Flagship Ventures Fund V SC 13G/A Codiak BioSciences / Flagship Ventures Fund V ownership change

UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

WASHINGTON, D.C. 20549

SCHEDULE 13G

Under the Securities Exchange Act of 1934

(Amendment No. 1)*

Codiak BioSciences, Inc.

(Name of Issuer)

Common Stock, $0.0001 par value per share

(Title of Class of Securities)

192010 10 6

(CUSIP Number)

December 31, 2022

(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)

* 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 the disclosures provided in a prior cover page.

The information required in 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. 192010 10 6 Page 2 of 12 Pages

1	NAMES OF REPORTING PERSONS   I.R.S. IDENTIFICATION NOS. OF ABOVE PERSONS (ENTITIES ONLY)   Flagship Ventures Fund V, 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
	6	SHARED VOTING POWER   2,588,357(1)
	7	SOLE DISPOSITIVE POWER   0
	8	SHARED DISPOSITIVE POWER   2,588,357(1)

9	AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON   2,588,357(1)
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   6.9%
12	TYPE OF REPORTING PERSON (SEE INSTRUCTIONS)   PN

(1) Includes 722,590 shares of Common Stock underlying warrants that are exercisable within 60 days of December 31, 2022.

CUSIP No. 192010 10 6 Page 3 of 12 Pages

1	NAMES OF REPORTING PERSONS   I.R.S. IDENTIFICATION NOS. OF ABOVE PERSONS (ENTITIES ONLY)   Flagship V VenturesLabs Rx 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
	6	SHARED VOTING POWER   1,399,663(1)
	7	SOLE DISPOSITIVE POWER   0
	8	SHARED DISPOSITIVE POWER   1,399,663(1)

9	AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON   1,399,663(1)
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   3.8%
12	TYPE OF REPORTING PERSON (SEE INSTRUCTIONS)   PN

(1) Includes 210,743 shares of Common Stock underlying warrants that are exercisable within 60 days of December 31, 2022.

CUSIP No. 192010 10 6 Page 4 of 12 Pages

1	NAMES OF REPORTING PERSONS   I.R.S. IDENTIFICATION NOS. OF ABOVE PERSONS (ENTITIES ONLY)   Flagship Ventures Fund V General Partner LLC
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
	6	SHARED VOTING POWER   3,988,020(1)
	7	SOLE DISPOSITIVE POWER   0
	8	SHARED DISPOSITIVE POWER   3,988,020(1)

9	AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON   3,988,020(1)
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   10.6%
12	TYPE OF REPORTING PERSON (SEE INSTRUCTIONS)   OO

(1) Includes 933,333 shares of Common Stock underlying warrants that are exercisable within 60 days of December 31, 2022.

CUSIP No. 192010 10 6 Page 5 of 12 Pages

1	NAMES OF REPORTING PERSONS   I.R.S. IDENTIFICATION NOS. OF ABOVE PERSONS (ENTITIES ONLY)   Flagship VenturesLabs V LLC
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
	6	SHARED VOTING POWER   485,949
	7	SOLE DISPOSITIVE POWER   0
	8	SHARED DISPOSITIVE POWER   485,949

9	AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON   485,949
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   1.3%
12	TYPE OF REPORTING PERSON (SEE INSTRUCTIONS)   OO

CUSIP No. 192010 10 6 Page 6 of 12 Pages

1	NAMES OF REPORTING PERSONS   I.R.S. IDENTIFICATION NOS. OF ABOVE PERSONS (ENTITIES ONLY)   Flagship VentureLabs V Manager LLC
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
	6	SHARED VOTING POWER   485,949
	7	SOLE DISPOSITIVE POWER   0
	8	SHARED DISPOSITIVE POWER   485,949

9	AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON   485,949
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   1.3%
12	TYPE OF REPORTING PERSON (SEE INSTRUCTIONS)   OO

CUSIP No. 192010 10 6 Page 7 of 12 Pages

1	NAMES OF REPORTING PERSONS   I.R.S. IDENTIFICATION NOS. OF ABOVE PERSONS (ENTITIES ONLY)   Flagship Pioneering, Inc.
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
	6	SHARED VOTING POWER   485,949
	7	SOLE DISPOSITIVE POWER   0
	8	SHARED DISPOSITIVE POWER   485,949

9	AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON   485,949
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   1.3%
12	TYPE OF REPORTING PERSON (SEE INSTRUCTIONS)   CO

CUSIP No. 192010 10 6 Page 8 of 12 Pages

1	NAMES OF REPORTING PERSONS   I.R.S. IDENTIFICATION NOS. OF ABOVE PERSONS (ENTITIES ONLY)   Noubar B. Afeyan, Ph.D.
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 of America

NUMBER OF SHARES  BENEFICIALLY  OWNED BY EACH REPORTING PERSON WITH:	5	SOLE VOTING POWER   0
	6	SHARED VOTING POWER   4,473,969(1)
	7	SOLE DISPOSITIVE POWER   0
	8	SHARED DISPOSITIVE POWER   4,473,969(1)

9	AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON   4,473,969(1)
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   11.8%
12	TYPE OF REPORTING PERSON (SEE INSTRUCTIONS)   IN

(1) Includes 933,333 shares of Common Stock underlying warrants that are exercisable within 60 days of December 31, 2022.

CUSIP No. 192010 10 6 Page 9 of 12 Pages

Item 1(a). Name of Issuer:

Codiak BioSciences, Inc. (the “Issuer”)

Item 1(b). Address of Issuer’s Principal Executive Offices:

35 CambridgePark Drive, Suite 500

Cambridge, MA 02140

Item 2(a). Names of Persons Filing:

The names of the persons filing this report (collectively, the “Reporting Persons”) are:

Flagship Ventures Fund V, L.P. (“Flagship Fund V”)

Flagship V VentureLabs Rx Fund, L.P. (“Flagship Fund V Rx”)

Flagship Ventures Fund V General Partner LLC (“Flagship V GP”)

Flagship VentureLabs V LLC (“VentureLabs V”)

Flagship VentureLabs V Manager LLC (“VentureLabs V Manager”)

Flagship Pioneering, Inc. (“Flagship Pioneering”)

Noubar B. Afeyan, Ph.D. (“Dr. Afeyan”)

Item 2(b). Address of Principal Business Office or, if None, Residence:

The address of the principal business office of each of the Reporting Persons is:

c/o Flagship Pioneering Inc.

55 Cambridge Parkway, Suite 800E

Cambridge, Massachusetts 02142

Item 2(c). Citizenship:

Flagship Fund V	Delaware
Flagship Fund V Rx	Delaware
Flagship V GP	Delaware
VentureLabs V	Delaware
VentureLabs V Manager	Delaware
Flagship Pioneering	Delaware
Dr. Afeyan	United States of America

Item 2(d). Title of Class of Securities:

Common Stock, $0.0001 par value per share (“Common Stock”).

Item 2(e). CUSIP Number:

192010 10 6

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:

Not applicable.

CUSIP No. 192010 10 6 Page 10 of 12 Pages

Item 4. Ownership.

The information required by this item with respect to each Reporting Person is set forth in Rows 5 through 9 and 11 of the cover page to this Schedule 13G. The ownership percentages reported are based on (i) 36,829,626 shares of outstanding Common Stock, as reported in the Issuer’s report on Form 10-Q filed with the Securities and Exchange Commission on November 3, 2022, plus (ii) the shares of Common Stock underlying warrants held by each Reporting Person that are exercisable within 60 days of December 31, 2022, which are treated as converted into Common Stock only for the purpose of computer the Reporting Person’s beneficial ownership percentage pursuant to Rule 13d-3 of the Securities Exchange Act of 1934.

Flagship V GP is the general partner of each of Flagship Fund V and Flagship Fund V Rx, and, as such, may be deemed to beneficially own the shares beneficially owned by Flagship Fund V and Flagship Fund V Rx.

Dr. Afeyan is the manager of Flagship V GP and, as such, may be deemed to beneficially own shares beneficially owned by Flagship V GP.

VentureLabs V Manager is the manager of VentureLabs V and, as such, may be deemed to beneficially own the shares beneficially owned by VentureLabs V.

Flagship Pioneering is the manager of VentureLabs V and, as such, may be deemed to beneficially own the shares beneficially owned by VentureLabs V Manager.

Dr. Afeyan is the Chief Executive Officer, sole stockholder and director of Flagship Pioneering and, as such, may be deemed to beneficially own shares beneficially owned by Flagship Pioneering.

Item 5. Ownership of Five Percent or Less of a Class.

If this statement is being filed to report the fact that as of the date hereof the Reporting Persons have ceased to be the beneficial owner of more than five percent of the class of securities, check the following ☐.

Item 6. Ownership of More than Five Percent on Behalf of Another Person.

Not applicable.

Item 7. Identification and Classification of the SubsidiaryWhich 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. Certification.

Not applicable.

CUSIP No. 192010 10 6 Page 11 of 12 Pages

SIGNATURE

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

Date: February 14, 2023

FLAGSHIP VENTURES FUND V, L.P.
By:	Flagship Ventures Fund V General Partner LLC
	General Partner
	By:	/s/ Noubar B. Afeyan, Ph.D.
		Noubar B. Afeyan, Ph.D.
		Manager
FLAGSHIP V VENTURELABS RX FUND, L.P.
By:	Flagship Ventures Fund V General Partner LLC
	General Partner
	By:	/s/ Noubar B. Afeyan, Ph.D.
		Noubar B. Afeyan, Ph.D.
		Manager
FLAGSHIP VENTURES FUND V GENERAL PARTNER LLC
	By:	/s/ Noubar B. Afeyan, Ph.D.
		Noubar B. Afeyan, Ph.D.
		Manager
FLAGSHIP VENTURELABS V LLC
By:	Flagship VentureLabs V Manager LLC, Manager
	By: Flagship Pioneering, Inc., Manager
	By:	/s/ Noubar B. Afeyan, Ph.D.
		Noubar B. Afeyan, Ph.D.
		Chief Executive Officer

CUSIP No. 192010 10 6 Page 12 of 12 Pages

FLAGSHIP VENTURELABS V MANAGER LLC
By:	Flagship Pioneering, Inc.
	Manager
	By:	/s/ Noubar B. Afeyan, Ph.D.
		Noubar B. Afeyan, Ph.D.
		Chief Executive Officer
FLAGSHIP PIONEERING, INC.
	By:	/s/ Noubar B. Afeyan, Ph.D.
		Noubar B. Afeyan, Ph.D.
		Chief Executive Officer
/s/ Noubar B. Afeyan, Ph.D.
Noubar B. Afeyan, Ph.D.