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

Page 1 of 21

The Reporting Persons have entered into a Joint Filing Agreement,
a copy of which is attached hereto as Exhibit 99.9.

Item 3.

Source and Amount of Funds or Other Consideration.

Item 3 of the Schedule 13D is hereby
amended by adding the following:

As previously reported
in Item 4 of the Schedule 13D, on June 22, 2017, Deerfield Private Design Fund IV, the Company and the other Investors entered
into the Purchase Agreement, a copy of which has been filed as Exhibit 10.20 to the Company’s Form 8-K filed with the Securities
and Exchange Commission on June 23, 2017, and is incorporated by reference as Exhibit 99.7 hereto. On August 2, 2017, pursuant
to the Purchase Agreement, Deerfield Private Design Fund IV purchased 16,000 Preferred Shares for an aggregate purchase price of
$16.0 million. Such Preferred Shares are initially convertible into an aggregate of 16,082,018 shares (“Series A Conversion
Shares”) of Common Stock, subject to adjustment pursuant to the terms of the Certificate of Designation. Deerfield Private
Design Fund IV utilized working capital to purchase such Preferred Shares.

Item 4.         Purpose of Transaction.

Item
4 of the Schedule 13D is hereby amended by adding the following:

On August 1, 2017, the Company filed the
Certificate of Designation with the Delaware Secretary of State, a copy of which was filed by the Company as Exhibit 3.1 to the
Company’s Form 8-K filed with the Securities and Exchange Commission on August 3, 2017.

On August 2, 2017, the Company closed the
Transaction, pursuant to which Deerfield Private Design Fund IV acquired 16,000 Preferred Shares. Deerfield Private Design Fund
IV acquired the Preferred Shares reported herein for investment purposes.

Item 5.          Interests in Securities of the
Issuer

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

(a) Throughout this report, the percentage
of outstanding Common Stock beneficially owned by the Reporting Persons has been determined based on 17,619,418 shares of Common
Stock outstanding as of August 2, 2017, based on information set forth in the Company’s Registration Statement on Form S-3,
filed with the Securities and Exchange Commission on August 3, 2017.

(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%