Filing Details

 UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

SCHEDULE 13G

(Rule 13d-102)

INFORMATION TO BE INCLUDED IN STATEMENTS FILED PURSUANT

TO RULES 13d-1(b), (c), AND (d) AND AMENDMENTS THERETO FILED

PURSUANT TO RULE 13d-2(b)

(Amendment No. 1)¹

 

Protagonist Therapeutics, Inc.

(Name of Issuer)

Common Stock, par value $0.00001 per share

(Title of Class of Securities)

74366E102

(CUSIP Number)

December 31, 2023

(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)

 

 

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).

 

	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		CITIZENSHIP OR PLACE OF ORGANIZATION
				Delaware
NUMBER OF				5		SOLE VOTING POWER
SHARES
BENEFICIALLY							0
OWNED BY				6		SHARED VOTING POWER
EACH
REPORTING							3,120,957
PERSON WITH				7		SOLE DISPOSITIVE POWER
							0
				8		SHARED DISPOSITIVE POWER
							3,120,957
	9		AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
				3,120,957
	10		CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES															☐
	11		PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9)
				5.4% (1)
	12		TYPE OF REPORTING PERSON
				PN

  

(1) Includes 19,100 Shares (as defined below) underlying certain Pre-Funded Warrants (as defined below).

	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		CITIZENSHIP OR PLACE OF ORGANIZATION
				Delaware
NUMBER OF				5		SOLE VOTING POWER
SHARES
BENEFICIALLY							0
OWNED BY				6		SHARED VOTING POWER
EACH
REPORTING							3,120,957 (1)
PERSON WITH				7		SOLE DISPOSITIVE POWER
							0
				8		SHARED DISPOSITIVE POWER
							3,120,957 (1)
	9		AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
				3,120,957 (1)
	10		CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES															☐
	11		PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9)
				5.4% (1)
	12		TYPE OF REPORTING PERSON
				OO

  

(1) Includes 19,100 Shares underlying certain Pre-Funded Warrants.

 

	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		CITIZENSHIP OR PLACE OF ORGANIZATION
				Delaware
NUMBER OF				5		SOLE VOTING POWER
SHARES
BENEFICIALLY							0
OWNED BY				6		SHARED VOTING POWER
EACH
REPORTING							2,344,241
PERSON WITH				7		SOLE DISPOSITIVE POWER
							0
				8		SHARED DISPOSITIVE POWER
							2,344,241
	9		AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
				2,344,241
	10		CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES															☐
	11		PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9)
				4.1%
	12		TYPE OF REPORTING PERSON
				PN

  

 

	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		CITIZENSHIP OR PLACE OF ORGANIZATION
				Delaware
NUMBER OF				5		SOLE VOTING POWER
SHARES
BENEFICIALLY							0
OWNED BY				6		SHARED VOTING POWER
EACH
REPORTING							2,344,241
PERSON WITH				7		SOLE DISPOSITIVE POWER
							0
				8		SHARED DISPOSITIVE POWER
							2,344,241
	9		AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
				2,344,241
	10		CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES															☐
	11		PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9)
				4.1%
	12		TYPE OF REPORTING PERSON
				OO

  

 

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

CITIZENSHIP OR PLACE OF ORGANIZATION

Cayman Islands

NUMBER OF

5

SOLE VOTING POWER

SHARES

BENEFICIALLY

0

OWNED BY

6

SHARED VOTING POWER

EACH

REPORTING

238,712

PERSON WITH

7

SOLE DISPOSITIVE POWER

0

8

SHARED DISPOSITIVE POWER

238,712

9

AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

238,712

10

CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES

☐

11

PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9)

Less than 1%

12

TYPE OF REPORTING PERSON

PN

  

 

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

CITIZENSHIP OR PLACE OF ORGANIZATION

Cayman Islands

NUMBER OF

5

SOLE VOTING POWER

SHARES

BENEFICIALLY

0

OWNED BY

6

SHARED VOTING POWER

EACH

REPORTING

238,712

PERSON WITH

7

SOLE DISPOSITIVE POWER

0

8

SHARED DISPOSITIVE POWER

238,712

9

AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

238,712

10

CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES

☐

11

PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9)

Less than 1%

12

TYPE OF REPORTING PERSON

CO

  

 

	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		CITIZENSHIP OR PLACE OF ORGANIZATION
				Delaware
NUMBER OF				5		SOLE VOTING POWER
SHARES
BENEFICIALLY							0
OWNED BY				6		SHARED VOTING POWER
EACH
REPORTING							5,465,198 (1)
PERSON WITH				7		SOLE DISPOSITIVE POWER
							0
				8		SHARED DISPOSITIVE POWER
							5,465,198 (1)
	9		AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
				5,465,198 (1)
	10		CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES															☐
	11		PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9)
				9.5% (1)
	12		TYPE OF REPORTING PERSON
				OO

  

(1) Includes 19,100 Shares underlying certain Pre-Funded Warrants.

 

	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		CITIZENSHIP OR PLACE OF ORGANIZATION
				Delaware
NUMBER OF				5		SOLE VOTING POWER
SHARES
BENEFICIALLY							0
OWNED BY				6		SHARED VOTING POWER
EACH
REPORTING							5,763,948 (1)
PERSON WITH				7		SOLE DISPOSITIVE POWER
							0
				8		SHARED DISPOSITIVE POWER
							5,763,948 (1)
	9		AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
				5,763,948 (1)
	10		CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES															☐
	11		PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9)
				9.99% (1)
	12		TYPE OF REPORTING PERSON
				PN, IA

  

(1) Includes 19,100 Shares underlying certain Pre-Funded Warrants.

 

	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		CITIZENSHIP OR PLACE OF ORGANIZATION
				Delaware
NUMBER OF				5		SOLE VOTING POWER
SHARES
BENEFICIALLY							0
OWNED BY				6		SHARED VOTING POWER
EACH
REPORTING							5,763,948 (1)
PERSON WITH				7		SOLE DISPOSITIVE POWER
							0
				8		SHARED DISPOSITIVE POWER
							5,763,948 (1)
	9		AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
				5,763,948 (1)
	10		CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES															☐
	11		PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9)
				9.99% (1)
	12		TYPE OF REPORTING PERSON
				CO

  

(1) Includes 19,100 Shares underlying certain Pre-Funded Warrants.

 

	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		CITIZENSHIP OR PLACE OF ORGANIZATION
				United States
NUMBER OF				5		SOLE VOTING POWER
SHARES
BENEFICIALLY							0
OWNED BY				6		SHARED VOTING POWER
EACH
REPORTING							5,763,948 (1)
PERSON WITH				7		SOLE DISPOSITIVE POWER
							0
				8		SHARED DISPOSITIVE POWER
							5,763,948 (1)
	9		AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
				5,763,948 (1)
	10		CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES															☐
	11		PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9)
				9.99% (1)
	12		TYPE OF REPORTING PERSON
				IN

  

(1) Includes 19,100 Shares underlying certain Pre-Funded Warrants.

 

Item 1(a).

Name of Issuer:

 

Protagonist Therapeutics, Inc., a Delaware corporation (the “Issuer”).

 

Item 1(b).

Address of Issuer’s Principal Executive Offices:

 

7707 Gateway Boulevard, Suite 140

Newark, California 94560

 

Item 2(a).

Name of Person Filing

Item 2(b).

Address of Principal Business Office or, if None, Residence

Item 2(c).

Citizenship

 

Biotechnology Value Fund, L.P. (“BVF”)

44 Montgomery St., 40th Floor

San Francisco, California 94104

Citizenship: Delaware

 

BVF I GP LLC (“BVF GP”)

44 Montgomery St., 40th Floor

San Francisco, California 94104

Citizenship: Delaware

 

Biotechnology Value Fund II, L.P. (“BVF2”)

44 Montgomery St., 40th Floor

San Francisco, California 94104

Citizenship: Delaware

 

BVF II GP LLC (“BVF2 GP”)

44 Montgomery St., 40th Floor

San Francisco, California 94104

Citizenship: Delaware

 

Biotechnology Value Trading Fund OS LP (“Trading Fund OS”)

PO Box 309 Ugland House

Grand Cayman, KY1-1104

Cayman Islands

Citizenship: Cayman Islands

 

BVF Partners OS Ltd. (“Partners OS”)

PO Box 309 Ugland House

Grand Cayman, KY1-1104

Cayman Islands

Citizenship: Cayman Islands

 

BVF GP Holdings LLC (“BVF GPH”)

44 Montgomery St., 40th Floor

San Francisco, California 94104

Citizenship: Delaware

 

BVF Partners L.P. (“Partners”)

44 Montgomery St., 40th Floor

San Francisco, California 94104

Citizenship: Delaware

 

BVF Inc.

44 Montgomery St., 40th Floor

San Francisco, California 94104

Citizenship: Delaware

 

Mark N. Lampert (“Mr. Lampert”)

44 Montgomery St., 40th Floor

San Francisco, California 94104

Citizenship: United States

 

Each of the foregoing is referred to as a “Reporting Person” and collectively as the “Reporting Persons.”

 

Item 2(d).

Title of Class of Securities:

 

Common Stock, par value $0.00001 per share (the “Shares”)

 

Item 2(e).

CUSIP Number:

 

74366E102

 

Item 3.

If This Statement is Filed Pursuant to Rule 13d-1(b), or 13d-2(b) or (c), Check Whether the Person Filing is a:

 

		/x/	Not applicable.
	(a)	/ /	Broker or dealer registered under Section 15 of the Exchange Act.
	(b)	/ /	Bank as defined in Section 3(a)(6) of the Exchange Act.
	(c)	/ /	Insurance company as defined in Section 3(a)(19) of the Exchange Act.
	(d)	/ /	Investment company registered under Section 8 of the Investment Company Act.
	(e)	/ /	An investment adviser in accordance with Rule 13d-1(b)(1)(ii)(E).
	(f)	/ /	An employee benefit plan or endowment fund in accordance with Rule 13d-1(b)(1)(ii)(F).
	(g)	/ /	A parent holding company or control person in accordance with Rule 13d-1(b)(1)(ii)(G).
	(h)	/ /	A savings association as defined in Section 3(b) of the Federal Deposit Insurance Act.
	(i)	/ /	A church plan that is excluded from the definition of an investment company under Section 3(c)(14) of the Investment Company Act.
	(j)	/ /	A non-U.S. institution, in accordance with Rule 13d-1(b)(1)(ii)(J).
	(k)	/ /	Group, in accordance with Rule 13d-1(b)(1)(ii)(K). If filing as a non-U.S. institution in accordance with Rule 13d-1(b)(1)(ii)(J), please specify the type of institution: ____

 

Item 4.

Ownership

 

(a)

Amount beneficially owned:

 

As of the close of business on December 31, 2023, the Reporting Persons and certain Partners managed accounts (the “Partners Managed Accounts”) held pre-funded warrants (the “Pre-Funded Warrants”) exercisable for an aggregate of 1,205,252 Shares. The Pre-Funded Warrants are immediately exercisable at an exercise price of $0.001 per Share and expire on the day they are exercised in full. The Pre-Funded Warrants held by the Reporting Persons and the Partners Managed Accounts may not be exercised if, after giving effect to such exercise, the Reporting Persons would beneficially own more than 9.99% of the outstanding Shares (the “Pre-Funded Warrants Blocker”). As of the close of business on December 31, 2023, the Pre-Funded Warrants Blocker limited the exercise of the Pre-Funded Warrants held by the Reporting Persons and the Partners Managed Accounts to 19,100 out of the 1,205,252 Shares underlying the Pre-Funded Warrants held by them.

 

As of the close of business on December 31, 2023, (i) BVF beneficially owned 3,120,957 Shares, including 19,100 Shares underlying certain Pre-Funded Warrants held by it and excluding 558,441 Shares underlying certain Pre-Funded Warrants held by it; (ii) BVF2 beneficially owned 2,344,241 Shares, excluding 454,455 Shares underlying the Pre-Funded Warrants held by it; and (iii) Trading Fund OS beneficially owned 238,172 Shares, excluding 88,264 Shares underlying the Pre-Funded Warrants held by it.

 

BVF GP, as the general partner of BVF, may be deemed to beneficially own the 3,120,957 Shares beneficially owned by BVF.

 

BVF2 GP, as the general partner of BVF2, may be deemed to beneficially own the 2,344,241 Shares beneficially owned by BVF2.

 

Partners OS, as the general partner of Trading Fund OS, may be deemed to beneficially own the 238,712 Shares beneficially owned by Trading Fund OS.

 

BVF GPH, as the sole member of each of BVF GP and BVF2 GP, may be deemed to beneficially own the 5,465,198 Shares beneficially owned in the aggregate by BVF and BVF2.

 

Partners, as the investment manager of BVF, BVF2 and Trading Fund OS, and the sole member of Partners OS, may be deemed to beneficially own the 5,763,948 Shares beneficially owned in the aggregate by BVF, BVF2 and Trading Fund OS and held in the Partners Managed Accounts, including 60,038 Shares held in the Partners Managed Accounts, excluding 84,992 Shares underlying the Pre-Funded Warrants held in the Partners Managed Accounts.

 

BVF Inc., as the general partner of Partners, may be deemed to beneficially own the 5,763,948 Shares beneficially owned by Partners.

 

Mr. Lampert, as a director and officer of BVF Inc., may be deemed to beneficially own the 5,763,948 Shares beneficially owned by BVF Inc.

 

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 Accounts, and the filing of this statement shall not be construed as an admission that any such person or entity is the beneficial owner of any such securities.

 

(b)

Percent of class:

 

The following percentages are based on a denominator which is the sum of: (i) 57,678,122 Shares outstanding as of October 27, 2023, which is the total number of Shares outstanding as disclosed in the Issuer’s Quarterly Report on Form 10-Q filed with the Securities and Exchange Commission on November 2, 2023, and (ii) 19,100 Shares underlying certain Pre-Funded Warrants held by the Reporting Persons, as applicable.

 

As of the close of business on December 31, 2023 (i) BVF beneficially owned approximately 5.4% of the outstanding Shares, (ii) BVF2 beneficially owned approximately 4.1% of the outstanding Shares, (iii) Trading Fund OS beneficially owned less than 1% of the outstanding Shares, (iv) BVF GP may be deemed to beneficially own approximately 5.4% of the outstanding Shares, (v) BVF2 GP may be deemed to beneficially own approximately 4.1% of the outstanding Shares, (vi) Partners OS may be deemed to beneficially own less than 1% of the outstanding Shares, (vii) BVF GPH may be deemed to beneficially own approximately 9.5% of the outstanding Shares, and (viii) each of Partners, BVF Inc. and Mr. Lampert may be deemed to beneficially own approximately 9.99% of the outstanding Shares (less than 1% of the outstanding Shares are held in the Partners Managed Accounts).

 

(c)

Number of shares as to which such person has:

 

(i)

Sole power to vote or to direct the vote

 

See Cover Pages Items 5-9.

 

(ii)

Shared power to vote or to direct the vote

 

See Cover Pages Items 5-9.

 

(iii)

Sole power to dispose or to direct the disposition of

 

See Cover Pages Items 5-9.

 

(iv)

Shared power to dispose or to direct the disposition of

 

See Cover Pages Items 5-9.

 

Item 5.

Ownership of Five Percent or Less of a Class.

 

Not applicable.

 

Item 6.

Ownership of More than Five Percent on Behalf of Another Person.

 

BVF GP, BVF GPH, Partners, BVF Inc. and Mr. Lampert share voting and dispositive power over the Shares beneficially owned by BVF. BVF GPH, Partners, BVF Inc. and Mr. Lampert share voting and dispositive power over the Shares beneficially owned by BVF2. Partners, BVF Inc. and Mr. Lampert share voting and dispositive power over the Shares beneficially owned by Trading Fund OS and held in the Partners Managed Accounts.

 

Item 7.

Identification and Classification of the Subsidiary That 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.

 

See Exhibit 99.1 to the Schedule 13G filed by the Reporting Persons with the Securities and Exchange Commission on March 20, 2023.

 

Item 9.

Notice of Dissolution of Group.

 

Not Applicable.

 

Item 10.

Certifications.

 

By signing below each of the undersigned certifies that, to the best of its 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.

 

SIGNATURE

 

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

 

Dated: February 14, 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