UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

SCHEDULE 13D

(Rule 13d-101)

INFORMATION TO BE INCLUDED IN STATEMENTS FILED PURSUANT

TO § 240.13d-1(a) AND AMENDMENTS THERETO FILED PURSUANT TO

§ 240.13d-2(a)

(Amendment No. 1)¹

Molecular Partners AG

(Name of Issuer)

Common Shares, CHF 0.10 nominal value per share

(Title of Class of Securities)

60853G106

(CUSIP Number)

JAMES KRATKY

BVF PARTNERS L.P.

44 Montgomery St., 40th Floor

San Francisco, California 94104

(415) 525-8830

(Name, Address and Telephone Number of Person

Authorized to Receive Notices and Communications)

October 25, 2024

(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 ☒.

Note:  Schedules filed in paper format shall include a signed original and five copies of the schedule, including all exhibits.  See § 240.13d-7 for other parties to whom copies are to be sent.

1              The remainder of this cover page shall be filled out for a reporting person’s initial filing on this form with respect to the subject class of securities, and for any subsequent amendment containing information which would alter disclosures provided in a prior cover page.

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).

CUSIP No. 60853G106

	1	NAME OF REPORTING PERSON
			Biotechnology Value Fund, L.P.
	2	CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP				(a) ☒
						(b) ☐
	3	SEC USE ONLY
	4	SOURCE OF FUNDS
			WC
	5	CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDINGS IS REQUIRED PURSUANT TO ITEM 2(d) OR 2(e)				☐
	6	CITIZENSHIP OR PLACE OF ORGANIZATION
			Delaware
NUMBER OF			7	SOLE VOTING POWER
SHARES
BENEFICIALLY					0
OWNED BY			8	SHARED VOTING POWER
EACH
REPORTING					5,077,491 (1)
PERSON WITH			9	SOLE DISPOSITIVE POWER
					0
			10	SHARED DISPOSITIVE POWER
					5,077,491 (1)
	11	AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
			5,077,491 (1)
	12	CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES CERTAIN SHARES				☐
	13	PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11)
			12.6% (1)
	14	TYPE OF REPORTING PERSON
			PN

(1) Includes 666,740 Shares (as defined below) represented by 666,740 American Depositary Shares (the “ADSs”) (each ADS represents 1 Share).

2

CUSIP No. 60853G106

	1	NAME OF REPORTING PERSON
			BVF I GP LLC
	2	CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP				(a) ☒
						(b) ☐
	3	SEC USE ONLY
	4	SOURCE OF FUNDS
			AF
	5	CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDINGS IS REQUIRED PURSUANT TO ITEM 2(d) OR 2(e)				☐
	6	CITIZENSHIP OR PLACE OF ORGANIZATION
			Delaware
NUMBER OF			7	SOLE VOTING POWER
SHARES
BENEFICIALLY					0
OWNED BY			8	SHARED VOTING POWER
EACH
REPORTING					5,077,491 (1)
PERSON WITH			9	SOLE DISPOSITIVE POWER
					0
			10	SHARED DISPOSITIVE POWER
					5,077,491 (1)
	11	AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
			5,077,491 (1)
	12	CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES CERTAIN SHARES				☐
	13	PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11)
			12.6% (1)
	14	TYPE OF REPORTING PERSON
			OO

(1) Includes 666,740 Shares represented by 666,740 ADSs (each ADS represents 1 Share).

3

CUSIP No. 60853G106

	1	NAME OF REPORTING PERSON
			Biotechnology Value Fund II, L.P.
	2	CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP				(a) ☒
						(b) ☐
	3	SEC USE ONLY
	4	SOURCE OF FUNDS
			WC
	5	CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDINGS IS REQUIRED PURSUANT TO ITEM 2(d) OR 2(e)				☐
	6	CITIZENSHIP OR PLACE OF ORGANIZATION
			Delaware
NUMBER OF			7	SOLE VOTING POWER
SHARES
BENEFICIALLY					0
OWNED BY			8	SHARED VOTING POWER
EACH
REPORTING					4,102,563 (1)
PERSON WITH			9	SOLE DISPOSITIVE POWER
					0
			10	SHARED DISPOSITIVE POWER
					4,102,563 (1)
	11	AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
			4,102,563 (1)
	12	CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES CERTAIN SHARES				☐
	13	PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11)
			10.2% (1)
	14	TYPE OF REPORTING PERSON
			PN

(1) Includes 549,879 Shares represented by 549,879 ADSs (each ADS represents 1 Share).

4

CUSIP No. 60853G106

	1	NAME OF REPORTING PERSON
			BVF II GP LLC
	2	CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP				(a) ☒
						(b) ☐
	3	SEC USE ONLY
	4	SOURCE OF FUNDS
			AF
	5	CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDINGS IS REQUIRED PURSUANT TO ITEM 2(d) OR 2(e)				☐
	6	CITIZENSHIP OR PLACE OF ORGANIZATION
			Delaware
NUMBER OF			7	SOLE VOTING POWER
SHARES
BENEFICIALLY					0
OWNED BY			8	SHARED VOTING POWER
EACH
REPORTING					4,102,563 (1)
PERSON WITH			9	SOLE DISPOSITIVE POWER
					0
			10	SHARED DISPOSITIVE POWER
					4,102,563 (1)
	11	AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
			4,102,563 (1)
	12	CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES CERTAIN SHARES				☐
	13	PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11)
			10.2% (1)
	14	TYPE OF REPORTING PERSON
			OO

(1) Includes 549,879 Shares represented by 549,879 ADSs (each ADS represents 1 Share).

5

CUSIP No. 60853G106

	1	NAME OF REPORTING PERSON
			Biotechnology Value Trading Fund OS LP
	2	CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP				(a) ☒
						(b) ☐
	3	SEC USE ONLY
	4	SOURCE OF FUNDS
			WC
	5	CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDINGS IS REQUIRED PURSUANT TO ITEM 2(d) OR 2(e)				☐
	6	CITIZENSHIP OR PLACE OF ORGANIZATION
			Cayman Islands
NUMBER OF			7	SOLE VOTING POWER
SHARES
BENEFICIALLY					0
OWNED BY			8	SHARED VOTING POWER
EACH
REPORTING					514,365 (1)
PERSON WITH			9	SOLE DISPOSITIVE POWER
					0
			10	SHARED DISPOSITIVE POWER
					514,365 (1)
	11	AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
			514,365 (1)
	12	CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES CERTAIN SHARES				☐
	13	PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11)
			1.3% (1)
	14	TYPE OF REPORTING PERSON
			PN

(1) Includes 69,612 Shares represented by 69,612 ADSs (each ADS represents 1 Share).

6

CUSIP No. 60853G106

	1	NAME OF REPORTING PERSON
			BVF Partners OS Ltd.
	2	CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP				(a) ☒
						(b) ☐
	3	SEC USE ONLY
	4	SOURCE OF FUNDS
			AF
	5	CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDINGS IS REQUIRED PURSUANT TO ITEM 2(d) OR 2(e)				☐
	6	CITIZENSHIP OR PLACE OF ORGANIZATION
			Cayman Islands
NUMBER OF			7	SOLE VOTING POWER
SHARES
BENEFICIALLY					0
OWNED BY			8	SHARED VOTING POWER
EACH
REPORTING					514,365 (1)
PERSON WITH			9	SOLE DISPOSITIVE POWER
					0
			10	SHARED DISPOSITIVE POWER
					514,365 (1)
	11	AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
			514,365 (1)
	12	CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES CERTAIN SHARES				☐
	13	PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11)
			1.3% (1)
	14	TYPE OF REPORTING PERSON
			CO

(1) Includes 69,612 Shares represented by 69,612 ADSs (each ADS represents 1 Share).

7

CUSIP No. 60853G106

	1	NAME OF REPORTING PERSON
			BVF GP Holdings LLC
	2	CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP				(a) ☒
						(b) ☐
	3	SEC USE ONLY
	4	SOURCE OF FUNDS
			AF
	5	CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDINGS IS REQUIRED PURSUANT TO ITEM 2(d) OR 2(e)				☐
	6	CITIZENSHIP OR PLACE OF ORGANIZATION
			Delaware
NUMBER OF			7	SOLE VOTING POWER
SHARES
BENEFICIALLY					0
OWNED BY			8	SHARED VOTING POWER
EACH
REPORTING					9,180,054 (1)
PERSON WITH			9	SOLE DISPOSITIVE POWER
					0
			10	SHARED DISPOSITIVE POWER
					9,180,054 (1)
	11	AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
			9,180,054 (1)
	12	CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES CERTAIN SHARES				☐
	13	PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11)
			22.8% (1)
	14	TYPE OF REPORTING PERSON
			OO

(1) Includes 1,216,619 Shares represented by 1,216,619 ADSs (each ADS represents 1 Share).

8

CUSIP No. 60853G106

	1	NAME OF REPORTING PERSON
			BVF Partners L.P.
	2	CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP				(a) ☒
						(b) ☐
	3	SEC USE ONLY
	4	SOURCE OF FUNDS
			AF
	5	CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDINGS IS REQUIRED PURSUANT TO ITEM 2(d) OR 2(e)				☐
	6	CITIZENSHIP OR PLACE OF ORGANIZATION
			Delaware
NUMBER OF			7	SOLE VOTING POWER
SHARES
BENEFICIALLY					0
OWNED BY			8	SHARED VOTING POWER
EACH
REPORTING					9,888,592 (1)
PERSON WITH			9	SOLE DISPOSITIVE POWER
					0
			10	SHARED DISPOSITIVE POWER
					9,888,592 (1)
	11	AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
			9,888,592 (1)
	12	CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES CERTAIN SHARES				☐
	13	PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11)
			24.5% (1)
	14	TYPE OF REPORTING PERSON
			PN, IA

(1) Includes 1,353,968 Shares represented by 1,353,968 ADSs (each ADS represents 1 Share).

9

CUSIP No. 60853G106

	1	NAME OF REPORTING PERSON
			BVF Inc.
	2	CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP				(a) ☒
						(b) ☐
	3	SEC USE ONLY
	4	SOURCE OF FUNDS
			AF
	5	CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDINGS IS REQUIRED PURSUANT TO ITEM 2(d) OR 2(e)				☐
	6	CITIZENSHIP OR PLACE OF ORGANIZATION
			Delaware
NUMBER OF			7	SOLE VOTING POWER
SHARES
BENEFICIALLY					0
OWNED BY			8	SHARED VOTING POWER
EACH
REPORTING					9,888,592 (1)
PERSON WITH			9	SOLE DISPOSITIVE POWER
					0
			10	SHARED DISPOSITIVE POWER
					9,888,592 (1)
	11	AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
			9,888,592 (1)
	12	CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES CERTAIN SHARES				☐
	13	PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11)
			24.5% (1)
	14	TYPE OF REPORTING PERSON
			CO

(1) Includes 1,353,968 Shares represented by 1,353,968 ADSs (each ADS represents 1 Share).

10

CUSIP No. 60853G106

	1	NAME OF REPORTING PERSON
			Mark N. Lampert
	2	CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP				(a) ☒
						(b) ☐
	3	SEC USE ONLY
	4	SOURCE OF FUNDS
			AF
	5	CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDINGS IS REQUIRED PURSUANT TO ITEM 2(d) OR 2(e)				☐
	6	CITIZENSHIP OR PLACE OF ORGANIZATION
			United States
NUMBER OF			7	SOLE VOTING POWER
SHARES
BENEFICIALLY					0
OWNED BY			8	SHARED VOTING POWER
EACH
REPORTING					9,888,592 (1)
PERSON WITH			9	SOLE DISPOSITIVE POWER
					0
			10	SHARED DISPOSITIVE POWER
					9,888,592 (1)
	11	AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
			9,888,592 (1)
	12	CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES CERTAIN SHARES				☐
	13	PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11)
			24.5% (1)
	14	TYPE OF REPORTING PERSON
			IN

(1) Includes 1,353,968 Shares represented by 1,353,968 ADSs (each ADS represents 1 Share).

11

CUSIP No. 60853G106

The following constitutes Amendment No. 1 to the Schedule 13D filed by the undersigned (“Amendment No. 1”). This Amendment No. 1 amends the Schedule 13D as specifically set forth herein.

Item 3. Source and Amount of Funds or Other Consideration.

Item 3 is hereby amended and restated to read as follows:

The securities of the Issuer purchased by each of BVF, BVF2 and Trading Fund OS, and held in the Partners Managed Account, were purchased with working capital (which may, at any given time, include margin loans made by brokerage firms in the ordinary course of business).

The aggregate purchase price of the 4,410,751 Shares owned directly by BVF and the 666,740 ADSs owned directly by BVF is approximately $45,162,615 and $6,848,297, respectively, including brokerage commissions. The aggregate purchase price of the 3,552,684 Shares owned directly by BVF2 and the 549,879 ADSs owned directly by BVF2 is approximately $33,713,632 and $5,593,918, respectively, including brokerage commissions. The aggregate purchase price of the 444,753 Shares owned directly by Trading Fund OS and the 69,612 ADSs owned directly by Trading Fund OS is approximately $4,380,194 and $382,170, respectively, including brokerage commissions. The aggregate purchase price of the 126,436 Shares held in the Partners Managed Account and the 67,737 ADSs held in the Partners Managed Account is approximately $1,571,093 and $435,114, respectively, including brokerage commissions.

Item 4. Purpose of Transaction.

Item 4 is hereby amended to add the following:

On October 25, 2024, certain of the Reporting Persons purchased an aggregate of 910,747 ADSs, representing 910,747 Shares, in the Issuer’s public offering (the “Offering”) at the Offering price of $5.4900 per ADS. Specifically, BVF, BVF2, Trading Fund OS and Partners, on behalf of the Partners Managed Account, purchased 440,841, 351,578, 69,612 and 48,716 ADSs, respectively.

Item 5. Interest in Securities of the Issuer.

Item 5(a) and (c) are hereby amended and restated to read as follows:

(a) The aggregate percentage of Shares reported owned by each person named herein is based on 40,325,575 Shares (including Shares represented by ADSs) outstanding as of the completion of the Offering as disclosed in the Issuer’s prospectus filed with the Securities and Exchange Commission on October 25, 2024.

As of the close of business on the date hereof, (i) BVF beneficially owned 5,077,491 Shares, including 666,740 Shares represented by 666,740 ADSs held by it, representing percentage ownership of approximately 12.6% of the Shares outstanding, (ii) BVF2 beneficially owned 4,102,563 Shares, including 549,879 Shares represented by 549,879 ADSs held by it, representing percentage ownership of approximately 10.2% of the Shares outstanding, and (iii) Trading Fund OS beneficially owned 514,365 Shares, including 69,612 Shares represented by 69,612 ADSs held by it, representing percentage ownership of approximately 1.3% of the Shares outstanding.

BVF GP, as the general partner of BVF, may be deemed to beneficially own the 5,077,491 Shares beneficially owned by BVF, representing percentage ownership of approximately 12.6% of the Shares outstanding.

12

CUSIP No. 60853G106

BVF2 GP, as the general partner of BVF2, may be deemed to beneficially own the 4,102,563 Shares beneficially owned by BVF2, representing percentage ownership of approximately 10.2% of the Shares outstanding.

Partners OS, as the general partner of Trading Fund OS, may be deemed to beneficially own the 514,365 Shares beneficially owned by Trading Fund OS, representing percentage ownership of approximately 1.3% of the Shares outstanding.

BVF GPH, as the sole member of each of BVF GP and BVF2 GP, may be deemed to beneficially own the 9,180,054 Shares beneficially owned in the aggregate by BVF and BVF2, representing percentage ownership of approximately 22.8% of the Shares outstanding.

Partners, as the investment manager of BVF, BVF2, Trading Fund OS and the Partners Managed Account, and the sole member of Partners OS, may be deemed to beneficially own the 9,888,592 Shares beneficially owned in the aggregate by BVF, BVF2 and Trading Fund OS and held in the Partners Managed Account, including 194,173 Shares held in the Partners Managed Account, including 67,737 Shares represented by 67,737 ADSs held in the Partners Managed Account, representing percentage ownership of approximately 24.5% of the Shares outstanding (less than 1% of the Shares outstanding are held in the Partners Managed Account).

BVF Inc., as the general partner of Partners, may be deemed to beneficially own the 9,888,592 Shares beneficially owned by Partners, representing percentage ownership of approximately 24.5% of the Shares outstanding.

Mr. Lampert, as the sole director and officer of BVF Inc., may be deemed to beneficially own the 9,888,592 Shares beneficially owned by BVF Inc., representing percentage ownership of approximately 24.5% of the Shares outstanding.

The foregoing should not be construed in and of itself as an admission by any Reporting Person as to beneficial ownership of any Shares owned by another Reporting Person. BVF GP disclaims beneficial ownership of the Shares beneficially owned by BVF. BVF2 GP disclaims beneficial ownership of the Shares beneficially owned by BVF2. Partners OS disclaims beneficial ownership of the Shares beneficially owned by Trading Fund OS. BVF GPH disclaims beneficial ownership of the Shares beneficially owned by BVF and BVF2. Each of Partners, BVF Inc. and Mr. Lampert disclaims beneficial ownership of the Shares beneficially owned by BVF, BVF2 and Trading Fund OS and held in the Partners Managed Account.

(c)       Other than as set forth in Item 4 above, none of the Reporting Persons has entered into any transactions in the securities of the Issuer during the past sixty days.

13

CUSIP No. 60853G106

SIGNATURES

After reasonable inquiry and to the best of his or its knowledge and belief, each of the undersigned certifies that the information set forth in this statement is true, complete and correct.

Dated: October 29, 2024

BIOTECHNOLOGY VALUE FUND, L.P.		BIOTECHNOLOGY VALUE TRADING FUND OS LP
By:	BVF I GP LLC, its general partner	By:	BVF Partners L.P., its investment manager
		By:	BVF Inc., its general partner
By:	/s/ Mark N. Lampert
	Mark N. Lampert	By:	/s/ Mark N. Lampert
	Chief Executive Officer		Mark N. Lampert
			President
BVF I GP LLC
		BVF GP HOLDINGS LLC
By:	/s/ Mark N. Lampert
	Mark N. Lampert	By:	/s/ Mark N. Lampert
	Chief Executive Officer		Mark N. Lampert
			Chief Executive Officer
BIOTECHNOLOGY VALUE FUND II, L.P.
		BVF PARTNERS L.P.
By:	BVF II GP LLC, its general partner
		By:	BVF Inc., its general partner
By:	/s/ Mark N. Lampert
	Mark N. Lampert	By:	/s/ Mark N. Lampert
	Chief Executive Officer		Mark N. Lampert
			President
BVF II GP LLC
		BVF INC.
By:	/s/ Mark N. Lampert
	Mark N. Lampert	By:	/s/ Mark N. Lampert
	Chief Executive Officer		Mark N. Lampert
			President
BVF PARTNERS OS LTD.
		/s/ Mark N. Lampert
By:	BVF Partners L.P., its sole member	MARK N. LAMPERT
By:	BVF Inc., its general partner
By:	/s/ Mark N. Lampert
	Mark N. Lampert
	President

14