SecProbe.io

CORRESP
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Correspondence

 650 Page Mill Road

Palo Alto, CA 94304-1050

650.493.9300

 650.493.6811

 www.wsgr.com

 CONFIDENTIAL TREATMENT REQUESTED

BY APPLIED MOLECULAR TRANSPORT INC.: AMTI-001

FOIA Confidential Treatment Requested Pursuant to 17 C.F.R. §200.83

The entity requesting confidential treatment is:

Applied Molecular Transport Inc.

 1 Tower Place, Suite 850

South San Francisco, CA 94080

 Attention: Tahir Mahmood, Ph.D.

 Chief Executive Officer

CERTAIN PORTIONS OF THIS LETTER HAVE BEEN OMITTED FROM THE VERSION FILED VIA EDGAR. CONFIDENTIAL TREATMENT
HAS BEEN REQUESTED WITH RESPECT TO THE OMITTED PORTIONS. INFORMATION THAT WAS OMITTED IN THE EDGAR VERSION HAS BEEN NOTED IN THIS LETTER WITH A PLACEHOLDER IDENTIFIED BY THE MARK “[*].”

May 20, 2020

 VIA EDGAR AND OVERNIGHT
DELIVERY

 Securities and Exchange Commission

Division of Corporation Finance

 Office of Life Sciences

100 F Street, N.E.

 Washington, D.C. 20549-3720

Attn:
 Michael Clampitt

 Jessica Livingston

 Vanessa Robertson

 David Burton

RE:
 Applied Molecular Transport Inc.

 Registration Statement on Form S-1

 CIK No. 0001801777; Reg. No. 333-238464

 Ladies and Gentlemen:

On behalf of our client, Applied Molecular Transport Inc. (the “Company” or “AMT”), we submit this letter in
response to Comment 1 of the comments received from the Division of Corporation Finance (the “Staff”) of the Securities and Exchange Commission (the “Commission”) by letter dated April 27, 2020 (the
“Comment Letter”), relating to the Company’s Registration Statement on Form S-1 (the “Registration Statement”), originally confidentially submitted in draft form to the
Commission on April 10, 2020 and filed via EDGAR on May 18, 2020.

 CONFIDENTIAL
TREATMENT REQUESTED BY

 APPLIED MOLECULAR TRANSPORT INC.

AUSTIN      BEIJING      BOSTON      BRUSSELS      HONG KONG
     LONDON      LOS ANGELES      NEW YORK      PALO ALTO

SAN DIEGO      SAN FRANCISCO      SEATTLE      SHANGHAI
WASHINGTON, DC     WILMINGTON, DE

 Securities and Exchange Commission

 May 20,
2020

  Page
 2

 CONFIDENTIAL TREATMENT REQUESTED

BY APPLIED MOLECULAR TRANSPORT INC.: AMTI-001

 Because of the commercially sensitive nature of information contained herein, this submission
is accompanied by the Company’s request for confidential treatment for selected portions of this letter. The Company has filed a separate letter with the Office of Freedom of Information and Privacy Act Operations in connection with the
confidential treatment request, pursuant to Rule 83 of the Commission’s Rules on Information and Requests, 17 C.F.R. § 200.83. For the Staff’s reference, we have enclosed a copy of the Company’s letter to the Office of Freedom of
Information and Privacy Act Operations, as well as a copy of this correspondence, marked to show the portions redacted from the version filed via EDGAR and for which the Company is requesting confidential treatment.

For the convenience of the Staff, we have recited the prior comment from the Staff in italicized type and have followed the comment with the
Company’s response.

 Management’s Discussion and Analysis of Financial Condition and Results of Operations

Critical Accounting Policies, Significant Judgments and Use of Estimates

Stock-Based Compensation Expense, page 93

1.
 Once you have an estimated offering price or range, please explain to us how you determined the
fair value of the common stock underlying your equity issuances and the reasons for any differences between the recent valuations of your common stock leading up to the IPO and the estimated offering price. This information will help facilitate our
review of your accounting for equity issuances including stock compensation and beneficial conversion features.

 Price
Range

 To assist the Staff in its evaluation of stock compensation disclosures and certain other matters, the Company advises the Staff
that the Company currently estimates a price range of $[*] to $[*] per share (the “Price Range”) for an initial public offering (the “IPO”) of the Company’s common stock, resulting in a midpoint of the Price
Range of $[*] per share (the “Midpoint Price”). The Price Range has been estimated based on a number of factors, including the progress of the Company’s preclinical studies and clinical trials, other developments in the
Company’s business, input received from the Company’s “testing the waters meetings,” current market conditions, including as a result of the disruptions and volatility in the market due to the
COVID-19 pandemic, and input received from BofA Securities, Inc., Jefferies LLC and SVB Leerink LLC (the “Underwriters”), including discussions that took place on May 15-18, 2020 among representatives of the Company and representatives of the Underwriters.

 The Price
Range does not consider any discount for the current lack of liquidity for the Company’s common stock and assumes a successful IPO with no weighting attributed to any other outcome for the Company’s business, such as remaining a privately
held company, being sold in an acquisition transaction or failing to continue as a going-concern. As is typical for IPOs, the Price Range was not derived using a formal determination of fair value, but was determined as a result of discussions among
representatives of the Company and the Underwriters. During these discussions, the parties considered quantitative factors, as well as non-quantitative factors, such as the valuations of recently completed
public offerings and evaluating those issuers’ respective stages of development as compared to the Company; current market conditions, including the volatility, disruptions and uncertainty caused by the
COVID-19 pandemic and its

 CONFIDENTIAL
TREATMENT REQUESTED BY

 APPLIED MOLECULAR TRANSPORT INC.

 Securities and Exchange Commission

 May 20,
2020

  Page
 3

 CONFIDENTIAL TREATMENT REQUESTED

BY APPLIED MOLECULAR TRANSPORT INC.: AMTI-001

impact on the capital markets; and the current valuations of public companies at a similar stage of clinical development as the Company, taking into account the number of programs of those
companies as compared to the Company. Prior to May 15, 2020, the Underwriters had not provided the Company with a specific estimated price range.

The actual bona fide price range to be included in the Registration Statement has not yet been determined and remains
subject to adjustment based on further discussions between the Company and the Underwriters, developments in the Company’s business, market conditions and other factors that are outside of the Company’s control. The actual price range to
be included in the Registration Statement will be reflected in an amendment to the Registration Statement that will be filed before the commencement of the road show and will comply with the Staff’s interpretation regarding the parameters of
a bona fide price range.

 Equity Grants and Common Stock Valuation

As stated in the Registration Statement, the Company has granted stock-based awards, consisting of stock options, to its employees, directors
and other service providers.

 The Company measures stock-based awards granted to employees, directors and other service providers based on
their estimated fair value on the date of grant and recognizes compensation expense for those awards over the requisite service period, which is generally the vesting period of the respective award. Generally, the Company issues stock options with
only service-based vesting conditions and records the expense for these awards using the straight-line method.

 The Registration Statement
describes the Company’s use of the Black-Scholes option-pricing model (“Black-Scholes”) for the purpose of calculating the estimated grant date fair value of the stock options. The Company’s board of directors (the
“Board”), with input from management, determined the estimated fair value per share of the Company’s common stock for financial reporting purposes to be as follows:

 Valuation Date

 Date of Underlying

Valuation Report

 Estimated Fair Value

Per Share
of Common Stock

 Valuation

Method

September 12, 2018

October 16, 2018

$ 2.38

OPM

December 31, 2018

February 7, 2020

$ 2.43

OPM

March 31, 2019

February 7, 2020

$ 2.46

OPM

June 30, 2019

February 7, 2020

$ 2.50

OPM

September 30, 2019

December 19, 2019

$ 4.62

PWERM

December 31, 2019

February 14, 2020

$ 6.14

PWERM

March 31, 2020

May 13, 2020

$ 4.61

PWERM

 In connection with the preparation of the Registration Statement, management prepared the Company’s
financial statements in 2020 for the annual audit of each of the years ended December 31, 2018 and 2019, and for the unaudited results for the quarter ended March 31, 2020. As noted in the table above, the Company obtained valuation
reports, and the Company used such valuations for determining the valuation of each share of common stock, for the December 31, 2018, March 31, 2019 and June 30, 2019 valuation dates on February 7, 2020. As a result, the
valuations for these valuation dates were determined for financial reporting purposes with the benefit of hindsight, which ranged from seven to thirteen months. Each of the other valuation determinations was completed on a more contemporaneous
basis, within one to three months’ time.

 CONFIDENTIAL
TREATMENT REQUESTED BY

 APPLIED MOLECULAR TRANSPORT INC.

 Securities and Exchange Commission

 May 20,
2020

  Page
 4

 CONFIDENTIAL TREATMENT REQUESTED

BY APPLIED MOLECULAR TRANSPORT INC.: AMTI-001

 These estimated fair values per share of common stock were determined after considering
valuation reports from an independent third-party valuation firm as well as other objective and subjective factors as appropriate, including the progress of the Company’s preclinical studies and clinical trials; the Company’s stage of
development and programs; the Company’s cash burn and cash balances; the value of public companies with similar profiles to the Company; the issuance of preferred stock and the rights, preferences and privileges of preferred stock as compared
to common stock; the need for and market related to additional private financings, such as preferred stock financings; the likelihood of achieving a liquidity event, including an IPO; and the other factors described below. A discussion of each
valuation and equity grant since January 1, 2019, along with a comparison of the estimated fair value of the Company’s common stock to the Midpoint Price is set forth below.

The following table sets forth all equity awards made by the Company since January 1, 2019 to the present:

 Grant date

Type of
award

Number of
shares

Exercise price
of options per
share

Estimated fair value
of common stock per
share on grant date
(utilized for ASC 718
calculation)

 March 26, 2019

Options

531,016

$
2.38

$
2.43

 April 26, 2019

Options

210,672

$
2.38

$
2.43

 May 30, 2019

Options

20,000

$
2.38

$
2.46

 July 3, 2019

Options

12,000

$
2.38

$
2.50

 March 6, 2020*

Options

1,126,066

$
4.61
*

$
6.14

 March 30, 2020*

Options

862,611

$
4.61
*

$
6.14

 May 14, 2020

Options

167,500

$
4.61

$
TBD

 * See the discussion below for additional details on the repricing of the March 6, 2020 and March 30, 2020 grants in
which the exercise price for all of these grants was repriced by the Company from $6.14 to $4.61 effective May 14, 2020 and as disclosed in the Registration Statement.

March 26, 2019, April 26, 2019, May 30, 2019 and July 3, 2019 Grants

The following section discusses the underlying valuations and analysis applicable to the March 26, 2019, April 26, 2019, May 30,
2019 and July 3, 2019 stock option grants.

 September 12, 2018 Valuation. In
preparing the September 12, 2018 valuation (based on a report issued on October 16, 2018), the Company determined its enterprise value using the option pricing method (“OPM”) “back solve” method. The resulting
estimated fair value of the Company’s common stock was $2.38 per share on a non-marketable, minority basis.

 CONFIDENTIAL
TREATMENT REQUESTED BY

 APPLIED MOLECULAR TRANSPORT INC.

 Securities and Exchange Commission

 May 20,
2020

  Page
 5

 CONFIDENTIAL TREATMENT REQUESTED

BY APPLIED MOLECULAR TRANSPORT INC.: AMTI-001

 In an OPM framework, the “back solve” method for inferring the equity value implied
by a recent financing transaction involves making assumptions for the expected time to liquidity, risk-free rate and volatility and then solving for the value of such equity such that the value for the most recent financing equal the amount paid.
The method was selected as it was concluded that the Company’s recent round of Series B preferred stock financing was a reasonable indication of value as it was considered to be an arm’s length transaction negotiated by sophisticated
investors and the financing terms were fairly negotiated and reasonably reflected the expected economics for the Company going forward. In September 2018 and October 2018, the Company issued and sold an aggregate of 3,992,919 shares of Series B
convertible preferred stock at a purchase price of $7.77 per share for aggregate gross proceeds of approximately $31.0 million.

 The
Series B convertible preferred stock per share price of $7.77 was then “back solved” to the capitalization of the Company to arrive at the per share fair market value of the Company’s common stock using the Black-Scholes method as
described in the Registration Statement. For the September 12, 2018 valuation, the Company used:

•

 an implied equity value of approximately $[*];

•

 a probability-weighted time to exit of 2.0 years after accounting for the Company’s approximation of the
time it would take the Company to reach an IPO or merger and acquisition (“M&A”) event;

•

 a risk-free interest rate of 2.74% based on the yield of 2.0-year U.S.
Treasury bonds as of September 12, 2018, a maturity which closely approximated the forecasted liquidity horizon of the Company; and

•

 an estimate for expected volatility of 70.0% based on an analysis of the historical volatility of guideline
public companies and factors specific to the Company.

 A discount for lack of marketability (“DLOM”) of
50.0% was then applied to account for the lack of an active trading market in the Company’s securities.

December 31, 2018 Valuation. The Company determined a December 31, 2018 valuation
(based on a report issued on February 7, 2020) based on the valuation determinations as of September 12, 2018 and June 30, 2019 (as discussed below). The Company used an interpolation method, assuming a straight-line linear movement
in value, for this December 31, 2018 valuation between the September 12, 2018 and June 30, 2019 valuations. The resulting estimated fair value of the Company’s common stock was $2.43 per share as of December 31, 2018 on a non-marketable, minority basis.

 March 31, 2019
Valuation. The Company determined a March 31, 2019 valuation (based on a report issued on February 7, 2020) based on the valuation determinations as of the September 12, 2018 and

 CONFIDENTIAL
TREATMENT REQUESTED BY

 APPLIED MOLECULAR TRANSPORT INC.

 Securities and Exchange Commission

 May 20,
2020

  Page
 6

 CONFIDENTIAL TREATMENT REQUESTED

BY APPLIED MOLECULAR TRANSPORT INC.: AMTI-001

June 30, 2019 (as discussed below). The Company used an interpolation method, assuming a straight-line linear movement in value, for March 31, 2019 valuation between the
September 12, 2018 and June 30, 2019 valuations. The resulting estimated fair value of the Company’s common stock was $2.46 per share as of March 31, 2019 on a non-marketable, minority
basis.

 June 30, 2019 Valuation. In preparing the June 30, 2019 valuation
(based on a report issued in February 7, 2020), the Company used the OPM. The resulting estimated fair value of the Company’s common stock was $2.50 per share on a non-marketable, minority basis. The
key drivers in the increased price included the continued grow