IP Library Granted Patent US 12,365,882
Granted Patent B2
US 12,365,882 · App. 18/476,753 · Granted Jul 22, 2025

P450-BM3 variants with improved activity

Inventors: Robert Osborne (Raleigh, NC); Vesna Mitchell (Santa Clara, CA); Khin Yu Naing Htwe (Daly City, CA); Xiyun Zhang (Fremont, CA); Erika M. Milczek (New York, NY); Jeffrey C. Moore (Westfield, NJ)
Assignee: Codexis, Inc.
C12N9/0071C07K14/80C12N9/0042C12P13/001C12Y114/14001C12Y106/02004
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Quick Facts
Patent No.
US 12,365,882
App. No.
18/476,753
Granted
Jul 22, 2025
Kind
B2
Abstract

The present invention provides improved P450-BM3 variants with improved activity. In some embodiments, the P450-BM3 variants exhibit improved activity over a wide range of substrates.

Claims (13)

1. A recombinant cytochrome P450-BM3 variant comprising the amino acid sequence of SEQ ID NO: 34.

2. The recombinant cytochrome P450-BM3 variant of claim 1 , wherein said variant oxidizes at least three organic substrates.

3. The recombinant cytochrome P450-BM3 variant of claim 2 , wherein the at least three organic substrates are selected from the group consisting of nifedipine, propranolol, verapamil, and diclofenac.

4. An isolated polynucleotide comprising a nucleotide sequence encoding the recombinant cytochrome P450-BM3 variant of claim 1 .

5. The isolated polynucleotide of claim 4 , wherein said nucleotide sequence comprises the nucleotide sequence of SEQ ID NO: 33.

6. An expression vector comprising the polynucleotide of claim 4 .

7. The expression vector of claim 6 , wherein said polynucleotide is operably linked with regulatory sequences for expression of said polynucleotide in a host cell.

8. The expression vector of claim 7 , wherein said host cell is a prokaryotic or eukaryotic cell.

9. The expression vector of claim 8 , wherein said host cell is a prokaryotic cell.

10. The expression vector of claim 8 , wherein said host cell is E. coli.

11. A host cell comprising the expression vector of claim 6 .

12. A method for producing at least one recombinant cytochrome P450-BM3 variant comprising culturing the host cell of claim 11 under conditions such that the at least one recombinant cytochrome P450-BM3 variant is produced.

13. The method of claim 12 , further comprising the step of recovering said at least one recombinant cytochrome P450-BM3 variant.

Assignments (1)
SECURITY INTEREST Recorded Feb 15, 2024
From: CODEXIS, INC.
To: INNOVATUS LIFE SCIENCES LENDING FUND I, LP, AS COLLATERAL AGENT
Reel/Frame 066600/0650 →
Continuity (7)
Continuation 17672542 · Feb 15, 2022
Continuation 15931310 · May 13, 2020
Continuation 16131252 · Sep 14, 2018
Continuation 15619176 · Jun 9, 2017
Division 14794249 · Jul 8, 2015
Provisional Application 62022442 · Jul 9, 2014
Related Publication 20240026313A1 · Jan 25, 2024
References Cited (170)
US 5538867A · Durliat et al. · 1996 [cited by applicant]
US 5605793A · Stemmer · 1997 [cited by applicant]
US 5811238A · Stemmer et al. · 1998 [cited by applicant]
US 5830721A · Stemmer et al. · 1998 [cited by applicant]
US 5834252A · Stemmer et al. · 1998 [cited by applicant]
US 5837458A · Minshull et al. · 1998 [cited by applicant]
US 5928905A · Stemmer et al. · 1999 [cited by applicant]
US 6096548A · Stemmer · 2000 [cited by applicant]
US 6117679A · Stemmer · 2000 [cited by applicant]
US 6132970A · Stemmer · 2000 [cited by applicant]
US 6165793A · Stemmer · 2000 [cited by applicant]
US 6180406B1 · Stemmer · 2001 [cited by applicant]
US 6251674B1 · Tobin et al. · 2001 [cited by applicant]
US 6277638B1 · Stemmer · 2001 [cited by applicant]
US 6287861B1 · Stemmer et al. · 2001 [cited by applicant]
US 6287862B1 · delCardayre et al. · 2001 [cited by applicant]
US 6291242B1 · Stemmer · 2001 [cited by applicant]
US 6297053B1 · Stemmer · 2001 [cited by applicant]
US 6303344B1 · Patten et al. · 2001 [cited by applicant]
US 6309883B1 · Minshull et al. · 2001 [cited by applicant]
US 6319713B1 · Patten et al. · 2001 [cited by applicant]
US 6319714B1 · Crameri et al. · 2001 [cited by applicant]
US 6323030B1 · Stemmer · 2001 [cited by applicant]
US 6326204B1 · delCardayre et al. · 2001 [cited by applicant]
US 6335160B1 · Patten et al. · 2002 [cited by applicant]
US 6335198B1 · delCardayre et al. · 2002 [cited by applicant]
US 6344356B1 · Stemmer · 2002 [cited by applicant]
US 6352859B1 · delCardayre et al. · 2002 [cited by applicant]
US 6355484B1 · Patten et al. · 2002 [cited by applicant]
US 6358740B1 · Patten et al. · 2002 [cited by applicant]
US 6358742B1 · Stemmer · 2002 [cited by applicant]
US 6365377B1 · Patten et al. · 2002 [cited by applicant]
US 6365408B1 · Stemmer · 2002 [cited by applicant]
US 6368861B1 · Crameri et al. · 2002 [cited by applicant]
US 6372497B1 · Stemmer · 2002 [cited by applicant]
US 6376246B1 · Crameri et al. · 2002 [cited by applicant]
US 6379964B1 · delCardayre et al. · 2002 [cited by applicant]
US 6387702B1 · Stemmer · 2002 [cited by applicant]
US 6391552B2 · Stemmer · 2002 [cited by applicant]
US 6391640B1 · Minshull et al. · 2002 [cited by applicant]
US 6395547B1 · Stemmer · 2002 [cited by applicant]
US 6406855B1 · Patten et al. · 2002 [cited by applicant]
US 6406910B1 · Patten et al. · 2002 [cited by applicant]
US 6413745B1 · Patten et al. · 2002 [cited by applicant]
US 6413774B1 · Stemmer · 2002 [cited by applicant]
US 6420175B1 · Stemmer · 2002 [cited by applicant]
US 6423542B1 · Crameri et al. · 2002 [cited by applicant]
US 6426224B1 · Crameri et al. · 2002 [cited by applicant]
US 6436675B1 · Welch et al. · 2002 [cited by applicant]
US 6444468B1 · Stemmer et al. · 2002 [cited by applicant]
US 6455253B1 · Patten et al. · 2002 [cited by applicant]
US 6479652B1 · Crameri et al. · 2002 [cited by applicant]
US 6482647B1 · Stemmer · 2002 [cited by applicant]
US 6489146B2 · Stemmer et al. · 2002 [cited by applicant]
US 6506602B1 · Stemmer · 2003 [cited by applicant]
US 6506603B1 · Stemmer · 2003 [cited by applicant]
US 6519065B1 · Colbourne et al. · 2003 [cited by applicant]
US 6521453B1 · Crameri et al. · 2003 [cited by applicant]
US 6528311B1 · delCardayre et al. · 2003 [cited by applicant]
US 6537746B2 · Arnold et al. · 2003 [cited by applicant]
US 6573098B1 · Stemmer · 2003 [cited by applicant]
US 6576467B1 · Stemmer · 2003 [cited by applicant]
US 6579678B1 · Patten et al. · 2003 [cited by applicant]
US 6586182B1 · Patten et al. · 2003 [cited by applicant]
US 6602986B1 · Stemmer et al. · 2003 [cited by applicant]
US 6613514B2 · Patten et al. · 2003 [cited by applicant]
US 6653072B1 · Patten et al. · 2003 [cited by applicant]
US 6716631B1 · delCardayre et al. · 2004 [cited by applicant]
US 6946296B2 · Patten et al. · 2005 [cited by applicant]
US 6961664B2 · Selfinov et al. · 2005 [cited by applicant]
US 6995017B1 · Stemmer · 2006 [cited by applicant]
US 7024312B1 · Selifonov et al. · 2006 [cited by applicant]
US 7058515B1 · Selifonov et al. · 2006 [cited by applicant]
US 7105297B2 · Minshull et al. · 2006 [cited by applicant]
US 7148054B2 · delCardayre et al. · 2006 [cited by applicant]
US 7288375B2 · Stemmer et al. · 2007 [cited by applicant]
US 7421347B2 · Selifonov et al. · 2008 [cited by applicant]
US 7430477B2 · Selifonov et al. · 2008 [cited by applicant]
US 7524664B2 · Arnold et al. · 2009 [cited by applicant]
US 7534564B2 · Patten et al. · 2009 [cited by applicant]
US 7620500B2 · Mundorff et al. · 2009 [cited by applicant]
US 7620502B2 · Selifonov et al. · 2009 [cited by applicant]
US 7629170B2 · delCardayre et al. · 2009 [cited by applicant]
US 7702464B1 · Emig et al. · 2010 [cited by applicant]
US 7747391B2 · Gustafsson et al. · 2010 [cited by applicant]
US 7747393B2 · Fox · 2010 [cited by applicant]
US 7751986B2 · Gustafsson et al. · 2010 [cited by applicant]
US 7776598B2 · Patten et al. · 2010 [cited by applicant]
US 7783428B2 · Gustafsson et al. · 2010 [cited by applicant]
US 7795030B2 · Minshull et al. · 2010 [cited by applicant]
US 7853410B2 · Selifonov et al. · 2010 [cited by applicant]
US 7868138B2 · Stemmer et al. · 2011 [cited by applicant]
US 7873499B2 · Selifonov et al. · 2011 [cited by applicant]
US 7904249B2 · Selifonov et al. · 2011 [cited by applicant]
US 7957912B2 · Selifonov et al. · 2011 [cited by applicant]
US 9683220B2 · Osborne et al. · 2017 [cited by applicant]
US 9708587B2 · Osborne et al. · 2017 [cited by applicant]
US 10100289B2 · Osborne et al. · 2018 [cited by applicant]
US 10113153B2 · Osborne et al. · 2018 [cited by applicant]
US 10450550B2 · Osborne et al. · 2019 [cited by applicant]
US 10689627B2 · Osborne et al. · 2020 [cited by applicant]
US 10704030B2 · Osborne et al. · 2020 [cited by applicant]
US 10982197B2 · Osborne et al. · 2021 [cited by applicant]
US 11279917B2 · Osborne et al. · 2022 [cited by applicant]
US 11591578B2 · Osborne · 2023 [cited by examiner]
US 11807874B2 · Osborne · 2023 [cited by examiner]
US 20080220990A1 · Fox · 2008 [cited by applicant]
US 20080268517A1 · Arnold et al. · 2008 [cited by applicant]
US 20090124515A1 · Arnold · 2009 [cited by examiner]
US 20090312196A1 · Colbeck et al. · 2009 [cited by applicant]
US 20100240106A1 · Wong et al. · 2010 [cited by applicant]
US 20110244537A1 · Arnold et al. · 2011 [cited by applicant]
WO 9522625A1 · 1995 [cited by applicant]
WO 9533836A1 · 1995 [cited by applicant]
WO 9600787A1 · 1996 [cited by applicant]
WO 970078A1 · 1997 [cited by applicant]
WO 9735966A1 · 1997 [cited by applicant]
WO 9827230A1 · 1998 [cited by applicant]
WO 200042651A1 · 2000 [cited by applicant]
WO 200175767A2 · 2001 [cited by applicant]
WO 2005017105A2 · 2005 [cited by applicant]
WO 2009152336A1 · 2009 [cited by applicant]
WO 2014070673A1 · 2014 [cited by applicant]
Altschul, S., et al., “Basic local alignment search tool,” J. Mol. Biol., 215: 403-410 (1990). [cited by applicant]
Altschul, S.F., et al., “Gapped BLAST and PSI-BLAST: a new generation of protein database search programs,” Nucleic Acids Res., 25(17):3389-3402 (1997). [cited by applicant]
Beaucage, S.L., et al., “Deoxynucleoside phosphoamidites—A new class of key intermediates for deoxypolynucleotide synthesis,” Tetrahedron Letters, 22(20):1859-62 (1981). [cited by applicant]
Black, M.E., et al., “Creation of drug-specific herpes simplex virus type 1 thymidine kinase mutants for gene therapy,” Proc Natl Acad Sci USA, 93:3525-3529 (1996). [cited by applicant]
Botstein, D., et al., “Strategies and applications of in vitro mutagenesis,” Science, 229(4719):1193-1201 [1985]. [cited by applicant]
Caldwell, R.C., et al., “Mutagenic PCR,” PCR Methods Appl., 3:S136-S140 (1994). [cited by applicant]
Capdevila, J.H, et al., “The Highly Stereoselective Oxidation of Polyunsaturated Fatty Acids by Cytochrome P450BM-3,” J. Biol. Chem., 271:22663-226671 [1996]. [cited by applicant]
Carter, P., “Site-directed mutagenesis,” Biochem. J., 237:1-7 (1986). [cited by applicant]
Christians, F.C., et al., “Directed evolution of thymidine kinase for AZT phosphorylation using DNA family shuffling,” Nat. Biotechnol., 17:259-264 (1999). [cited by applicant]
Crameri, A., et al., “DNA shuffling of a family of genes from diverse species accelerates directed evolution”, Nature, 391:288-291 (1998). [cited by applicant]
Crameri, A., et al., “Improved green fluorescent protein by molecular evolution using DNA shuffling,” Nat. Biotechnol., 14(3):315-319 (1996). [cited by applicant]
Crameri, A., et al., “Molecular evolution of an arsenate detoxification pathway by DNA shuffling,” Nat. Biotechnol., 15 (5):436-438 (1997). [cited by applicant]
Dale, S.J., et al., “Oligonucleotide-directed random mutagenesis using the phosphorothioate method,” Methods Mol. Biol., 57:369-74 (1996). [cited by applicant]
Damsten, M.C., et al., “Application of drug metabolising mutants of cytochrome P450 BM3 (CYP102A1) as biocatalysts for the generation of reactive metabolites,” Chem. Biol. Interact., 171:96-107 [2008]. [cited by applicant]
De Boer, H.A., et al., “The tac promoter: A functional hybrid derived from the trp and lac promoters,” Proc. Natl Acad. Sci. USA, 80: 21-25 (1983). [cited by applicant]
Di Nardo, G., et al., “Optimization of the Bacterial Cytochrome P450 BM3 System for the Production of Human Drug Metabolites,” Int. J. Mol. Sci., 13(12):15901-15924 [2012]. [cited by applicant]
Guo, Z., et al., “3′-End-Forming Signals of Yeast mRNA,” Mol. Cell. Biol., 15(11):5983-5990 [1995]. [cited by applicant]
Henikoff, S., et al., “Amino acid substitution matrices from protein blocks,” Proc. Natl. Acad. Sci., 89: 10915-10919 (1992). [cited by applicant]
Kramer, B., et al., “Different base/base mismatches are corrected with different efficiencies by the methyl-directed DNA mismatch-repair system of [cited by applicant]
Ling, M., et al., “Approaches to DNA Mutagenesis:An Overview,” Anal. Biochem., 254:157-78 (1997). [cited by applicant]
Matthes, H.W.D., et al., “Simultaneous rapid chemical synthesis of over one hundred oligonucleotides on a microscale,” EMBO J., 3(4):801-05 (1984). [cited by applicant]
Minshull, J., et al., “Protein evolution by molecular breeding,” Curr. Op. Chem. Biol., 3(3):284-290 (1999). [cited by applicant]
Munro, A.W., et al., “Probing electron transfer in flavocytochrome P-450 BM3 and its component domains,” Eur. J. Biochem., 239:403-409 [1996]. [cited by applicant]
Narhi, L.O., et al., “Characterization of a catalytically self-sufficient 119,000-dalton cytochrome P-450 monooxygenase induced by barbiturates in Bacillus megaterium,” J. Biol. Chem., 261(18):7160-7169 [1986]. [cited by applicant]
Needleman, S., et al., “A general method applicable to the search for similarities in the amino acid sequence of two proteins,” J. Mol. Biol. 48:443-453 (1970). [cited by applicant]
Noble, M.A., et al., “Roles of key active-site residues in flavocytochrome P450 BM3,” Biochem. J., 339:371-379 [1999]. [cited by applicant]
Otey, C.R., et al., “Preparation of human metabolites of propranolol using laboratory-evolved bacterial cytochromes P450,” Biotechnol. Bioeng., 93(3):494-499 [2006]. [cited by applicant]
Pearson, W.R., “Improved tools for biological sequence comparison,” Proc. Nat'l. Acad. Sci. USA, 85:2444-2448 (1988). [cited by applicant]
Romanos, M.A., et al., “Foreign gene expression in yeast: a review,” Yeast 8:423-488 [1992]. [cited by applicant]
Sawayama, A.M., et al., “A panel of cytochrome P450 BM3 variants to produce drug metabolites and diversify lead compounds,” Chem., 15(43):11723-11729 [2009]. [cited by applicant]
Simonen, M., et al., “Protein Secretion in [cited by applicant]
Smith, M., “In vitro mutagenesis,” Ann. Rev. Genet., 19:423-462 (1985). [cited by applicant]
Smith, T., et al., “Comparison of Biosequences,” Adv. Appl. Math, 2:482-489 (1981). [cited by applicant]
Stemmer, W., “Dna Shuffling by Random Fragmentation and Reassembly: In vitro Recombination for Molecular Evolution,” Proc. Natl. Acad. Sci. USA, 91:10747-10751 (1994). [cited by applicant]
Stemmer, W.P.C., “Rapid evolution of a protein in vitro by DNA shuffling”, Nature, 370:389-391 (1994). [cited by applicant]
Villa-Komaroff, L., et al., “A bacterial clone synthesizing proinsulin,” Proc. Natl Acad. Sci. USA, 75:3727-3731 (1978). [cited by applicant]
Wells, J.A., et al., “Cassette mutagenesis: an efficient method for generation of multiple mutations at defined sites,” Gene, 34:315-323 (1985). [cited by applicant]
Zhang, J-H., et al., “Directed evolution of a fucosidase from a galactosidase by DNA shuffling and screening ,” Proc. Nat. Acad. Sci., U.S.A., 94:4504-4509 (1997). [cited by applicant]
Zhao, H., et al., “Molecular evolution by staggered extension process (StEP) in vitro recombination,” Nat. Biotechnol., 16:258-261 (1998). [cited by applicant]
Ruettinger, R.T., et al., “Coding nucleotide, 5′ regulatory, and deduced amino acid sequences of P-450BM-3, a single peptide cytochrome P-450:NADPH-P-450 reductase from Bacillus megaterium,” J. Biol. Chem., 264 (19):109… [cited by applicant]
Wen, L-P., et al., “Cloning of the gene encoding a catalytically self-sufficient cytochrome P-450 fatty acid monooxygenase induced by barbiturates in Bacillus megaterium and its functional expression and regulation in h… [cited by applicant]
Tsotsou, G.E., et al., “Identification of Mutant Asp251Gly/Gln307His of Cytochrome P450 BM3 for the Generation of Metabolites of Diclofenac, Ibuprofen and Tolbutamide,” Chem. Eur. J., 18:3582-3588 [2012]. [cited by applicant]
Sang, H., “Prospects for transgenesis in the chick,” Mechanisms of Development, 121:1179-1186 [2004]. [cited by applicant]
Yun, C., et al., “The bacterial P450 BM3: a prototype for a biocatalyst with human P450 activities,” Trends in Biotechnology, 25(7):289-298 [2007]. [cited by applicant]
Goswami, R., et al., “Gene Therapy Leaves a Vicious Cycle,” Frontiers in Oncology, 9(297):1-25 [2019]. [cited by applicant]
Zhang, M., et al., “Propagated Perturbations from a Peripheral Mutation Show Interactions Supporting WW Domain Thermostability,” Structure, 26:1474-1485 [2018]. [cited by applicant]
Singh, K.S., et al., “Protein Engineering Approaches in the Post-Genomic Era,” Current Protein and Peptide Science, 18(4):1-11 [2017]. [cited by applicant]