[SCHEDULE 13D/A] PepGen Inc. SEC Filing

Rhea-AI Filing Summary

PepGen Inc. (PEPG) is the subject of Amendment No. 4 to a Schedule 13D filed by RA Capital Management, L.P., Peter Kolchinsky, Rajeev Shah and RA Capital Healthcare Fund, L.P. Collectively the Reporting Persons beneficially own 20,099,753 shares, equal to 29.2% of the outstanding common stock based on 68,737,224 shares outstanding. The Fund acquired 9,375,000 shares in PepGen's 2025 public offering at $3.20 per share for an aggregate purchase price of $30.0 million, funded from the Fund's working capital. Certain employee options totaling up to 11,667 shares vest on schedule and a customary 60-day lock-up from the offering applies to directors and officers.

Positive

• Significant ownership stake: Reporting Persons beneficially own 20,099,753 shares (29.2%), indicating substantial influence.
• Strategic capital deployment: Fund purchased 9,375,000 shares in the 2025 offering for $30.0 million, funded from working capital.
• Clear governance disclosures: Delegation of voting and disposition powers to RA Capital and joint filing agreement are documented.

Negative

• No majority control: The 29.2% stake is large but does not constitute control or a majority.
• Potential concentration risk: Large position may create liquidation or market-impact risk if sold.
• Insider lock-up: 60-day lock-up on officers/directors may constrain immediate insider selling but also delays market liquidity clarity.

Insights

Securities Analyst

TL;DR: Large passive stake established via public offering increases influence but not majority control.

The Reporting Persons disclose a substantial 29.2% beneficial position in PepGen following a $30.0 million purchase of 9.375 million shares in the 2025 offering. The share count and percent are calculated off the prospectus figure of 68,737,224 outstanding shares. RA Capital functions as adviser with shared voting/dispositive power reported for 20,099,753 shares, which signals material influence though not outright control. The 60-day lock-up on insiders may temporarily limit secondary share supply.

Corporate Governance Specialist

TL;DR: Reporting structure and delegations suggest coordinated ownership but include standard disclaimers.

The filing details delegated voting and disposition powers from the Fund and Nexus Fund II to RA Capital, and clarifies disclaimers of beneficial ownership by certain entities and individuals. This joint filing and the disclosed shared powers indicate a coordinated group approach under Rule 13d-1(k). Vesting employee options and the lock-up agreement are disclosed; no litigation or convictions are reported for the Reporting Persons.

SECURITIES AND EXCHANGE COMMISSION
Washington, D.C. 20549

SCHEDULE 13D

Under the Securities Exchange Act of 1934

(Amendment No. 4)

PEPGEN INC.

(Name of Issuer)

Common stock, par value $0.0001 per share

(Title of Class of Securities)

713317105

(CUSIP Number)

Peter Kolchinsky
RA Capital Management, L.P., 200 Berkeley Street, 18th Floor
Boston, MA, 02116
617.778.2500

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

09/26/2025

(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.

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

CUSIP No. 713317105

1

Name of reporting person

RA Capital Management, L.P.

2

Check the appropriate box if a member of a Group (See Instructions)

(a)
(b)

3

SEC use only

4

Source of funds (See Instructions)

AF

5

Check if disclosure of legal proceedings is required pursuant to Items 2(d) or 2(e)

6

Citizenship or place of organization

DELAWARE

Number of Shares Beneficially Owned by Each Reporting Person With:

7	Sole Voting Power 0.00
8	Shared Voting Power 20,099,753.00
9	Sole Dispositive Power 0.00
10	Shared Dispositive Power 20,099,753.00

11

Aggregate amount beneficially owned by each reporting person

20,099,753.00

12

Check if the aggregate amount in Row (11) excludes certain shares (See Instructions)

13

Percent of class represented by amount in Row (11)

29.2 %

14

Type of Reporting Person (See Instructions)

IA, PN

SCHEDULE 13D

CUSIP No. 713317105

1

Name of reporting person

Peter Kolchinsky

2

Check the appropriate box if a member of a Group (See Instructions)

(a)
(b)

3

SEC use only

4

Source of funds (See Instructions)

AF

5

Check if disclosure of legal proceedings is required pursuant to Items 2(d) or 2(e)

6

Citizenship or place of organization

UNITED STATES

Number of Shares Beneficially Owned by Each Reporting Person With:

7	Sole Voting Power 0.00
8	Shared Voting Power 20,099,753.00
9	Sole Dispositive Power 0.00
10	Shared Dispositive Power 20,099,753.00

11

Aggregate amount beneficially owned by each reporting person

20,099,753.00

12

Check if the aggregate amount in Row (11) excludes certain shares (See Instructions)

13

Percent of class represented by amount in Row (11)

29.2 %

14

Type of Reporting Person (See Instructions)

HC, IN

SCHEDULE 13D

CUSIP No. 713317105

1

Name of reporting person

Rajeev Shah

2

Check the appropriate box if a member of a Group (See Instructions)

(a)
(b)

3

SEC use only

4

Source of funds (See Instructions)

AF

5

Check if disclosure of legal proceedings is required pursuant to Items 2(d) or 2(e)

6

Citizenship or place of organization

UNITED STATES

Number of Shares Beneficially Owned by Each Reporting Person With:

7	Sole Voting Power 0.00
8	Shared Voting Power 20,099,753.00
9	Sole Dispositive Power 0.00
10	Shared Dispositive Power 20,099,753.00

11

Aggregate amount beneficially owned by each reporting person

20,099,753.00

12

Check if the aggregate amount in Row (11) excludes certain shares (See Instructions)

13

Percent of class represented by amount in Row (11)

29.2 %

14

Type of Reporting Person (See Instructions)

HC, IN

SCHEDULE 13D

CUSIP No. 713317105

1

Name of reporting person

RA Capital Healthcare Fund, L.P.

2

Check the appropriate box if a member of a Group (See Instructions)

(a)
(b)

3

SEC use only

4

Source of funds (See Instructions)

WC

5

Check if disclosure of legal proceedings is required pursuant to Items 2(d) or 2(e)

6

Citizenship or place of organization

DELAWARE

Number of Shares Beneficially Owned by Each Reporting Person With:

7	Sole Voting Power 0.00
8	Shared Voting Power 18,554,273.00
9	Sole Dispositive Power 0.00
10	Shared Dispositive Power 18,554,273.00

11

Aggregate amount beneficially owned by each reporting person

18,554,273.00

12

Check if the aggregate amount in Row (11) excludes certain shares (See Instructions)

13

Percent of class represented by amount in Row (11)

27.0 %

14

Type of Reporting Person (See Instructions)

PN

SCHEDULE 13D

Item 1.	Security and Issuer
(a)	Title of Class of Securities: Common stock, par value $0.0001 per share
(b)	Name of Issuer: PEPGEN INC.
(c)	Address of Issuer's Principal Executive Offices: 321 Harrison Avenue, 8th Floor, Boston, MASSACHUSETTS , 02118.
Item 1 Comment: This Amendment No. 4 (this "Amendment No. 4" or this "Schedule 13D/A") amends and supplements the statement on Schedule 13D originally filed with the Securities and Exchange Commission (the "SEC") on May 20, 2022 and amended on June 23, 2022, February 13, 2024 and March 11, 2024 (as amended, the "Statement") by the Reporting Persons. Unless otherwise defined herein, capitalized terms used in this Amendment No. 4 shall have the meanings ascribed to them in the Statement. Unless amended or supplemented below, the information in the Statement remains unchanged.
Item 2.	Identity and Background
(a)	This Schedule 13D/A is being filed on behalf of RA Capital Management, L.P. ("RA Capital"), Peter Kolchinsky, Rajeev Shah, and RA Capital Healthcare Fund, L.P. (the "Fund"). RA Capital, Dr. Kolchinsky, Mr. Shah and the Fund are collectively referred to herein as the "Reporting Persons." The agreement among the Reporting Persons to file this Schedule 13D/A jointly in accordance with Rule 13d-1(k) of the Securities Exchange Act of 1934, as amended, (the "Act") is attached hereto as Exhibit 99.1. The Reporting Persons' beneficial ownership of the Issuer's common stock consists of (i) 18,554,273 shares of common stock directly held by the Fund; (ii) 1,302,600 shares of common stock directly held by the RA Capital Nexus Fund II, L.P. (the "Nexus Fund II"); (iii) 207,672 shares of common stock directly held by a separately managed account (the "Account"); and (iv) a total of 34,722 shares underlying vested stock options (right to buy), and 486 shares underlying stock options (right to buy) which shall vest within 60 days of this filing held by Dr. Joshua Resnick for the benefit of RA Capital. RA Capital Healthcare Fund GP, LLC is the general partner of the Fund and RA Capital Nexus Fund II GP, LLC is the general partner of the Nexus Fund II. The general partner of RA Capital is RA Capital Management GP, LLC, of which Dr. Kolchinsky and Mr. Shah are the controlling persons. RA Capital serves as investment adviser for the Fund, the Nexus Fund II, and the Account and may be deemed a beneficial owner, for purposes of Section 13(d) of the Act, of any securities of the Issuer held by the Fund, the Nexus Fund II or the Account. The Fund and the Nexus Fund II have delegated to RA Capital the sole power to vote and the sole power to dispose of all securities held in the Fund and the Nexus Fund II, and each of these funds has divested themselves of voting and investment power over the reported securities they hold and may not revoke that delegation on less than 61 days' notice. The Fund and the Nexus Fund II disclaim beneficial ownership of the securities they hold for purposes of Section 13(d) of the Act and therefore disclaim any obligation to report ownership of the reported securities under Section 13(d) of the Act. As managers of RA Capital, Dr. Kolchinsky and Mr. Shah may be deemed beneficial owners, for purposes of Section 13(d) of the Act, of any securities of the Issuer beneficially owned by RA Capital. RA Capital, Dr. Kolchinsky, and Mr. Shah disclaim beneficial ownership of the securities reported in this Statement other than for the purpose of determining their obligations under Section 13(d) of the Act, and the filing of the Statement shall not be deemed an admission that either RA Capital, Dr. Kolchinsky, or Mr. Shah is the beneficial owner of such securities for any other purpose.
(b)	The address of the principal business office of each of the Reporting Persons is 200 Berkeley Street, 18th Floor, Boston, MA 02116.
(c)	The Fund is a private investment vehicle. RA Capital provides investment management services to the Fund, the Nexus Fund II and the Account. The principal occupation of each of Dr. Kolchinsky and Mr. Shah is investment management.
(d)	During the last five years, none of the Reporting Persons has been convicted in a criminal proceeding (excluding traffic violations or similar misdemeanors).
(e)	During the last five years, none of the Reporting Persons has been a party to a civil proceeding of a judicial or administrative body of competent jurisdiction and as a result of such proceeding was or is subject to a judgment, decree of final order enjoining future violations of, or prohibiting or mandating activities subject to, federal or state securities laws or finding any violation with respect to such laws.
(f)	See Item 6 of the cover pages.
Item 3.	Source and Amount of Funds or Other Consideration
	Item 3 of the Statement is hereby amended and supplemented as follows: On September 26, 2025, the Fund purchased 9,375,000 shares of common stock at a price of $3.20 per share from the underwriters of the Issuer's public offering (the "2025 Public Offering"). The aggregate purchase price for all securities acquired by the Fund in the 2025 Public Offering was $30.0 million, which was funded by the working capital of the Fund.
Item 5.	Interest in Securities of the Issuer
(a)	Rows 11 and 13 of each Reporting Person's cover page to this Schedule 13D/A set forth the aggregate number of shares of common stock and percentages of the shares of common stock beneficially owned by such Reporting Person and are incorporated by reference. The percentage set forth in each row 13 is based upon 68,737,224 shares of common stock outstanding as of September 26, 2025, as disclosed in the Issuer's prospectus supplement dated September 24, 2025 filed with the SEC on September 25, 2025, and giving effect to stock options, to the extent exercisable within 60 days hereof, as referenced herein.
(b)	Rows 7 through 10 of each Reporting Person's cover page to this Schedule 13D/A set forth the number of shares of common stock as to which such Reporting Person has the sole or shared power to vote or direct the vote and sole or shared power to dispose or to direct the disposition and are incorporated by reference.
(c)	Except as set forth herein, none of the Reporting Persons has effected any transactions with respect to the securities of the Issuer during the past sixty days. No. Price Per Transaction Purchaser Date Shares Share ($) Vest Stock Option (Right to Buy) RA Capital 08/06/2025 243 (1) Vest Stock Option (Right to Buy) RA Capital 09/06/2025 243 (1) Purchase (2025 Public Offering) Fund 09/26/2025 9,375,000 3.20 Vest Stock Option (Right to Buy) RA Capital 10/06/2025 243 (1)(2) Vest Stock Option (Right to Buy) RA Capital 11/06/2025 243 (1)(2) (1) This option represents a right to purchase a total of 11,667 shares of the Issuer's common stock, which began vesting from May 6, 2022 and vested with respect to 25% of the shares on May 6, 2023, with the remainder vesting in 36 equal monthly installments, subject to Dr. Joshua Resnick's continuous service to the Issuer through each vesting date. These options have an exercise price of $12.00 per share. (2) Represents future vesting within 60 days from the filing date of this Schedule 13D/A.
(d)	No person (other than the Reporting Persons) is known to have the right to receive or the power to direct the receipt of dividends from, or the proceeds from the sale of, the securities subject to this Schedule 13D/A.
(e)	Not applicable.
Item 6.	Contracts, Arrangements, Understandings or Relationships With Respect to Securities of the Issuer
	Item 6 of the Statement is hereby amended and supplemented as follows: Lock Up Agreement In connection with the 2025 Public Offering, each of the Issuer's directors and executive officers, including Dr. Resnick, entered into a customary lock-up agreement with the underwriters with respect to its common stock, for a period of 60 days (the " 2025 Lock-up Agreement"). The foregoing description of the 2025 Lock-up Agreement is not complete and is qualified in its entirety by reference to the full text of the form of the lock-up agreement attached hereto as Exhibit 99.2 and incorporated by reference herein.
Item 7.	Material to be Filed as Exhibits.
	Exhibit 99.1 Joint Filing Agreement (incorporated by reference to Exhibit 1 to the Reporting Persons' Schedule 13D/A filed with the SEC on March 11, 2024). Exhibit 99.2 Form of Lock-Up Agreement (incorporated by reference to Exhibit A to the Underwriting Agreement dated September 24, 2025 filed as Exhibit 1.1 to the Issuer's Current Report on Form 8-K, filed with the SEC on September 26, 2025).

SIGNATURE

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

RA Capital Management, L.P.

Signature:	/s/ Peter Kolchinsky
Name/Title:	By Peter Kolchinsky, Authorized Signatory
Date:	09/30/2025

Peter Kolchinsky

Signature:	/s/ Peter Kolchinsky
Name/Title:	Peter Kolchinsky
Date:	09/30/2025

Rajeev Shah

Signature:	/s/ Rajeev Shah
Name/Title:	Rajeev Shah
Date:	09/30/2025

RA Capital Healthcare Fund, L.P.

Signature:	/s/ Peter Kolchinsky
Name/Title:	By RA Capital Healthcare Fund GP, LLC, its General Partner, By Peter Kolchinsky, Manager
Date:	09/30/2025

FAQ

How many PepGen (PEPG) shares do the Reporting Persons beneficially own?

They beneficially own 20,099,753 shares, representing 29.2% of PepGen's outstanding common stock as reported.

What purchase did the RA Capital Healthcare Fund make in the 2025 offering?

The Fund purchased 9,375,000 shares at $3.20 per share, for an aggregate of $30.0 million, funded by the Fund's working capital.

What is the basis for the percentage ownership reported?

The percentage is based on 68,737,224 shares outstanding disclosed in the Issuer's prospectus supplement dated September 24, 2025.

Are there any lock-up restrictions disclosed?

Yes. PepGen's directors and executive officers entered into a customary 60-day lock-up with the underwriters in connection with the 2025 public offering.

Do RA Capital, Kolchinsky or Shah claim sole beneficial ownership?

No. The filing discloses shared voting and dispositive power of 20,099,753 shares and contains disclaimers that certain entities and individuals do not claim beneficial ownership beyond Section 13(d) filing obligations.