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. 3)*

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)

November
30, 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 17 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. and Deerfield Partners, 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. and Deerfield Partners, 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. and Deerfield Partners, 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 17

This Amendment No. 3 (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 Nos. 1 and 2 to the
Schedule 13D filed on August 4, 2017 and August 22, 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 3 of the Schedule 13D is hereby
amended by adding the following:

On December 1, 2017, Deerfield Partners
purchased from Deerfield International Master Fund 110,557 shares of Common Stock in a private transaction for an aggregate purchase
price of $193,474.75. Deerfield Partners utilized cash on hand to fund the purchase price for such shares.

Items 5(a), (b) (c) and (e) of the Schedule
13D are hereby amended and restated as follows:

(a)

(1) Deerfield Management

Number of shares: 17,306,917

Percentage of shares: 9.985%*

(2) Deerfield Mgmt

Number of shares: 347,100

Percentage of shares: 1.97%*

(3) Deerfield Mgmt III

Number of
Shares: 877,799

Percentage
of Shares: 4.98%*

Page 13 of 17

(4) Deerfield Partners

Number of shares: 197,424

Percentage of shares: 1.12%*

(5) Deerfield Special Situations
Fund

Number of shares: 149,676

Percentage of shares: 0.85%*

(6) Deerfield International Master
Fund

Number of
Shares: 0

Percentage
of Shares: 0.00%

(7) Deerfield Private Design
Fund III

Number of
Shares: 877,799

Percentage
of Shares: 4.98%*

(8) Deerfield Private Design
Fund IV

Number of
Shares: 16,082,018

Percentage
of Shares: 9.985%*

(9) Deerfield Mgmt IV

Number of
Shares: 16,082,018

Percentage
of Shares: 9.985%*

(10) Flynn

Number of shares: 17,306,917

Percentage of shares: 9.985%*

*Percentage beneficial ownership reported
herein reflects 17,619,418 shares of Common Stock outstanding as of October 31, 2017, as reported in the Company’s Quarterly
Report on Form 10-Q for the quarterly period ended September 30, 2017.

(b)

(1) Deerfield Management

Sole power to vote or direct the
vote: 0

Shared power to vote or direct
the vote: 17,306,917

Sole power to dispose or to direct
the disposition: 0

Shared power to dispose or direct
the disposition: 17,306,917

Page 14 of 17

(2) Deerfield Mgmt

Sole power to vote or direct the
vote: 0

Shared power to vote or direct
the vote: 347,100

Sole power to dispose or to direct
the disposition: 0

Shared power to dispose or direct
the disposition: 347,100

(3) Deerfield Mgmt III

Sole power to vote or direct the
vote: 0

Shared power to vote or direct
the vote: 877,799

Sole power to dispose or to direct
the disposition: 0

Shared power to dispose or direct
the disposition: 877,799

(4) Deerfield Partners

Sole power to vote or direct the
vote: 0

Shared power to vote or direct
the vote: 197,424

Sole power to dispose or to direct
the disposition: 0

Shared power to dispose or direct
the disposition: 197,424

(5) Deerfield Special Situations
Fund

Sole power to vote or direct the
vote: 0

Shared power to vote or direct
the vote: 149,676

Sole power to dispose or to direct
the disposition: 0

Shared power to dispose or direct
the disposition: 149,676

(6) Deerfield International Master
Fund

Sole power to vote or direct the
vote: 0

Shared power to vote or direct
the vote: 0

Sole power to dispose or to direct
the disposition: 0

Shared power to dispose or direct
the disposition: 0

(7) Deerfield Private Design
Fund III

Sole power to vote or direct the
vote: 0

Shared power to vote or direct
the vote: 877,799

Sole power to dispose or to direct
the disposition: 0

Shared power
to dispose or direct the disposition: 877,799

(8) Deerfield Private Design
Fund IV

Sole power to vote or direct the
vote: 0

Shared power to vote or direct
the vote: 16,082,018

Sole power to dispose or to direct
the disposition: 0

Shared power
to dispose or direct the disposition: 16,082,018

Page 15 of 17

(9) Deerfield Mgmt IV

Sole power to vote or direct the
vote: 0

Shared power to vote or direct
the vote: 16,082,018

Sole power to dispose or to direct
the disposition: 0

Shared power to dispose or direct
the disposition: 16,082,018

(10) Flynn

Sole power to vote or direct the
vote: 0

Shared power to vote or direct
the vote: 17,306,917

Sole power to dispose or to direct
the disposition: 0

Shared power to dispose or direct
the disposition: 17,306,917

Flynn is the sole member of the general partner of each of Deerfield
Mgmt, Deerfield Mgmt III, Deerfield Mgmt IV and Deerfield Management.  Deerfield Mgmt is the general partner of Deerfield
Special Situations Fund, Deerfield Partners and Deerfield International Master Fund. Deerfield Mgmt III is the general partner
of Deerfield Private Design Fund III. Deerfield Mgmt IV is the general partner of Deerfield Private Design Fund IV. Deerfield Management
is the investment manager of each of Deerfield Special Situations Fund, Deerfield Private Design Fund III, Deerfield Partners,
Deerfield International Master Fund and Deerfield Private Design Fund IV.

(c) On November 30, 2017, Deerfield International Master Fund
transferred an aggregate of 110,557 shares of Common Stock to Deerfield Partners at a price of $1.75 per share in a private transaction.

(e) On November 30, 2017, Deerfield International Master Fund
ceased to beneficially own more than five percent of the outstanding Common Stock.

Page 16 of 17

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: December 4, 2017

Page
17 of 17