IP Library › Granted Patent US 12,503,688
Granted Patent B2
US 12,503,688 · App. 17/420,378 · Granted Dec 23, 2025

Engineered transaminase polypeptides

Inventors: Jovana Nazor (Milpitas, CA); Christopher Michael Micklitsch (Philadelphia, PA); Da Duan (Foster City, CA); Auric Anthony Sowell-Kantz (Fairfax, CA); Steven Miller (Rahway, NJ); Birgit Kosjek (Westfield, NJ); Iman Farasat (Rahway, NJ); Nicholas M. Marshall (Rahway, NJ)
Assignee: Codexis, Inc.
C12N9/1096C12P13/001
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Quick Facts
Patent No.
US 12,503,688
App. No.
17/420,378
Granted
Dec 23, 2025
Kind
B2
Abstract

The present invention provides engineered transaminase polypeptides and compositions thereof, as well as polynucleotides encoding the engineered transaminase polypeptides. Methods for producing transaminase enzymes are also provided. In some embodiments, the engineered transaminase polypeptides are optimized to provide improved enzyme properties under minimal aqueous conditions in wet organic solvents.

Claims (37)

1 . An engineered polypeptide having transaminase activity comprising a polypeptide sequence having at least 90% sequence identity to SEQ ID NO: 2, wherein the polypeptide sequence of said engineered polypeptide comprises at least the substitutions L155W/P244G/T/L/E/D and wherein the amino acid positions of said polypeptide sequence are numbered with reference to SEQ ID NO: 2, and further wherein the engineered polypeptide has increased thermoactivity in a wet organic solvent relative to the engineered polypeptide of SEQ ID NO:6.

2 . The engineered polypeptide of claim 1 , wherein the polypeptide sequence of said engineered polypeptide comprises at least one substitution or substitution set at one or more positions in said polypeptide sequence selected from 20, 23, and 284, wherein the amino acid positions of said polypeptide sequence are numbered with reference to SEQ ID NO:2.

3 . The engineered polypeptide of claim 1 , wherein said polypeptide sequence has at least 90% sequence identity to SEQ ID NO:6, and wherein the polypeptide sequence of said engineered polypeptide comprises at least one substitution or substitution set at one or more positions in said polypeptide sequence selected from 5T/35Y, 9H/T, 9T/20T/23Q/24F/134S/244G, 9T/20T/23Q/101S/244L, 9T/20T/24F/101S/244G/249G, 9T/23Q/24F, 9T/23Q/24F/29M/244G, 9T/23Q/24F/101S/262V, 9T/23Q/24F/244L/262T, 9T/23Q/29M, 9T/24F/244G, 9T/24F/244G/262T, 9T/24F/249G, 9T/79G/101S/244G, 9T/101S/244G, 9T/244G/249G, 9T/244G/262T/264N, 9T/262T, 15I/T, 15I/16I/18R/20H/89M/93M/160L, 15I/24P/26P/89M/93M/160L, 15T/35G/273K, 15T/218R/273K, 15T/249M/273K, 16I, 17I/25R, 17I/25R/41F, 17I/25R/160V, 17I/160V, 18G/K/R, 18G/26H/246V/273T, 18G/146L, 18G/146L/262V, 18G/168P, 18G/244G, 18G/244G/248M, 18G/244L/273V, 18G/273T, 18G/273V, 18K/146L, 18K/146L/168P, 18K/168P, 18K/168P/244L, 18K/168P/262V/324W, 18K/244G/246V, 18K/244G/246V/284G, 18K/244L, 18K/244L/246V, 18K/244T/262V/273T, 18K/262V, 18K/273T, 20H/T, 20H/24P/89M/197T, 20H/33L/160L, 20H/324C, 20T/23Q/24F/55F/134G/244G/262T, 20T/23Q/134S/244G, 22H/L/W, 22L/102L, 22L/160V, 23H/Q, 23H/25R/55L/321Y, 23H/25R/102L/142L, 23H/102L, 23H/321Y, 24D/F/P, 25R, 25R/33M, 25R/104V, 25R/160V, 25R/321Y, 26H/273K, 26P, 29K/M, 29K/89Q, 32L/S, 33L/M/S, 35G, 35G/215L/218R/249T, 35G/218R/249T/273K, 35G/221D, 40M, 40M/168P/208L/244G, 40M/244G/248M, 41F/102L, 41K/Y, 42T, 45L, 46C, 50T, 55F/G/K/S, 56R, 71Y/102P, 74A, 79G, 79H, 82P, 82S/244D, 82T, 89L/M/Q/W, 89M/93M/156L/324C, 89M/93M/321V/324C, 90A/C/S/T, 93H/M/P, 93M/324C, 95P/T, 98M, 101L/S, 101L/160Y/244E/249M, 102L, 104I/S, 106S, 111L/T/, 114T, 117D, 119A, 134G, 134G/244L, 134G/262V, 134S, 139A, 140N/266N, 142L/321Y, 142T, 145N, 146A/H/I/L, 146A/244D, 146L/244L, 146L/273V, 156E/L/T, 160A/L/V/Y, 160Y/215L/216G/218R, 160Y/273K, 168P, 168P/244L/273T, 179R, 186R, 186R/200R, 197L, 197T, 203P, 207Y, 208K/L/P/R, 208L/246V, 215L, 215L/216G/249M, 216G/P/S, 216P/273V, 218N/313H, 218R/S, 218R/249M, 234H, 236T, 244E/G/L/T, 244G/248M, 244G/248M/284G, 244L/273C, 244L/273V, 246A/L/V, 246V/248M/273V, 248M/V, 249G/M/T, 249M/273K, 256C, 262L/P/T/V, 264A/E/G/N/P/R/W, 265R, 266G/S, 271C, 273L/M/T/V, 284G, 301E/M, 316R, 320R/W, 321L/V/Y, 324C/V/W, and 329R, wherein the amino acid positions of said polypeptide sequence are numbered with reference to SEQ ID NO:6.

4 . The engineered polypeptide of claim 1 , wherein said engineered polypeptide comprises a polypeptide sequence that has at least 90% sequence identity to SEQ ID NO: 332, 518, or 656.

5 . The engineered polypeptide of claim 1 , wherein said engineered polypeptide comprises a variant engineered polypeptide comprising the amino acid sequence of SEQ ID NO: 332, SEQ ID NO:518, or SEQ ID NO:656.

6 . The engineered polypeptide of claim 1 , wherein said engineered polypeptide comprises a polypeptide sequence selected from the group consisting of SEQ ID NO: 172, 186, 198, 208, 228, 294, 296, 298, 302, 306, 310, 312, 318, 322, 324, 328, 330, 332, 334, 360, 366, 426, 432, 434, 436, 442, 444, 454, 466, 468, 470, 474, 476, 480, 482, 488, 494, 244, 518, 520, 522, 524, 526, 528, 530, 532, 534, 536, 538, 540, 542, 544, 546, 548, 550, 552, 554, 556, 558, 560, 562, 564, 568, 570, 572, 574, 576, 578, 580, 582, 584, 586, 588, 590, 592, 594, 596, 598, 600, 602, 604, 606, 608, 610, 612, 614, 616, 618, 620, 622, 624, 626, 628, 630, 632, 634, 636, 638, 640, 642, 644, 646, 648, 650, 652, 654, 656, 658, 660,662, 664, 668, 670, 672, 674, 676, 678, 680, 682, 684, 686, 688, 690, 700, 702, 704, 706, 708, 710, 712, 714, 716, 718, 720, 722, 724, 726, 728, 730, 732, 734, 736, 738, 740, 742, 744, 746, 748, 750, 752, 754, 756, 758, 760, 762, 764, 766, 768, 770, 772, 774, 776, 778, 780, 782, 784, 786, 788, 790, 792, 794, 796, 798, 800, 802, 804, 806, 808, 810, 812, 814, 816, 818, 820, 822, 824, 826, 828, 830, 832, 834, 836, 838, 840, 842, 844 and 846.

7 . A polynucleotide sequence encoding at least one engineered polypeptide of claim 1 .

8 . A process for preparing a compound of structural Formula (I):

having the indicated stereochemical configuration at the stereogenic center marked with an *; in an enantiomeric excess of at least 70% over the opposite enantiomer,

wherein

Z is a linear C1-6 alkyl or a branched C1-6 alkyl, optionally substituted with one or more hydroxy, cyano, or nitro groups; and

R1 is C1-6 alkyl, aryl-C1-2 alkyl, heteroaryl-C1-2 alkyl, or a 5- to 6-membered heterocyclic ring system optionally containing an additional heteroatom selected from O, S, and N, the heterocyclic ring being unsubstituted or substituted with one to three substituents independently selected from oxo, hydroxy, halogen, C1-4 alkoxy, and C1-4 alkyl; the process comprising the step of contacting a compound of structural Formula (II):

with an engineered polypeptide of claim 1 in the presence of an amino group donor under suitable reaction conditions.

9 . The process of claim 8 , wherein the compound of structural Formula (II)

excludes compound (2)

and the compound of structural Formula (I)

excludes compound (1)

10 . A process of preparing compound (1),

the process comprising a step of contacting a substrate of compound (2)

with an engineered polypeptide of claim 1 , in the presence of an amino group donor under suitable reaction conditions.

11 . The process of claim 8 , wherein the compound of Formula (I) is produced in at least 90% enantiomeric excess.

12 . The process of claim 8 , wherein the compound of Formula (I) is produced in at least 99% enantiomeric excess.

13 . The process of claim 8 , wherein the amino group donor is selected from isopropylamine, alanine, 3-aminobutyric acid, or methylbenzylamine.

14 . The process of claim 8 , wherein the amino group donor is isopropylamine, optionally at a concentration of about 0.1 to about 3.0 M, 0.2 to about 2.5 M, about 0.5 to about 2 M, or about 1 to about 2 M.

15 . The process of claim 8 , wherein the suitable reaction conditions comprise a temperature of about 45° C. to about 60° C.

16 . The process of claim 8 , wherein the suitable reaction conditions comprise a wet organic solvent.

17 . The process of claim 16 , wherein the wet organic solvent is selected from wet isopropyl acetate, wet toluene, wet methyl tertiary-butyl ether, wet acetonitrile, or wet isopropyl alcohol.

18 . The process of claim 17 , wherein the wet organic solvent is isopropyl acetate.

19 . The process of claim 10 , wherein the suitable reaction conditions comprise the substrate compound at a loading of about 5 g/L to about 200 g/L, about 10 g/L to about 150 g/L, or about 50 g/L to about 100 g/L.

20 . The process of claim 8 , wherein the suitable reaction conditions comprise the engineered polypeptide at a concentration of from about 0.5 g/L to about 5 g/L, about 0.5 g/L to about 3 g/L, about 0.5 g/L to about 2 g/L, or from about 0.5 g/L to about 1 g/L.

21 . The process of claim 10 , wherein the suitable reaction conditions comprise: (a) substrate loading of about 10 to 220 g/L of substrate compound (2); (b) engineered polypeptide concentration of about 0.5 g/L to 25 g/L; (c) isopropylamine concentration of about 0.1 to 3 M; (d) a wet organic solvent; and (e) temperature of about 30° C. to 60° C.

22 . The process of claim 10 , wherein the suitable reaction conditions comprise: (a) about 20 g/L of substrate compound (2); (b) about 20 g/L engineered polypeptide; (c) wet isopropyl acetate; (d) about 0.55 M isopropylamine; and (e) about 50° C.

23 . The process of claim 8 , further comprising the step of isolating the compound of Formula (I) from the reaction.

24 . The process of claim 10 , wherein the compound (1) is produced in at least 90% enantiomeric excess.

25 . The process of claim 10 , wherein the compound (1) is produced in at least 99% enantiomeric excess.

26 . The process of claim 10 , further comprising the step of isolating the compound (1) from the reaction.

27 . The engineered polypeptide of claim 1 , wherein said engineered polypeptide comprises a polypeptide sequence that has at least 90% sequence identity to a polypeptide sequence selected from the group consisting of SEQ ID NO: 172, 186, 198, 208, 228, 294, 296, 298, 302, 306, 310, 312, 318, 322, 324, 328, 330, 332, 334, 360, 366, 426, 432, 434, 436, 442, 444, 454, 466, 468, 470, 474, 476, 480, 482, 488, 494, 244, 518, 520, 522, 524, 526, 528, 530, 532, 534, 536, 538, 540, 542, 544, 546, 548, 550, 552, 554, 556, 558, 560, 562, 564, 568, 570, 572, 574, 576, 578, 580, 582, 584, 586, 588, 590, 592, 594, 596, 598, 600, 602, 604, 606, 608, 610, 612, 614, 616, 618, 620, 622, 624, 626, 628, 630, 632, 634, 636, 638, 640, 642, 644, 646, 648, 650, 652, 654, 656, 658, 660,662, 664, 668, 670, 672, 674, 676, 678, 680, 682, 684, 686, 688, 690, 700, 702, 704, 706, 708, 710, 712, 714, 716, 718, 720, 722, 724, 726, 728, 730, 732, 734, 736, 738, 740, 742, 744, 746, 748, 750, 752, 754, 756, 758, 760, 762, 764, 766, 768, 770, 772, 774, 776, 778, 780, 782, 784, 786, 788, 790, 792, 794, 796, 798, 800, 802, 804, 806, 808, 810, 812, 814, 816, 818, 820, 822, 824, 826, 828, 830, 832, 834, 836, 838, 840, 842, 844 and 846.

Assignments (2)
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: NAZOR, JOVANA; DUAN, DA; SOWELL-KANTZ, AURIC ANTHONY; MICKLITSCH, CHRISTOPHER MICHAEL; NAZOR, JOVANA; DUAN, DA; SOWELL-KANTZ, AURIC ANTHONY; MICKLITSCH, CHRISTOPHER MICHAEL
To: CODEXIS, INC.
Reel/Frame 066431/0879 →
Continuity (2)
Provisional Application 62792518 · Jan 15, 2019
Related Publication 20220090033A1 · Mar 24, 2022
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