IP Library › Granted Patent US 12,215,359
Granted Patent B2
US 12,215,359 · App. 17/600,357 · Granted Feb 4, 2025

Engineered glucose dehydrogenases and methods for the reductive amination of ketone and amine compounds

Inventors: Xiang Yi (San Carlos, CA); Oscar Alvizo (Fremont, CA); Ravi David Garcia (Los Gatos, CA); David Entwistle (San Carlos, CA); Charlene Ching (San Jose, CA); James Nicholas Riggins (San Francisco, CA); Nandhitha Subramanian (Cambridge, GB)
Assignee: Codexis, Inc.
C12N9/0006C12N1/20C12N15/72
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Quick Facts
Patent No.
US 12,215,359
App. No.
17/600,357
Granted
Feb 4, 2025
Kind
B2
Abstract

The present application provides engineered glucose dehydrogenase polypeptides having imine reductase activity, polynucleotides encoding the engineered polypeptides, host cells capable of expressing the engineered polypeptides, and methods of using these engineered polypeptides with a range of ketone and amine substrate compounds to prepare secondary and tertiary amine product compounds.

Claims (25)

1. An engineered glucose dehydrogenase polypeptide comprising a polypeptide sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO:4, wherein said engineered glucose dehydrogenase polypeptide comprises a substitution at amino acid position 147 in said polypeptide sequence selected from the group consisting of H147A/S/I/T/Q/R, wherein the amino acid positions of said polypeptide sequence are numbered with reference to SEQ ID NO:4, and wherein said engineered glucose dehydrogenase polypeptide exhibits improved production of compound (1)

compared to the engineered glucose dehydrogenase polypeptide of SEQ ID NO:4.

2. The engineered glucose dehydrogenase polypeptide of claim 1 , wherein said polypeptide sequence has at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% sequence identity to SEQ ID NO:4, wherein said engineered glucose dehydrogenase polypeptide further comprises at least one substitution or substitution set in said polypeptide sequence at one or more amino acid positions selected from 96, 96/118,155, 155/253, 195, 200, and 256, and wherein the amino acid positions of said polypeptide sequence are numbered with reference to SEQ ID NO: 4.

3. The engineered glucose dehydrogenase polypeptide of claim 1 , wherein said polypeptide sequence has at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% sequence identity to SEQ ID NO:14, wherein said engineered glucose dehydrogenase polypeptide comprises at least one substitution or substitution set in said polypeptide sequence at one or more amino acid positions selected from 17, 95/96, 95/96/118, 95/96/118/156/200/253, 95/96/147, 95/96/147/200, 95/96/147/200/253, 95/96/155/156, 95/96/155/195/200, 95/96/159/195/253, 95/155/156, 95/155/159/200, 95/155/200, 96, 96/147/195/200/253, 96/155, 96/155/159, 96/155/159/195, 96/155/159/200, 96/156/159/195, 96/156/159/195/200, 96/195,147/155, 147/155/156, 147/155/156/200, 147/155/159, 147/195/200/253, 155, 155/156, 155/156/195/200/253, 155/159/200, and 253, and wherein the amino acid positions of said polypeptide sequence are numbered with reference to SEQ ID NO: 14.

4. The engineered glucose dehydrogenase polypeptide of claim 1 , wherein said polypeptide sequence has at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% sequence identity to SEQ ID NO:34, wherein said engineered glucose dehydrogenase polypeptide comprises at least one substitution or substitution set in said polypeptide sequence at one or more amino acid positions selected from 17, 17/21, 17/21/42, 17/21/42/155/260, 17/21/49, 17/21/49/51, 17/21/49/51/96, 17/21/49/51/260, 17/21/49/96/155/260, 17/21/49/260, 17/21/51/96, 17/21/51/195, 17/21/96, 17/21/96/155, 17/21/96/195/260, 17/21/96/253, 17/21/147/155/253, 17/21/155/253, 17/21/195, 17/21/253, 17/42, 17/42/49/195/260, 17/42/96, 17/44, 17/44/47/51/96, 17/44/47/51/96/114/147/195/199/253, 17/44/47/51/96/114/147/199, 17/44/47/51/96/114/195/199, 17/44/47/51/96/147/253, 17/44/47/51/178/195, 17/44/47/195/199, 17/44/51/114/195/253, 17/46/47/51/96/147, 17/46/47/51/96/195/253, 17/46/47/51/155, 17/46/47/51/155/195/199, 17/46/47/96/195, 17/46/47/178, 17/46/96/253, 17/47, 17/47/51, 17/47/51/96/114/147/195, 17/47/51/96/114/155/178/253, 17/47/51/96/195, 17/47/51/96/195/199, 17/47/96/114/155/253, 17/47/96/147/155/195/199, 17/47/96/147/195/199/253, 17/47/96/155, 17/47/96/195/199, 17/47/114, 17/47/114/155/195/199/253, 17/47/147/195/199/253, 17/49, 17/49/51, 17/49/51/96/195/253, 17/49/51/155/253, 17/49/51/155/253/260, 17/49/51/155/260, 17/49/51/253, 17/49/96, 17/49/96/155/253, 17/49/96/195, 17/49/260, 17/51, 17/51/96/114, 17/51/96/155/178, 17/51/96/155/195/199/253, 17/51/96/155/199, 17/51/96/155/253, 17/51/96/178/195/199, 17/51/96/195, 17/51/96/260, 17/51/114, 17/51/114/253, 17/51/147, 17/51/155/195, 17/51/178/195/253, 17/51/253, 17/96, 17/96/114/147/155, 17/96/114/147/155/178/195/199, 17/96/147, 17/96/147/155, 17/96/155/178, 17/96/155/178/253, 17/96/155/195, 17/96/155/195/199, 17/96/178, 17/96/178/195, 17/96/195, 17/96/195/199, 17/96/195/199/253, 17/96/253, 17/114, 17/114/253, 17/147/155/253, 17/147/178,17/147/199, 17/155, 17/155/178, 17/155/178/195, 17/155/195, 17/155/195/253, 17/155/199, 17/155/253, 17/178, 17/178/195/253, 17/195, 17/195/199, 17/195/199/253, 17/195/253, 17/199, 17/253, 17/260, 21/49/51, 21/49/96/195, 21/49/96/253, 21/49/195, 21/51/96/155, 21/96, 21/96/195, 21/96/253, 44/46/47/51/114/178/253, 44/46/47/51/155/178/253, 44/46/47/96/155/195, 44/46/51/96/147/178/195/199, 44/46/51/96/155/195/199/253, 44/46/51/96/195, 44/46/51/147/155/178/195/253, 44/47/51/96/114, 44/47/51/96/177/178/199/253, 44/47/51/114/178/253, 44/47/96/114, 44/47/96/195/253, 44/47/147/155, 44/47/147/155/199, 44/96/155/178, 46/47/51/96/114/178, 46/47/51/114/147/195/199, 46/47/51/155/195/199, 46/47/96/114/195/199, 46/47/96/155/178/195/253, 46/47/155/195/199, 46/114/147/155/178/195/199, 46/114/195/199/253, 47/51/96, 47/51/96/114, 47/51/96/147/155/195/199, 47/51/96/147/195/199, 47/51/96/178/195/199/253, 47/51/96/195, 47/51/96/195/199/253, 47/51/114/253, 47/51/155/178/195, 47/51/155/195/253, 47/96/114, 47/96/114/253, 47/96/155/178/195, 47/96/155/195, 47/96/155/195/199, 47/96/178/195/253, 47/96/178/253, 47/96/195/199/253, 47/96/195/253, 47/114, 47/114/155/195/199, 47/114/178, 47/147/195, 47/155/253, 47/178/195, 47/178/195/199, 47/195/199, 49/51/96, 49/96, 49/96/253, 51/96, 51/96/114/155/195/199/253, 51/96/155/178, 51/96/155/178/195/253, 51/96/155/195, 51/96/155/195/253, 51/96/195/253, 51/96/199, 51/96/253, 51/114/155/195/199, 51/114/195/199, 51/147/253, 51/155/195/199, 51/195, 51/253, 96, 96/114/147/155/195/199, 96/114/155/178/195/199/253, 96/114/155/195/253, 96/114/199, 96/147, 96/147/155/178/195/253, 96/147/178/195/199, 96/147/195, 96/147/195/199, 96/147/253, 96/155/178/199, 96/155/195, 96/155/199, 96/155/253, 96/178/195, 96/178/195/199, 96/195, 96/195/199, 96/195/253, 96/199, 96/199/253, 96/253,114, 114/147/155/253, 114/178/195/199/253, 114/195, 114/195/199/253, 132, 147/155, 149, 154, 155/178, 155/178/195/199, 155/195, 155/195/199, 155/195/199/253, 155/195/253, 155/253, 157, 167, 170, 178, 178/195, 178/199, 195, 196, 198, 214, 218, 251, 252, 256, 257, 259, and 260, and wherein the amino acid positions of said polypeptide sequence are numbered with reference to SEQ ID NO: 34.

5. The engineered glucose dehydrogenase polypeptide of claim 1 , wherein said polypeptide sequence has at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% sequence identity to SEQ ID NO: 112, wherein said engineered glucose dehydrogenase polypeptide comprises at least one substitution or substitution set in said polypeptide sequence at one or more amino acid positions selected from 21/42/96/178/195/253, 21/42/96/195, 21/96, 21/96/147/195, 21/96/149, 21/96/155/195/253, 21/96/167, 21/96/167/195, 21/96/178, 21/96/179/195/251/253, 21/96/195, 21/147/149, 21/147/253, 21/149/178/195, 21/155/178/253/256, 21/178/195/256, 42/96/149/253/256, 94, 96, 96/114/155/198/218/253/256/257, 96/114/155/252/253/257, 96/114/155/253, 96/114/196/214/253/256, 96/114/214/253/256, 96/147, 96/147/149, 96/147/149/155, 96/147/167/195, 96/149/155/167/178/253, 96/149/155/195,96/149/178/179/251/256, 96/149/178/253, 96/149/198/252/253/257, 96/155, 96/155/167, 96/155/167/178, 96/155/195, 96/155/196/218/253/256/257, 96/155/196/252/253, 96/155/198, 96/155/252/253, 96/167, 96/178, 96/178/179/195, 96/195, 96/196, 96/196/198, 96/196/201/256, 96/251/253/256, 96/253/257, 96/256/257, 98, 103, 114/253/256/257, 147/149, 149/167, 149/195, 149/218, 149/253, 149/257, 155/167, 155/178/195, 155/178/195/251/253, 155/195/251/253/256, 155/195/253/256, 155/196/198/253, 167, 167/195, 167/195/251/253, 196, 196/253/256/257, 198/253/256, 198/256, 205, 214/253/256, 251, and 257, and wherein the amino acid positions of said polypeptide sequence are numbered with reference to SEQ ID NO: 112.

6. The engineered glucose dehydrogenase polypeptide of claim 1 , wherein said polypeptide sequence has at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% sequence identity to SEQ ID NO: 736, wherein said engineered glucose dehydrogenase polypeptide comprises at least one substitution or substitution set in said polypeptide sequence at one or more amino acid positions selected from 21/47/96/114/155/251, 21/47/149/257, 21/47/155/178/257, 21/47/178, 21/47/178/251/256/257, 21/96/114/155/178, 21/114/155/251/257, 21/114/178/179, 21/155/178/209/256, 25/155, 25/178/256, 42/47/155/178, 47/114/149/178/251, 47/114/178/257, 47/149, 47/178, 47/178/179/251/257, 47/178/251/257, 96/114/155/198, 96/114/155/253/257, 96/253,114/149/155/251/256, 114/149/178/256/257, 114/155/195/198/256, 114/209/256/257, 149, 149/256/257, 155, 155/178/179, 155/178/198/252/253, 155/195/198, 155/195/198/253/256/257, 155/256/257, 178/253, 178/256, 179/256/257, 251, and 253, and wherein the amino acid positions of said polypeptide sequence are numbered with reference to SEQ ID NO: 736.

7. The engineered glucose dehydrogenase polypeptide of claim 1 , wherein said polypeptide sequence has at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% sequence identity to SEQ ID NO: 908, wherein said engineered glucose dehydrogenase polypeptide comprises at least one substitution or substitution set in said polypeptide sequence at one or more amino acid positions selected from 21/42/149, 21/42/149/214/253, 21/42/179/214/244/253, 21/42/253/260/261, 21/149, 21/149/179, 21/149/179/253, 21/149/179/253/260, 21/149/179/253/260/261, 21/149/179/261, 21/149/260/261, 21/149/261, 21/179/214/253, 21/179/253, 21/179/261, 21/214/253, 21/253, 40, 42/149/179/253/260, 42/149/179/260/261, 42/149/214/253, 42/179/253/261, 42/253,104, 111, 149, 149/179, 149/179/253, 149/179/253/260/261, 149/179/260, 149/179/260/261, 149/179/261, 149/253, 149/261, 160, 178, 179/214/253, 179/253, 179/253/260, 179/253/260/261, 179/253/261, 179/260/261, 179/261, 253,253/260/261, 253/261, and 255, and wherein the amino acid positions of said polypeptide sequence are numbered with reference to SEQ ID NO: 908.

8. The engineered glucose dehydrogenase polypeptide of claim 1 , wherein said polypeptide sequence has at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% sequence identity to SEQ ID NO: 956 wherein said engineered glucose dehydrogenase polypeptide comprises at least one substitution or substitution set in said polypeptide sequence at one or more amino acid positions selected from 3, 21/104/160/178/179, 21/104/160/255/258, 21/104/178/179/255, 21/104/178/255/258, 21/104/255, 21/104/255/258, 21/178/179/255/260, 21/255/260, 31, 32, 40, 40/104/178/179, 40/160/178, 46/82/259, 103, 104/149/255/258/260, 104/149/258, 104/160, 104/160/178,104/160/178/179/255, 104/160/178/179/260, 104/160/178/255/260, 104/160/179, 104/178/179/255/258, 104/178/255/258/260, 104/178/255/260,104/179,104/255/260,104/258/260, 111/149/255/258,111/149/255/260,111/160/178/179/255/258/260, 111/160/255/260,154,156,160, 160/178/179, 174, 194, 197, 205, 205/229, 222, 253, 257, 258/260, and 260, and wherein the amino acid positions of said polypeptide sequence are numbered with reference to SEQ ID NO: 956.

9. The engineered glucose dehydrogenase polypeptide of claim 1 , wherein said polypeptide sequence has at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% sequence identity to SEQ ID NO: 1062, wherein said engineered glucose dehydrogenase polypeptide comprises at least one substitution or substitution set in said polypeptide sequence at one or more amino acid positions selected from 3/31/154/205/257, 3/31/205, 3/154/205, 31/55/154/205, 31/55/205, 31/154/205, 31/154/205/257, 31/205, 31/205/222,40/55/205,40/154/205, 40/154/205/257, 40/174/205/229, 40/205/229, 54/205/253, 63, 63/149/154/174/178/253, 63/149/154/174/205/253, 63/149/156/178/205/253, 63/149/205,63/149/205/229/253, 63/149/205/253,63/154, 63/154/178/205/253, 63/154/205,63/154/205/229,63/154/205/229/253, 63/154/205/253,63/156, 63/156/205, 63/205, 63/205/253, 63/253, 67, 98,149/154, 149/154/205, 149/156/253, 149/205, 149/205/253, 154, 154/160, 154/160/205, 154/160/205/222/257, 154/160/253, 154/174, 154/174/178/205, 154/174/205/229, 154/205, 154/205/222, 154/205/222/257, 154/205/229, 154/205/253, 154/205/257, 154/229,154/253, 156/205, 156/205/253, 156/229/253, 160,160/205, 160/205/229, 194, 205, 205/222, 205/229, 205/229/253, 205/253, 208, 226, and 253, and wherein the amino acid positions of said polypeptide sequence are numbered with reference to SEQ ID NO: 1062.

10. The engineered glucose dehydrogenase polypeptide of claim 1 , wherein said engineered glucose dehydrogenase polypeptide comprises a polypeptide sequence that is at least 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to SEQ ID NO:4.

11. The engineered glucose dehydrogenase polypeptide of claim 1 , wherein said engineered glucose dehydrogenase polypeptide comprises SEQ ID NO: 14.

12. The engineered glucose dehydrogenase polypeptide of claim 1 , wherein said engineered glucose dehydrogenase polypeptide comprises an amino acid sequence with at least 92% sequence identity to any even-numbered sequence set forth in SEQ ID NO:6, 8, 14, and 32-1384.

13. The engineered glucose dehydrogenase polypeptide of claim 1 , wherein said engineered glucose dehydrogenase polypeptide comprises a polypeptide sequence set forth in the even numbered sequences of SEQ ID NOs: 6-1384.

14. The engineered glucose dehydrogenase polypeptide of claim 1 , wherein said engineered glucose dehydrogenase polypeptide further exhibits improved production of a compound of structural Formula (IV)

wherein R 1 is selected from a hydrogen atom, or optionally substituted alkyl, alkenyl, alkynyl, alkoxy, arylalkoxy, hydroxyalkyl, heteroalkyl, heteroalkenyl, heteroalkynyl, haloalkyl, alkylthioalkyl, cycloalkyl, aryl, arylalkyl, heterocycloalkyl, heteroaryl, and heteroarylalkyl; and wherein R2 is independently selected from alkyl, alkenyl, alkynyl, hydroxyalkyl, carboxy, aminocarbonyl, heteroalkyl, heteroalkenyl, heteroalkynyl, carboxyalkyl, alkylamino, haloalkyl, alkylthioalkyl, cycloalkyl, aryl, arylalkyl, heterocycloalkyl, heteroaryl, and heteroarylalkyl; and wherein R3 is independently selected from methyl, D 3 -methyl and ethyl.

15. The engineered glucose dehydrogenase polypeptide of claim 1 , wherein said engineered glucose dehydrogenase polypeptide further exhibits improved utilization of compound (2)

16. The engineered glucose dehydrogenase polypeptide of claim 1 , wherein said engineered glucose dehydrogenase polypeptide further exhibits improved utilization of compound (3)

17. The engineered glucose dehydrogenase polypeptide of claim 1 , wherein said engineered glucose dehydrogenase polypeptide exhibits improved production of compound (1) (1)

from compound (2)

and compound (3)

18. The engineered glucose dehydrogenase polypeptide of claim 1 , wherein said engineered glucose dehydrogenase polypeptide further exhibits improved enantioselectivity.

19. The engineered glucose dehydrogenase polypeptide of claim 1 , wherein said engineered glucose dehydrogenase polypeptide further exhibits improved stability.

20. The engineered glucose dehydrogenase polypeptide of claim 1 , wherein said engineered glucose dehydrogenase polypeptide is purified.

21. A composition comprising at least one glucose dehydrogenase polypeptide provided in claim 1 .

Assignments (3)
SECURITY INTEREST Recorded Feb 15, 2024
From: CODEXIS, INC.
To: INNOVATUS LIFE SCIENCES LENDING FUND I, LP, AS COLLATERAL AGENT
Reel/Frame 066600/0650 →
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Feb 9, 2024
From: YI, XIANG; ALVIZO, OSCAR; GARCIA, RAVI DAVID; ENTWISTLE, DAVID; CHING, CHARLENE; RIGGINS, JAMES NICHOLAS; SUBRAMANIAN, NANDHITHA
To: CODEXIS, INC.
Reel/Frame 066425/0173 →
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Feb 8, 2024
From: ALVIZO, OSCAR; GARCIA, RAVI DAVID; ENTWISTLE, DAVID; CHING, CHARLENE; YI, XIANG; RIGGINS, JAMES NICHOLAS; SUBRAMANIAN, NANDHITHA
To: CODEXIS, INC.
Reel/Frame 066420/0511 →
Continuity (2)
Provisional Application 62841666 · May 1, 2019
Related Publication 20220145268A1 · May 12, 2022
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