[SCHEDULE 13G] Assembly Biosciences, Inc SEC Filing

Rhea-AI Filing Summary

RA Capital Management, L.P., RA Capital Healthcare Fund, L.P., and principals Peter Kolchinsky and Rajeev Shah reported collective beneficial ownership of 1,530,615 shares of Assembly Biosciences, Inc. common stock, representing 9.5% of the class based on 15,560,009 shares outstanding plus 510,205 shares issuable upon exercise of Class A Warrants. The Fund directly holds 1,020,410 shares and warrants exercisable for up to 510,205 shares (Class A immediately exercisable; Class B exercisable beginning November 15, 2026). The warrants include a Beneficial Ownership Blocker preventing exercise that would raise ownership above 9.99%.

The Fund delegated sole voting and dispositive power over its holdings to RA Capital, and RA Capital and the individual managers disclaim beneficial ownership except as required for Section 13(d) reporting. The filing states the positions were not acquired to influence control of the issuer.

Positive

• Clear disclosure of total position (1,530,615 shares) and the basis for the percentage (15,560,009 shares outstanding plus exercisable Class A warrants).
• Warrants include a Beneficial Ownership Blocker that prevents accidental exercise above 9.99%, limiting unintended control changes.
• Delegation of voting and dispositive power to the investment adviser is explicitly stated, clarifying who manages the securities.

Negative

• Position close to 10% threshold (9.5%) which leaves limited room before triggering higher ownership consequences.
• Class B Warrants become exercisable in late 2026 and could alter the ownership picture subject to contractual limits.

Insights

Securities Analyst

TL;DR: A significant 9.5% position disclosed with warrants and ownership limits; RA Capital exercises voting/dispositive control via delegation.

This Schedule 13G shows RA Capital and affiliated persons collectively reported economic exposure to 1,530,615 shares (including warrants) of ASMB, equal to 9.5% of the diluted class as calculated by the filing. Material features include immediate exercisable Class A Warrants for 510,205 shares and a Class B tranche with a delayed exercise window in late 2026. Crucially, the warrants contain a contractual blocker that stops exercise above a 9.99% ownership threshold, which constrains potential dilution or control shifts. The Fund delegated sole voting and dispositive power to RA Capital, clarifying who directs trading and voting actions while the parties disclaim broader beneficial ownership for other purposes.

Corporate Governance Expert

TL;DR: Disclosure emphasizes passive reporting posture and procedural limits on escalating ownership above 9.99%.

The filing explicitly disclaims formation of a group and states the securities were not acquired to change control. The delegation of voting and dispositive powers from the Fund to the adviser is documented and irrevocable on less than 61 days' notice, which affects how ownership is characterized under Section 13(d). The Beneficial Ownership Blocker in the warrants is a material contractual protection that prevents the Fund from exceeding the 9.99% threshold, reducing the likelihood of an unintended regulatory trigger for additional filings or control presumptions.

SECURITIES AND EXCHANGE COMMISSION
Washington, D.C. 20549

SCHEDULE 13G

UNDER THE SECURITIES EXCHANGE ACT OF 1934

Assembly Biosciences, Inc.

(Name of Issuer)

Common Stock, par value $0.001 per share

(Title of Class of Securities)

045396207

(CUSIP Number)

08/11/2025

(Date of Event Which Requires Filing of this Statement)

Check the appropriate box to designate the rule pursuant to which this Schedule is filed:

Rule 13d-1(b)

Rule 13d-1(c)

Rule 13d-1(d)

SCHEDULE 13G

CUSIP No. 045396207

1

Names of Reporting Persons

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

Citizenship or Place of Organization

DELAWARE

Number of Shares Beneficially Owned by Each Reporting Person With:

5	Sole Voting Power 0.00
6	Shared Voting Power 1,530,615.00
7	Sole Dispositive Power 0.00
8	Shared Dispositive Power 1,530,615.00

9

Aggregate Amount Beneficially Owned by Each Reporting Person

1,530,615.00

10

Check box if the aggregate amount in row (9) excludes certain shares (See Instructions)

11

Percent of class represented by amount in row (9)

9.5 %

12

Type of Reporting Person (See Instructions)

IA, PN

SCHEDULE 13G

CUSIP No. 045396207

1

Names of Reporting Persons

Peter Kolchinsky

2

Check the appropriate box if a member of a Group (see instructions)

(a)
(b)

3

Sec Use Only

4

Citizenship or Place of Organization

UNITED STATES

Number of Shares Beneficially Owned by Each Reporting Person With:

5	Sole Voting Power 0.00
6	Shared Voting Power 1,530,615.00
7	Sole Dispositive Power 0.00
8	Shared Dispositive Power 1,530,615.00

9

Aggregate Amount Beneficially Owned by Each Reporting Person

1,530,615.00

10

Check box if the aggregate amount in row (9) excludes certain shares (See Instructions)

11

Percent of class represented by amount in row (9)

9.5 %

12

Type of Reporting Person (See Instructions)

HC, IN

SCHEDULE 13G

CUSIP No. 045396207

1

Names of Reporting Persons

Rajeev Shah

2

Check the appropriate box if a member of a Group (see instructions)

(a)
(b)

3

Sec Use Only

4

Citizenship or Place of Organization

UNITED STATES

Number of Shares Beneficially Owned by Each Reporting Person With:

5	Sole Voting Power 0.00
6	Shared Voting Power 1,530,615.00
7	Sole Dispositive Power 0.00
8	Shared Dispositive Power 1,530,615.00

9

Aggregate Amount Beneficially Owned by Each Reporting Person

1,530,615.00

10

Check box if the aggregate amount in row (9) excludes certain shares (See Instructions)

11

Percent of class represented by amount in row (9)

9.5 %

12

Type of Reporting Person (See Instructions)

HC, IN

SCHEDULE 13G

CUSIP No. 045396207

1

Names of Reporting Persons

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

Citizenship or Place of Organization

DELAWARE

Number of Shares Beneficially Owned by Each Reporting Person With:

5	Sole Voting Power 0.00
6	Shared Voting Power 1,530,615.00
7	Sole Dispositive Power 0.00
8	Shared Dispositive Power 1,530,615.00

9

Aggregate Amount Beneficially Owned by Each Reporting Person

1,530,615.00

10

Check box if the aggregate amount in row (9) excludes certain shares (See Instructions)

11

Percent of class represented by amount in row (9)

9.5 %

12

Type of Reporting Person (See Instructions)

PN

SCHEDULE 13G

Item 1.
(a)	Name of issuer: Assembly Biosciences, Inc.
(b)	Address of issuer's principal executive offices: Two Tower Place, 7th Floor, South San Francisco, CA, 94080.
Item 2.
(a)	Name of person filing: The names of the persons filing this report (collectively, the "Reporting Persons") are: RA Capital Management, L.P. ("RA Capital") Peter Kolchinsky Rajeev Shah RA Capital Healthcare Fund, L.P. (the "Fund") The Reporting Persons expressly disclaim status as a "group" for purposes of this Schedule 13G.
(b)	Address or principal business office or, if none, residence: The address of the principal business office of each of the Reporting Persons is: c/o RA Capital Management, L.P., 200 Berkeley Street, 18th Floor, Boston MA 02116
(c)	Citizenship: RA Capital and the Fund are Delaware limited partnerships. Dr. Kolchinsky and Mr. Shah are United States citizens.
(d)	Title of class of securities: Common Stock, par value $0.001 per share
(e)	CUSIP No.: 045396207
Item 3.	If this statement is filed pursuant to §§ 240.13d-1(b) or 240.13d-2(b) or (c), check whether the person filing is a:
(a)	Broker or dealer registered under section 15 of the Act (15 U.S.C. 78o);
(b)	Bank as defined in section 3(a)(6) of the Act (15 U.S.C. 78c);
(c)	Insurance company as defined in section 3(a)(19) of the Act (15 U.S.C. 78c);
(d)	Investment company registered under section 8 of the Investment Company Act of 1940 (15 U.S.C. 80a-8);
(e)	An investment adviser in accordance with § 240.13d-1(b)(1)(ii)(E);
(f)	An employee benefit plan or endowment fund in accordance with § 240.13d-1(b)(1)(ii)(F);
(g)	A parent holding company or control person in accordance with § 240.13d-1(b)(1)(ii)(G);
(h)	A savings associations as defined in Section 3(b) of the Federal Deposit Insurance Act (12 U.S.C. 1813);
(i)	A church plan that is excluded from the definition of an investment company under section 3(c)(14) of the Investment Company Act of 1940 (15 U.S.C. 80a-3);
(j)	A non-U.S. institution in accordance with § 240.13d-1(b)(1)(ii)(J). If filing as a non-U.S. institution in accordance with § 240.13d-1(b)(1)(ii)(J), please specify the type of institution:
(k)	Group, in accordance with Rule 240.13d-1(b)(1)(ii)(K).
Item 4.	Ownership
(a)	Amount beneficially owned: Row 9 of each Reporting Person's cover page to this Schedule 13G sets forth the aggregate number of securities of the Issuer beneficially owned by such Reporting Person and is incorporated by reference. The Fund directly holds (i) 1,020,410 shares of common stock, (ii) warrants (the "Class A Warrants") exercisable for up to 510,205 shares of common stock and (iii) warrants (the "Class B Warrants" and, together with the Class A Warrants, the "Warrants") exercisable for up to 510,205 shares of common stock. The Class A Warrants are immediately exercisable and will expire upon the earlier of (i) five years from the date of issuance and (ii) the date that is 30 days after the public announcement that the Issuer has achieved a predefined clinical milestone. The Class B Warrants are exercisable on or after November 15, 2026 and will expire on December 31, 2026, subject to their automatic termination in full in the event that the Issuer announces the completion of a non-dilutive capital raise of at least $75.0 million prior to November 15, 2026. The Warrants contain a provision (the "Beneficial Ownership Blocker") which precludes exercise of the Warrants to the extent that, following exercise, the Fund, together with its affiliates and other attribution parties, would own more than 9.99% of the common stock outstanding. RA Capital Healthcare Fund GP, LLC is the general partner of the Fund. 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 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 Fund has delegated to RA Capital the sole power to vote and the sole power to dispose of all securities held in the Fund's portfolio, including the shares of the Issuer's common stock reported herein. Because the Fund has divested voting and investment power over the reported securities it holds and may not revoke that delegation on less than 61 days' notice, the Fund disclaims beneficial ownership of the securities it holds for purposes of 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 Schedule 13G other than for the purpose of determining their obligations under Section 13(d) of the Act, and the filing of this Schedule 13G 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)	Percent of class: Row 11 of each Reporting Person's cover page to this Schedule 13G sets forth the percentages of common stock of the Issuer beneficially owned by such Reporting Person and is incorporated by reference. Such percentage is based upon the sum of (i) 15,560,009 shares of the Issuer's common stock outstanding as of August 11, 2025, as disclosed in the Issuer's prospectus supplement dated August 8, 2025 filed with the Securities and Exchange Commission (the "SEC") on August 11, 2025 and (ii) 510,205 shares of common stock issuable upon the exercise of the Class A Warrants.
(c)	Number of shares as to which the person has:
	(i) Sole power to vote or to direct the vote: Row 5 of each Reporting Person's cover page to this Schedule 13G sets forth the sole power to vote or to direct the vote of securities of the Issuer beneficially owned by such Reporting Person and is incorporated by reference.
	(ii) Shared power to vote or to direct the vote: Row 6 of each Reporting Person's cover page to this Schedule 13G sets forth the shared power to vote or to direct the vote of securities of the Issuer beneficially owned by such Reporting Person and is incorporated by reference.
	(iii) Sole power to dispose or to direct the disposition of: Row 7 of each Reporting Person's cover page to this Schedule 13G sets forth the sole power to dispose or to direct the disposition of securities of the Issuer beneficially owned by such Reporting Person and is incorporated by reference.
	(iv) Shared power to dispose or to direct the disposition of: Row 8 of each Reporting Person's cover page to this Schedule 13G sets forth the shared power to dispose or to direct the disposition of securities of the Issuer beneficially owned by such Reporting Person and is incorporated by reference.
Item 5.	Ownership of 5 Percent or Less of a Class.
Item 6.	Ownership of more than 5 Percent on Behalf of Another Person.
	Not Applicable
Item 7.	Identification and Classification of the Subsidiary Which Acquired the Security Being Reported on by the Parent Holding Company or Control Person.
	Not Applicable
Item 8.	Identification and Classification of Members of the Group.
	Not Applicable
Item 9.	Notice of Dissolution of Group.
	Not Applicable

Item 10.

Certifications:

By signing below I certify that, to the best of my knowledge and belief, the securities referred to above were not acquired and are not held for the purpose of or with the effect of changing or influencing the control of the issuer of the securities and were not acquired and are not held in connection with or as a participant in any transaction having that purpose or effect, other than activities solely in connection with a nomination under ?? 240.14a-11.

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:	08/18/2025

Peter Kolchinsky

Signature:	/s/ Peter Kolchinsky
Name/Title:	Peter Kolchinsky
Date:	08/18/2025

Rajeev Shah

Signature:	/s/ Rajeev Shah
Name/Title:	Rajeev Shah
Date:	08/18/2025

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:	08/18/2025

Exhibit Information

Exhibit 99.1 Joint Filing Agreement

FAQ

How many Assembly Biosciences (ASMB) shares do RA Capital and affiliates report owning?

They report beneficial ownership of 1,530,615 shares, representing 9.5% of the class as disclosed in the filing.

What instruments make up the reported 1,530,615 shares in ASMB?

The Fund directly holds 1,020,410 shares plus warrants exercisable for up to 510,205 shares (Class A and Class B Warrants).

Are the warrants immediately exercisable and are there limits on exercise?

The Class A Warrants are immediately exercisable; the Class B Warrants are exercisable on or after November 15, 2026. A Beneficial Ownership Blocker prevents exercise that would raise ownership above 9.99%.

Who has voting and dispositive power over the Fund's ASMB shares?

The Fund delegated sole voting and sole dispositive power over its ASMB securities to RA Capital, the investment adviser.

Did the filing state the holdings were intended to influence control of ASMB?

Yes; the certification states the securities were not acquired and are not held to change or influence control of the issuer.