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CORRESP
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CORRESP

 June 9, 2017

Suzanne Hayes

 Mary Beth Breslin

Office of Healthcare and Insurance

 Division of Corporation
Finance

 Securities and Exchange Commission

 100 F Street,
N.E.

 Washington, D.C. 20549

Re:
Aerpio Pharmaceuticals, Inc.

 Amendment No. 1 to Registration Statement on Form
S-1

 Filed May 22, 2017

File No. 333-217320

 Dear
Ms. Breslin,

 This letter is confidentially submitted on behalf of Aerpio Pharmaceuticals, Inc. (the
“Company”) in response to comments of the staff of the Division of Corporate Finance (the “Staff”) of the U.S. Securities and Exchange Commission (the “Commission”) with respect to the
Company’s confidential submission of the draft Amendment No. 1 to Registration Statement on Form S-1 submitted on May 22, 2017 (the “Amendment No. 1”), as set forth in the Staff’s letter dated June 7,
2017 to Joseph Gardner, President and Chief Executive Officer (the “Comment Letter”). The Company is concurrently filing Amendment No. 2 to the Registration Statement (“Amendment No. 2”), which includes
changes to reflect responses to the Staff’s comments and other updates.

 For reference purposes, the text of the Comment
Letter has been reproduced and italicized herein with responses below each numbered comment. Unless otherwise indicated, page references in the descriptions of the Staff’s comments refer to the Amendment No. 1, and page references in the
responses refer to Amendment No. 2. All capitalized terms used and not otherwise defined herein shall have the meanings set forth in Amendment No. 2.

The responses provided herein are based upon information provided to Goodwin Procter LLP by the Company. In addition to confidentially
submitting this letter via EDGAR, we are sending via Federal Express four (4) copies of each of this letter and Amendment No. 2 (marked to show changes from Amendment No. 1).

 Ms. Breslin

Securities and Exchange Commission

 June 9, 2017

 Page
 2

 Description of our Business

Our solution, page 58

1.
We note your response to prior comment 5; however, the revised disclosure indicates that the sole patient you highlight in Figure 4 represented only about 29% of all patients in the cohort (i.e., patients who
achieved a retinal thickness of less than 300 microns). Please revise the graphic so that it also illustrates, by comparison, the mean change in retinal thickness achieved by all 48 patients in the cohort. Alternatively, please remove the
graphic.

 RESPONSE: The Company respectfully advises the Staff that it has updated its disclosure on pages 57-58 in
response to the Staff’s comment.

 Changes in and Disagreements with Accountants on Accounting and Financial Disclosure, page 98

2.
LWBJ, LLP’s letter dated April 14, 2017 filed as Exhibit 16.1 to Form S-1 filed on April 14, 2017 refers to disclosure that is not included in that filing. As such, incorporating that letter by
reference into your S-1/A filed May 22, 2017 does not appear appropriate. Please amend your filing to include an updated exhibit 16.1 that refers to disclosure herein.

RESPONSE: The Company respectfully advises the Staff that it has updated Exhibit 16.1 of Amendment No. 2 in response to the Staff’s
comment.

 Selling Stockholders, page 129

3.
We note the last paragraph of your response to prior comment 8 that the selling shareholders are “longtime investors” in Aerpio Therapeutics, Inc. With respect to each of the selling shareholders that were
affiliates of Aerpio, such as the “major shareholders” with board representation or pre-merger officers and directors you reference in your response, please expand your response to tell us how long they have held the Aerpio shares, the
circumstances under which they received them, their relationship to the issuer, the amount of shares involved, and whether the shareholders are in the business of underwriting securities.

RESPONSE: The Company respectfully advises the Staff that detailed information regarding shares held by the “major stockholders”,
pre-merger directors and officers, and affiliates (the “Affiliated Stockholders”) of Aerpio Therapeutics, Inc. (“Aerpio”) has been included below. It should be noted that the following description is historical and
has not been adjusted to give effect to the Merger (as defined in Amendment No. 2) or the share conversion ratio pursuant to the Merger Agreement. In connection with the Merger, each 2.3336572 shares of Aerpio regardless of the series or class
of such share, were converted into one share of common stock of the Company.

 Shares in Aerpio held by the Affiliated Stockholders

 On December 23, 2011, Aerpio issued an aggregate of 3,094,774 shares of Series A convertible preferred stock at a price per share
of $1.83. The table below sets forth the number of shares of Series A convertible preferred stock sold to the Affiliated Stockholders.

 Ms. Breslin

Securities and Exchange Commission

 June 9, 2017

 Page
 3

 Purchaser

 Shares of Series A Preferred Stock

Novartis Bioventures Ltd.

1,004,507

Trusts and Other Entities affiliated with Muneer A. Satter

202,599

Venture Investors Early Stage Fund IV

573,450

Entities affiliated with Kearny Venture

164,402

Triathlon Medical Ventures

462,678

Joseph Gardner

34,830

Anupam Dalal (1)

148,991

Kevin Peters

1,126

 (1) Anupam Dalal, a director in Aerpio, has claimed beneficial ownership over shares held by TWHVP SPV, LLC
and Revelation TWHVP, LLC.

 On August 28, 2012, Aerpio issued an aggregate of 9,528,622 shares of Series A1 convertible preferred
stock at a price per share of $1.70. The table below sets forth the number of shares of Series A1 convertible preferred stock sold to the Affiliated Stockholders.

 Purchaser

 Shares of Series A1 Preferred Stock

Novartis Bioventures Ltd.

4,164,374

Trusts and Other Entities affiliated with Muneer A. Satter

1,061,004

Venture Investors Early Stage Fund IV

1,122,007

Entities affiliated with Kearny Venture

945,680

Triathlon Medical Ventures

753,812

Joseph Gardner

121,752

Kevin Peters

14,863

 Ms. Breslin

Securities and Exchange Commission

 June 9, 2017

 Page
 4

 On August 23, 2013, Aerpio issued an aggregate of 4,705,882 shares of Series A1
convertible preferred stock at a price per share of $1.70. The table below sets forth the number of shares of Series A1 convertible preferred stock sold to the Affiliated Stockholders.

 Purchaser

 Shares of Series A1 Preferred Stock

Novartis Bioventures Ltd.

2,324,605

Trusts and Other Entities affiliated with Muneer A. Satter

570,723

Venture Investors Early Stage Fund IV

357,092

Entities affiliated with Kearny Venture

446,625

Triathlon Medical Ventures

166,947

Joseph Gardner

64,573

Kevin Peters

10,762

Duane Nash

75,000

 On November 1, 2013, Aerpio issued an aggregate of 5,294,118 shares of Series A1 convertible preferred
stock at a price per share of $1.70. The table below sets forth the number of shares of Series A1 convertible preferred stock sold to the Affiliated Stockholders.

 Purchaser

 Shares of Series A1 Preferred Stock

Novartis Bioventures Ltd.

1,176,471

Trusts and Other Entities affiliated with Muneer A. Satter

1,794,121

Venture Investors Early Stage Fund IV

357,038

Entities affiliated with Kearny Venture

446,558

Triathlon Medical Ventures

166,922

Joseph Gardner

64,563

 On April 22, 2014, Aerpio issued an aggregate of 10,476,182 shares of Series A2 convertible preferred
stock at a price per share of $2.10. The table below sets forth the number of shares of Series A2 convertible preferred stock sold to the Affiliated Stockholders.

 Ms. Breslin

Securities and Exchange Commission

 June 9, 2017

 Page
 5

 Purchaser

 Shares of Series A2 Preferred Stock

Novartis Bioventures Ltd.

1,585,609

Orbimed Private Investments V, L.P.

7,142,857

Trusts and Other Entities affiliated with Muneer A. Satter

519,973

Venture Investors Early Stage Fund IV

139,598

Entities affiliated with Kearny Venture

349,749

Triathlon Medical Ventures

65,264

Joseph Gardner

44,043

Kevin Peters

7,340

 In March 2016, Aerpio issued convertible promissory notes for an aggregate principal amount of $4,496,533. The
convertible notes accrued interest at 8% per annum, compounding annually. The table below sets forth the principal amount of the convertible promissory notes sold and the interest outstanding as of the date of the Merger for the Affiliated
Stockholders. All outstanding principal and interest under these convertible notes were automatically converted into shares of Aerpio common stock, in the numbers set forth in the table below, immediately prior to the Merger, which were then
converted into shares of Company Common Stock (as defined in Amendment No. 2) on a 2.3336572:1 basis at the effective time of the Merger.

 Purchaser

 Principal Price

 Interest

 Number of Shares of Aerpio Common
Stock Upon Conversion

Entities affiliated with Novartis Bioventures Ltd.

$1,394,279

$106,653

714,729

Orbimed Private Investments V, L.P.

$971,096

$74,282

497,798

Trusts and Other Entities affiliated with Muneer A. Satter

$563,992

$43,142

289,111

Venture Investors Early Stage Fund IV

$346,570

$26,510

177,657

Entities affiliated with Kearny Venture

$319,900

$24,470

163,985

Triathlon Medical Ventures

$219,649

$16,802

112,595

Joseph Gardner

$44,832

$3,429

22,981

Kevin Peters

$4,635

$355

2,375

Duane Nash

$10,197

$749

5,211

 Ms. Breslin

Securities and Exchange Commission

 June 9, 2017

 Page
 6

 In July 2016, Aerpio issued convertible promissory notes for an aggregate principal amount
of $4,496,533. The convertible notes accrued interest at 8% per annum, compounding annually. The table below sets forth the principal amount of the convertible promissory notes sold and the interest outstanding as of the date of the Merger for
the Affiliated Stockholders. All outstanding principal and interest under these convertible notes were automatically converted into shares of Aerpio common stock, in the numbers set forth in the table below, immediately prior to the Merger which
were then converted into shares of Company Common Stock (as defined in Amendment No. 2) on a 2.3336572:1 basis at the effective time of the Merger.

 Purchaser

 Principal Price

 Interest

 Number of Shares of Aerpio Common
Stock Upon Conversion

Entities affiliated with Novartis Bioventures Ltd.

$1,394,279

$74,260

699,304

Orbimed Private Investments V, L.P.

$971,096

$51,721

487,055

Trusts and Other Entities affiliated with Muneer A. Satter

$563,992

$30,038

282,871

Venture Investors Early Stage Fund IV

$346,570

$18,458

173,823

Entities affiliated with Kearny Venture

$319,900

$17,038

160,446

Triathlon Medical Ventures

$219,649

$11,699

110,165

Joseph Gardner

$44,832

$2,388

22,485

Kevin Peters

$4,635

$247

2,324

Duane Nash

$10,197

$543

5,114

 Ms. Breslin

Securities and Exchange Commission

 June 9, 2017

 Page
 7

 In October 2016, Aerpio issued convertible promissory notes for an aggregate principal
amount of $3,469,141. The convertible notes accrued interest at 8% per annum, compounding annually. The table below sets forth the principal amount of the convertible promissory notes sold and the interest outstanding as of the date of the
Merger for the Affiliated Stockholders. All outstanding principal and interest under these convertible notes were automatically converted into shares of Aerpio common stock, in the numbers set forth in the table below, immediately prior to the
Merger which were then converted into shares of Company Common Stock (as defined in Amendment No. 2) on a 2.3336572:1 basis at the effective time of the Merger.

 Purchaser

 Principal Price

 Interest

 Number of Shares of Aerpio Common
Stock Upon Conversion

Entities affiliated with Novartis Bioventures Ltd.

$1,075,707

$31,829

527,397

Orbimed Private Investments V, L.P.

$749,214

$22,169

367,325

Trusts and Other Entities affiliated with Muneer A. Satter

$435,128

$12,875

213,334

Venture Investors Early Stage Fund IV

$267,384

$7,912

131,093

Entities affiliated with Kearny Venture

$246,808

$7,303

121,005

Triathlon Medical Ventures

$169,463

$5,014

83,084

Joseph Gardner

$34,589

$1,023

16,958

Kevin Peters

$3,576

$106

1,753

Duane Nash

$7,867

$233

3,856

 Ms. Breslin

Securities and Exchange Commission

 June 9, 2017

 Page
 8

 In January 2017, Aerpio issued convertible promissory notes for an aggregate principal
amount of $297,355. The convertible notes accrued interest at 8% per annum, compounding annually. The table below sets forth the principal amount of the convertible promissory notes sold and the interest outstanding as of the date of the Merger
for the Affiliated Stockholders. All outstanding principal and interest under these convertible notes were automatically converted into shares of Aerpio common stock, in the numbers set forth in the table below, immediately prior to the Merger which
were then converted into shares of Company Common Stock (as defined in Amendment No. 2) on a 2.3336572:1 basis at the effective time of the Merger.

 Purchaser

 Principal Price

 Interest

 Number of Shares of Aerpio Common
Stock Upon Conversion

Entities affiliated with Novartis Bioventures Ltd.

$92,203

$869

44,320

Orbimed Private Investments V, L.P.

$64,218

$605

30,868

Trusts and Other Entities affiliated with Muneer A. Satter

$37,297

$352

17,927

Venture Investors Early Stage Fund IV

$22,919

$216

11,016

Entities affiliated with Kearny Venture

$21,155

$199

10,168

Triathlon Medical Ventures

$14,525

$137

6,982

Joseph Gardner

$2,965

$28

1,425

Kevin Peters

$307

$3

147

Duane Nash

$674

$6

324

 Ms. Breslin

Securities and Exchange Commission

 June 9, 2017

 Page
 9

 In 2011, Joseph Gardner received 8,000 shares of Aerpio common stock as part of his
compensation package for his services as the President and Chief Executive Officer. In 2011, 2013 and 2014, Joseph Gardner received 75,221, 264,229 and 409,496 shares of restricted common stock, respectively, in Aerpio as part of his compensation
package for his services as the President and Chief Executive Officer. In 2011, 2013 and 2014, Kevin Peters received 38,538, 256,373 and 403,929 shares of restricted common stock, respectively, in Aerpio as part of his compensation package for his
services as the Senior Vice President and Chief Scientific Officer. In 2014, Adrienne Graves received 30,788 shares of restricted common stock in Aerpio as part of her compensation package for her services as a consultant to Aerpio.

Relationship to the Company

The Affiliated Stockholders are either private investment funds or individual investors.

Reinhard Ambros and Campbell Murray, affiliates of Novartis Bioventures Ltd., Chau Khuong, an affiliate of Orbimed Private Investments V, L.P.,
Muneer Satter, Paul Weiss, an affiliate of Venture Investors Early Stage Fund IV, Caley Castelein, an affiliate of Kearny Venture, and John Rice, an affiliate of Triathlon Medical Ventures were each directors of Aerpio prior to the closing of the
Merger. Each of these individuals were nominated to the Board in connection with an investment by their respective fund and they did not have any special contractual or other rights, other than those provided in the investment agreements.

Joseph Gardner was an officer and director of Aerpio, Kevin Peters was an officer of Aerpio, and Anupam Dalal, Adrienne Graves and Duane Nash
were directors of Aerpio. Joseph Gardner, Anupam Dalal, Adrienne Graves and Duane Nash were each designated as directors by the holders of a majority of Aerpio’s outstanding common stock.

The Company advises the Staff that the respective equity purchase and convertible note purchase agreements pursuant to which each of these
investors acquired Aerpio securities were the product of extensive arm’s length negotiations among the applicable parties and were subject to customary terms and conditions