[SCHEDULE 13D/A] Assembly Biosciences, Inc SEC Filing

Rhea-AI Filing Summary

Gilead Sciences purchased a significant stake in Assembly Biosciences and acquired related warrants. Under a Securities Purchase Agreement dated August 8, 2025, Gilead paid a combined price of $19.60 per share to buy 2,295,920 shares of Assembly common stock plus accompanying warrants, with the transaction closing on August 11, 2025 for approximately $45 million funded from Gilead's cash resources. After the purchase, Gilead beneficially owns 4,505,391 shares, representing 29.0% of the outstanding common stock based on 15,560,009 shares outstanding following the issuer's public offering.

The purchase included a Series A Warrant exercisable immediately at an exercise price of $21.60 (expiring August 11, 2030 or earlier upon a public announcement of a specified Phase 2 enrollment milestone) and a Series B Warrant exercisable on or after November 15, 2026 at $21.60 (expiring December 31, 2026 and subject to termination if the issuer receives at least $75 million of specified non-dilutive capital before November 15, 2026). Each warrant is subject to a 19.99% beneficial ownership limitation, and 2,475,420 underlying shares from warrants are not deemed beneficially owned due to that limitation.

Positive

• Material capital commitment: Gilead invested approximately $45 million from available cash resources to acquire equity and warrants.
• Significant ownership stake: After the transaction Gilead beneficially owns 4,505,391 shares (29.0%) of Assembly's common stock based on 15,560,009 shares outstanding.
• Warrants provide upside exposure: Acquisition included a Series A Warrant exercisable immediately and a Series B Warrant exercisable later, each exercisable at $21.60 per share, offering potential future ownership.

Negative

• Beneficial ownership cap: Each warrant contains a 19.99% beneficial ownership limitation, which prevents Gilead from exercising warrants to exceed that threshold and limits immediate further accumulation.
• Series B termination condition: The Series B Warrant will terminate if Assembly publicly announces receiving at least $75.0 million of non-dilutive capital before November 15, 2026, reducing potential warrant upside under that scenario.
• Warrant exercise price above purchase price: Both Series A and Series B warrants have an exercise price of $21.60, which is higher than the $19.60 per-share purchase price paid for the common stock portion.

Insights

Financial Analyst

TL;DR: Gilead's ~$45M investment creates a material 29% stake and option exposure via warrants, increasing strategic and capital alignment.

Gilead's acquisition of 2.3 million shares and accompanying warrants for approximately $45 million materially increases its economic and voting stake to 29.0% of Assembly's outstanding common stock. The Series A and B warrants provide potential additional upside at a $21.60 exercise price but include a 19.99% ownership cap that prevents immediate accumulation beyond that threshold. For investors, this is a significant capital commitment from a large biopharma, which may affect liquidity, shareholder base concentration, and potential strategic optionality, while the warrants' expiration and termination mechanics (including a $75 million non-dilutive capital trigger for Series B) limit certain upside scenarios.

Corporate Governance Expert

TL;DR: The filing documents a large minority stake without disclosed control agreements or board changes; governance effects are possible but not explicit.

The Schedule 13D shows sole voting and dispositive power over 4,505,391 shares (29.0%) but does not disclose any director nominations, change-of-control provisions, or contractual governance arrangements. The 19.99% beneficial ownership limitation tied to the warrants constrains immediate additional ownership through exercise. Absent further agreements or disclosures, this remains a substantial minority stake that could influence corporate decisions indirectly, but no direct governance changes are described in this amendment.

SECURITIES AND EXCHANGE COMMISSION
Washington, D.C. 20549

SCHEDULE 13D

Under the Securities Exchange Act of 1934

(Amendment No. 3)

ASSEMBLY BIOSCIENCES, INC.

(Name of Issuer)

Common Stock, par value $0.001

(Title of Class of Securities)

045396108

(CUSIP Number)

Gilead Sciences, Inc.
333 Lakeside Drive,
Foster City, CA, 94404
650-574-3000

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

08/08/2025

(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. 045396108

1

Name of reporting person

GILEAD SCIENCES, INC.

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 4,505,391.00
8	Shared Voting Power 0.00
9	Sole Dispositive Power 4,505,391.00
10	Shared Dispositive Power 0.00

11

Aggregate amount beneficially owned by each reporting person

4,505,391.00

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 %

14

Type of Reporting Person (See Instructions)

CO

Comment for Type of Reporting Person:

Comment relating to row 13: Based upon 15,560,009 shares of Common Stock of the Issuer issued and outstanding upon the closing of the Issuer's most recent public offering, which was completed on August 11, 2025, as disclosed in the prospectus supplement (the "Prospectus Supplement") filed with the Securities and Exchange Commission (the "SEC") on August 11, 2025.

SCHEDULE 13D

Item 1.	Security and Issuer
(a)	Title of Class of Securities: Common Stock, par value $0.001
(b)	Name of Issuer: ASSEMBLY BIOSCIENCES, INC.
(c)	Address of Issuer's Principal Executive Offices: Two Tower Place, 7th Floor, South San Francisco, CALIFORNIA , 94080.
Item 1 Comment: This Amendment No. 3 ("Amendment No. 3") amends and supplements the Schedule 13D filed by the Reporting Person with the SEC on October 25, 2023, as amended by Amendment No. 1 filed with the SEC on June 20, 2024 and Amendment No. 2 filed with the SEC on December 23, 2024 (as amended by Amendment No. 2, the "Schedule 13D"), which relates to the Common Stock of the Issuer. Unless otherwise indicated, all capitalized terms used herein shall have the meanings set forth in the Schedule 13D and, unless amended hereby, all information previously disclosed remains unchanged.
Item 2.	Identity and Background
(c)	Item 2(c) is amended and restated to read as follows: The principal business of the Reporting Person is to develop and commercialize innovative medicines in areas of unmet medical need and engage in any other activity or business lawfully carried on by a corporation organized under the laws of the State of Delaware. The directors and executive officers of the Reporting Person are set forth on Exhibit 99.1 filed herewith. Exhibit 99.1 sets forth the following information with respect to each such person: (i) name; (ii) business address; (iii) position with the Reporting Person and present principal occupation or employment and, for persons not employed by the Reporting Person, the name, principal business and address of any corporation or other organization in which such employment is conducted; and (iv) citizenship.
(f)	Item 2(f) is amended and restated to read as follows: The jurisdiction of organization of the Reporting Person is set forth in subsection (a) above. The citizenship of each of the individuals referred to in Exhibit 99.1 is set forth on Exhibit 99.1.
Item 3.	Source and Amount of Funds or Other Consideration
	Item 3 is amended to add the following paragraph immediately following the last paragraph: On August 8, 2025, Gilead entered into a Securities Purchase Agreement with the Issuer (the "2025 Purchase Agreement"), pursuant to which Gilead purchased from the Issuer 2,295,920 shares of Common Stock, a Series A warrant to purchase 1,147,960 shares of Common Stock (the "Series A Warrant"), and a Series B warrant to purchase 1,147,960 shares of Common Stock (the "Series B Warrant"), at a combined purchase price of $19.60 per share of Common Stock and accompanying one half of one Series A Warrant and one half of one Series B Warrant, which purchase closed on August 11, 2025. The total consideration for such purchase was approximately $45 million and such consideration was obtained from the available cash resources of Gilead.
Item 4.	Purpose of Transaction
	Item 4 is amended to add the following immediately following the last paragraph: 2025 Securities Purchase Agreement and Warrants On August 8, 2025, pursuant to the 2025 Purchase Agreement, Gilead purchased from the Issuer 2,295,920 shares of Common Stock, the Series A Warrant, and the Series B Warrant, at a combined purchase price of $19.60 per share of Common Stock and accompanying one half of one Series A Warrant and one half of one Series B Warrant. The Series A Warrant is exercisable, in whole or in part, immediately at an exercise price of $21.60 per share and expires on the earlier of (i) 5:00 p.m. (New York City time) on August 11, 2030 and (ii) the date that is 30 days after the public announcement (whether by press release, document filed or furnished with the SEC, or other form of public announcement) that the Issuer has completed enrollment (of at least 200 patients total) for its Phase 2 clinical study evaluating ABI-5366 vs. valacyclovir. The Series B Warrant is exercisable, in whole or in part, on or after November 15, 2026 at an exercise price of $21.60 per share and expires on December 31, 2026, provided that the Series B Warrant will automatically terminate in full and be extinguished and shall no longer be exercisable in the event that the Issuer publicly announces prior to November 15, 2026 that it has received at least $75.0 million in the aggregate of non-dilutive capital in connection with a collaboration agreement. Each of the Series A Warrant and the Series B Warrant cannot be exercised by Gilead if, after giving effect thereto, Gilead would beneficially own, as determined in accordance with Section 13(d) of the Securities Exchange Act of 1934, as amended, more than 19.99% of the Issuer's outstanding shares of Common Stock, subject to certain exceptions. The foregoing descriptions of the 2025 Purchase Agreement, the Series A Warrant, and the Series B Warrant are not complete and are subject to and qualified in their entirety by reference to the full text of such documents, which are attached as Exhibits 99.2, 99.3, and 99.4 hereto and incorporated herein by reference.
Item 5.	Interest in Securities of the Issuer
(a)	Item 5(a) of the Schedule 13D is hereby amended and restated to read as follows: Number of shares beneficially owned: Gilead Sciences, Inc. - 4,505,391 Shares Percent of class: Gilead Sciences, Inc. - 29.0% The percent ownership was calculated based upon 15,560,009 shares of Common Stock of the Issuer issued and outstanding upon the closing of the Issuer's most recent public offering, which was completed on August 11, 2025, as disclosed in the Prospectus Supplement.
(b)	Item 5(b) of the Schedule 13D is hereby amended and restated to read as follows: (i) Sole power to vote or to direct the vote: Gilead Sciences, Inc. - 4,505,391 shares (ii) Shared power to vote or to direct the vote: Gilead Sciences, Inc. - 0 shares (iii) Sole power to dispose or to direct the disposition of: Gilead Sciences, Inc. - 4,505,391 shares (iv) Shared power to dispose or to direct the disposition of: Gilead Sciences, Inc. - 0 shares To the best knowledge of the Reporting Person, none of the individuals listed on Exhibit 99.1 beneficially owns any of the Issuer's Common Stock. The Reporting Person beneficially owns a warrant to purchase 179,500 shares of Common Stock (the "2024 Warrant") that was acquired from the Issuer on June 17, 2024, the Series A Warrant, and the Series B Warrant (collectively, the "Warrants"). Each of the Warrants is subject to a limitation pursuant to which the Reporting Persons may not exercise such Warrant if such exercise would cause the Reporting Person to beneficially own Common Stock in an amount exceeding the "Beneficial Ownership Limitation" (as defined in such Warrant) then in effect. The Beneficial Ownership Limitation with respect to each Warrant is subject to adjustment upon 61 days' notice by the holder of such Warrant to the Issuer and, as of the date of this Amendment No. 3, was 19.99% of the number of shares of Common Stock outstanding. As a result, none of the aggregate of 2,475,420 shares of Common Stock underlying the Warrants are deemed to be beneficially owned by the Reporting Persons.
(c)	Item 5(c) of the Schedule 13D is hereby amended and restated to read as follows: Except as reported in this Amendment No. 3, neither the Reporting Person nor, to the best knowledge of the Reporting Person, any of the individuals listed on Exhibit 99.1 have effected any transactions in the Common Stock during the past sixty (60) days.
Item 7.	Material to be Filed as Exhibits.
	Exhibit 99.1 - List of Executive Officers and Directors of Gilead Sciences, Inc. Exhibit 99.2 - Securities Purchase Agreement, dated August 8, 2025, by and between the Company and Gilead Sciences, Inc. (incorporated by reference to Exhibit 10.1 to the Issuer's Current Report on Form 8-K filed with the SEC on August 11, 2025) Exhibit 99.3 - Private Placement Class A Warrant (incorporated by reference to Exhibit 4.4 to the Issuer's Current Report on Form 8-K filed with the SEC on August 11, 2025) Exhibit 99.4 - Private Placement Class B Warrant (incorporated by reference to Exhibit 4.5 to the Issuer's Current Report on Form 8-K filed with the SEC on August 11, 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.

GILEAD SCIENCES, INC.

Signature:	/s/ Andrew D. Dickinson
Name/Title:	Andrew D. Dickinson, Chief Financial Officer
Date:	08/12/2025

FAQ

What stake does Gilead (ASMB) own after the transaction?

Gilead beneficially owns 4,505,391 shares, or 29.0% of Assembly's common stock based on 15,560,009 shares outstanding after the issuer's public offering.

What did Gilead purchase and for how much?

Gilead purchased 2,295,920 shares of common stock plus a Series A and Series B warrant at a combined price of $19.60 per share, with total consideration of approximately $45 million.

What are the key terms of the Series A and Series B warrants?

The Series A Warrant is exercisable immediately at $21.60 per share and expires by August 11, 2030 or 30 days after a specified Phase 2 enrollment announcement; the Series B Warrant is exercisable on or after November 15, 2026 at $21.60 and expires December 31, 2026, but will terminate if Assembly announces receiving $75.0 million of specified non-dilutive capital before November 15, 2026.

Are the warrants counted in Gilead's beneficial ownership?

No. The filing states that 2,475,420 shares underlying the warrants are not deemed beneficially owned because each warrant is subject to a beneficial ownership limitation (currently 19.99%).

How was the purchase funded?

The filing states the total consideration of approximately $45 million was obtained from Gilead's available cash resources.