Polynucleotides encoding engineered ketoreductase polypeptides

Patent metadata

Field	Value
Publication number	US-9228213-B2
Application number	US-201414503578-A
Country	US
Kind code	B2
Filing date	Oct 1, 2014
Priority date	Aug 27, 2008
Publication date	Jan 5, 2016
Grant date	Jan 5, 2016

Abstract

The present disclosure provides engineered ketoreductase enzymes having improved properties as compared to a naturally occurring wild-type ketoreductase enzyme. Also provided are polynucleotides encoding the engineered ketoreductase enzymes, host cells capable of expressing the engineered ketoreductase enzymes, and methods of using the engineered ketoreductase enzymes to synthesize a variety of chiral compounds. The engineered ketoreductase polypeptides are optimized for catalyzing the conversion of N-methyl-3-keto-3-(2-thienyl)-1-propanamine to (S)—N-methyl-3-hydroxy-3-(2-thienyl)-1-propanamine.

First claim

What is claimed is:

1. A ketoreductase polypeptide capable of converting substrate N-methyl-3-keto-3-(2-thienyl)-1-propanamine to product (S)—N-methyl-3-hydroxy-3- (2-thienyl)-1-propanamine at a rate that is improved over a reference polypeptide having the amino acid sequence of SEQ ID NO: 6, wherein the polypeptide has an amino acid sequence that is at least about 90% identical to a reference sequence based on SEQ ID NO:2, comprising a substitution at position 199, wherein the residue corresponding to residue X46 is arginine; residue X60 is isoleucine; residue X64 is valine; residue X108 is histidine; residue 152 is asparagine; residue X153 is valine; residue X157 is serine; residue X198 is asparagine; residue X199 is aspartic acid, valine, arginine, or phenylalanine; and/or residue X245 is isoleucine.

2. The ketoreductase polypeptide of claim 1 , wherein the polypeptide is capable of converting the substrate to the product with a percent stereomeric excess of at least 95%.

3. The ketoreductase polypeptide of claim 1 , wherein the polypeptide is capable of converting the substrate to the product with a percent stereomeric excess of at least 99%.

4. The ketoreductase polypeptide of claim 1 , wherein the polypeptide is capable of converting the substrate to the product at a rate that is at least 10-15 times greater than the rate of conversion of the substrate to the product by the reference polypeptide of SEQ ID NO:6.

5. The ketoreductase polypeptide of claim 1 , wherein the polypeptide is capable of converting the substrate to the product at a rate that is at least 15 times greater than the rate of conversion of the substrate to the product by the reference polypeptide of SEQ ID NO:6.

6. The ketoreductase polypeptide of claim 1 , wherein the polypeptide is capable of converting at least 95% of the substrate to the product in less than 24 hours when carried out with greater than 100 g/L of substrate and less than 5 g/L of the polypeptide.

7. A composition comprising the compound of structural formula I and/or structural formula (II) and the ketoreductase polypeptide of claim 1 .

8. The composition of claim 7 , wherein the compound has the structural formula of (III).

9. The composition of claim 7 , further comprising a cofactor regenerating system.

10. The composition of claim 9 , wherein the cofactor regenerating system is selected from the group consisting of glucose dehydrogenase and glucose, formate dehydrogenase and formate, isopropanol and a secondary alcohol dehydrogenase, and phosphite and phosphite dehydrogenase.

11. A method for producing an (S)-3-aryl-3-hydroxypropanamine, said method comprising:
(a) providing a 3-aryl-3-ketopropanamine substrate having the structure of formula (I):

(b) contacting the 3-aryl-3-ketopropanamine substrate with the ketoreductase polypeptide of claim 1 , in a reaction mixture under conditions suitable for reduction or conversion of the substrate to an (S) 3-aryl-3-hydroxypropanamine product having the structural formula (II):

wherein for (I) and (II), R 1 and R 2 are each independently selected from the group consisting of hydrogen, an optionally substituted lower alkyl, an optionally substituted cycloalkyl, an optionally substituted aryl, or alternatively, wherein R 1 and R 2 together form an optionally substituted cycloalkyl or an optionally substituted cycloaryl having 3-7 carbon atoms; R 3 , R 4 , R 5 , and R 6 are each independently selected from the group consisting of hydrogen and an optionally substituted lower alkyl; and R 7 is an optionally substituted aryl.

12. The method of claim 11 , wherein R 3 , R 4 , R 5 , and R 6 are hydrogen, and at least one of R 1 and R 2 is methyl.

13. The method of claim 12 , wherein R 7 is thienyl.

14. The method of claim 13 , wherein the substrate is reduced to product with a stereomeric excess of greater than 99%.

15. The method of claim 11 , wherein the method further comprises a NADH/NADPH cofactor regenerating system.

16. The method of claim 11 , wherein the contacting is carried out at a pH of <8.

17. The method of claim 11 , wherein the contacting is in presence of at least 50% v/v isopropanol.

18. The method of claim 11 , wherein step (b) is carried out with whole cells that express the ketoreductase enzyme, or an extract or lysate of such cells.

19. The method of claim 11 , wherein the ketoreductase is isolated and/or purified and the reduction reaction is carried out in the presence of a cofactor for the ketoreductase and optionally a regeneration system for the cofactor.

20. The method of claim 19 , wherein the cofactor regenerating system is selected from the group consisting of glucose dehydrogenase and glucose, formate dehydrogenase and formate, isopropanol and a secondary alcohol dehydrogenase, and phosphite and phosphite dehydrogenase.

21. The method of claim 20 , wherein the secondary alcohol dehydrogenase is the ketoreductase.

22. A method of making an (S)—N-methyl-3-hydroxy-3-(aryl)-propanamine, said method comprising:
(a) providing a 3-aryl-3-ketopropanamine substrate having the structure of formula (I):

wherein R 1 and R 2 are each methyl, R 3 , R 4 , R 5 , and R 6 are each independently selected from the group consisting of hydrogen and an optionally substituted lower alkyl, and R 7 is an optionally substituted aryl;
(b) contacting the 3-aryl-3-ketopropanamine substrate with one or more ketoreductase polypeptides of claim 1 , in a reaction mixture under conditions suitable for reduction or conversion of the substrate to an (S)-3-aryl-3-hydroxypropanamine product having the structural formula (II):

wherein R 1 and R 2 are each methyl, R 3 , R 4 , R 5 , and R 6 are each independently selected from the group consisting of hydrogen and a an optionally substituted lower alkyl, and R 7 is an optionally substituted aryl; and
(c) demethylating the (S)-3-aryl-3-hydroxypropanamine product of step (b) in a reaction mixture under conditions suitable for producing an (S)—N-methyl-3-hydroxy-3-(aryl)-propanamine having the formula of structure (II), wherein one of R 1 and R 2 are is methyl and the other is hydrogen, R 3 , R 4 , R 5 , and R 6 are each independently selected from the group consisting of hydrogen and an optionally substituted lower alkyl, and R 7 is an optionally substituted aryl.

23. A method for making a 3-aryloxy-3-(aryl)-propanamine, the method comprising:
(a) providing a 3-aryl-3-ketopropanamine having the structure of formula (I):

(b) contacting the 3-aryl-3-ketopropanamine with a ketoreductase polypeptide of claim 1 , in a reaction mixture under conditions sufficient to produce an (S)-3-aryl-3-hydroxypropanamine having the structure of formula (II):

and
(c) contacting the (S)-3-aryl-3-hydropropanamine with an activated aryl compound in a reaction mixture under conditions suff

Assignees

• Codexis Inc

Inventors

• Savile Christopher
• Gruber John M
• Mundorff Emily
• Huisman Gjalt W
• Collier Steven J

Classifications

• C12N9/0006

  acting on CH-OH groups as donors (1.1) · CPC title

• C12P13/001 Primary

  Amines; Imines · CPC title

• C12Y101/01164

  Hexadecanol dehydrogenase (1.1.1.164) · CPC title

• C12Y101/01184

  Carbonyl reductase (NADPH) (1.1.1.184) · CPC title

• C12P17/00 Primary

  Preparation of heterocyclic carbon compounds with only O, N, S, Se or Te as ring hetero atoms (C12P13/04 - C12P13/24 take precedence) · CPC title