D-2(a)

(Amendment No. 2)*

Proteon
Therapeutics, Inc.

(Name
of Issuer)

Common
Stock

(Title
of Class of Securities)

74371L109

(CUSIP
Number)

(Name,
Address and Telephone Number of Person Authorized to Receive Notices and Communications)

August
21, 2017

(Date
of Event which Requires Filing of this Statement)

If the filing person
has previously filed a statement on Schedule 13G to report the acquisition that is the subject of this Schedule 13D, and is filing
this schedule because of §§ 240.13d-1(e), 240.13d-1(f) or 240.13d-1(g), check the following box ☐.

Note: Schedules
filed in paper format shall include a signed original and five copies of the schedule, including all exhibits. See § 240.13d-7
for other parties to whom copies are to be sent.

(Continued on following
pages)
(Page 1 of 14 Pages)

* The remainder of this cover page shall be filled out for a
reporting person’s initial filing on this form with respect to the subject class of securities, and for any subsequent amendment
containing information which would alter disclosures provided in a prior cover page.

The information required on the remainder of this cover page
shall not be deemed to be “filed” for the purpose of Section 18 of the Securities Exchange Act of 1934 (“Act”)
or otherwise subject to the liabilities of that section of the Act but shall be subject to all other provisions of the Act (however,
see the Notes).

SCHEDULE 13D

SCHEDULE 13D

SCHEDULE 13D

SCHEDULE 13D

SCHEDULE 13D

(1) Comprised of shares of common stock issuable upon conversion
of shares of the Issuer’s Series A Convertible Preferred Stock (“Series A Convertible Preferred Stock”).

(2) The provisions of the Series A Convertible Preferred Stock beneficially owned by the reporting person
restrict the conversion of such securities to the extent that, upon such conversion, the number of shares of the Issuer’s
common stock then beneficially owned by the holder and its affiliates and any other person or entities with which such holder
would constitute a Section 13(d) “group” would exceed 9.985% of the total number of shares of the Issuer’s common
stock then outstanding (the “Ownership Cap”). Accordingly, notwithstanding the number of shares reported, the reporting
person disclaims beneficial ownership of the shares of common stock issuable upon conversion of such preferred stock to the extent
that upon such conversion the number of shares beneficially owned by all reporting persons hereunder, in the aggregate, would
exceed the Ownership Cap.

SCHEDULE 13D

(3) Comprised of shares of common stock held by Deerfield Special
Situations Fund, L.P., Deerfield Partners, L.P. and Deerfield International Master Fund, L.P., of which Deerfield Mgmt, L.P. is
the general partner.

SCHEDULE 13D

(4) Comprised of shares of Common Stock held by Deerfield Private
Design Fund III, L.P., of which Deerfield Mgmt III, L.P. is the general partner.

SCHEDULE 13D

(5) Comprised of shares of common stock issuable upon conversion
of shares of the Issuer’s Series A Convertible Preferred Stock held by Deerfield Private Design Fund IV, L.P., of which Deerfield
Mgmt IV, L.P. is the general partner.

(6) See footnote 2.

SCHEDULE 13D

(7) Comprised of (i) an aggregate of 1,224,899 shares of common
stock held by Deerfield Private Design Fund III, L.P., Deerfield Special Situations Fund, L.P., Deerfield Partners, L.P. and Deerfield
International Master Fund, L.P., and (ii) 16,082,018 shares of common stock issuable upon conversion of shares of the Issuer’s
Series A Convertible Preferred Stock held by Deerfield Private Design Fund IV, L.P. Deerfield Management Company, L.P. is the investment
manager of Deerfield Private Design Fund III, L.P., Deerfield Special Situations Fund, L.P., Deerfield Partners, L.P., Deerfield
International Master Fund, L.P. and Deerfield Private Design Fund IV, L.P.

(8) See footnote 2.

SCHEDULE 13D

(9) Comprised of (i) an aggregate of 1,224,899 shares of common
stock held by Deerfield Private Design Fund III, L.P., Deerfield Special Situations Fund, L.P., Deerfield Partners, L.P. and Deerfield
International Master Fund, L.P., and (ii) 16,082,018 shares of common stock issuable upon conversion of shares of the Issuer’s
Series A Convertible Preferred Stock held by Deerfield Private Design Fund IV, L.P. James E. Flynn is the sole member of the general
partner of each of Deerfield Mgmt, L.P., Deerfield Mgmt III, L.P., Deerfield Mgmt IV, L.P. and Deerfield Management Company, L.P.
Deerfield Management Company, L.P. is the investment manager of Deerfield Special Situations Fund, L.P., Deerfield Private Design
Fund III, L.P., Deerfield Private Design Fund IV, L.P., Deerfield Partners, L.P. and Deerfield International Master Fund, L.P.
Deerfield Mgmt III, L.P is the general partner of Deerfield Private Design Fund III, L.P. Deerfield Mgmt IV, L.P. is the general
partner of Deerfield Private Design Fund IV, L.P. Deerfield Mgmt, L.P. is the general partner of each of Deerfield Special Situations
Fund, L.P., Deerfield Partners, L.P. and Deerfield International Master Fund, L.P.

(10) See footnote 2.

Page 12 of 14 pages

This Amendment No.
2 (this “Amendment”) to Schedule 13D amends the Schedule 13D (as previously amended, the “Schedule
13D”) filed by (i) Deerfield Mgmt, L.P. (“Deerfield Mgmt”), (ii) Deerfield Management Company, L.P.
(“Deerfield Management”), (iii) Deerfield Mgmt III, L.P. (“Deerfield Mgmt III”), (iv) Deerfield
Special Situations Fund, L.P. (“Deerfield Special Situations Fund”), (v) Deerfield Partners, L.P. (“Deerfield
Partners”), (vi) Deerfield International Master Fund, L.P. (“Deerfield International Master Fund”),
(vii) Deerfield Private Design Fund III, L.P. (“Deerfield Private Design Fund III”), (viii) Deerfield Private
Design Fund IV, L.P. (“Deerfield Private Design Fund IV”), (ix) Deerfield Mgmt, L.P. (“Deerfield Mgmt
IV”) and (x) James E. Flynn (“Flynn” and, collectively with Deerfield Mgmt, Deerfield Management,
Deerfield Mgmt III, Deerfield Special Situations Fund, Deerfield Partners, Deerfield International Master Fund, Deerfield Private
Design Fund III, Deerfield Private Design Fund IV and Deerfield Mgmt IV, the “Reporting Persons”), with respect
to the securities of Proteon Therapeutics, Inc., as amended by Amendment No. 1 to the Schedule 13D filed on August 4, 2017. Deerfield
Special Situations Fund, Deerfield Partners, Deerfield International Master Fund, Deerfield Private Design Fund III and Deerfield
Private Design Fund IV are collectively referred to herein as the “Funds”.

Capitalized terms used
herein but not otherwise defined herein shall have the meanings ascribed to them in the Schedule 13D.

Item 2(e) of the Schedule 13D is hereby
amended by adding the following:

On August 21, 2017, Deerfield Management
voluntarily agreed to settle an SEC administrative proceeding relating to alleged violations of Section 204A of the Investment
Advisers Act of 1940 (the “Advisers Act”), without admitting or denying the SEC’s allegations, pursuant to an
order under Section 203(e) and 203(k) of the Advisers Act (the “Order”).  The Order resolved the SEC’s allegations
that Deerfield Management, from 2012 through 2014, violated Section 204A of the Advisers Act by failing to establish, maintain,
and enforce policies and procedures reasonably designed to prevent the misuse of material, nonpublic information, particularly
taking into consideration the nature of Deerfield Management’s business.  The Order alleged that, as part of Deerfield
Management’s research in the healthcare sector, Deerfield Management engaged third party consultants and research firms,
including firms that specialized in providing “political intelligence” regarding upcoming regulatory and legislative
decisions, that Deerfield Management employees based certain trading recommendations on such information, and that hedge funds
advised by Deerfield Management then made those trades.  The Order required Deerfield Management to cease and desist from
committing or causing any violations and any future violations of Section 204A of the Advisers Act, censured Deerfield Management
and provided that Deerfield Management will pay disgorgement and interest of $811,695 and a civil money penalty of $3,946,267.

Page 13 of 14 pages

SIGNATURE

After reasonable inquiry
and to the best of their knowledge and belief, the undersigned certify that the information set forth in this statement is true,
complete and correct.

Dated: August 22, 2017

Page 14 of 14 pages