1
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Fansher D, Besna JN, Fendri A, Pelletier JN. Choose Your Own Adventure: A Comprehensive Database of Reactions Catalyzed by Cytochrome P450 BM3 Variants. ACS Catal 2024; 14:5560-5592. [PMID: 38660610 PMCID: PMC11036407 DOI: 10.1021/acscatal.4c00086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 03/11/2024] [Accepted: 03/12/2024] [Indexed: 04/26/2024]
Abstract
Cytochrome P450 BM3 monooxygenase is the topic of extensive research as many researchers have evolved this enzyme to generate a variety of products. However, the abundance of information on increasingly diversified variants of P450 BM3 that catalyze a broad array of chemistry is not in a format that enables easy extraction and interpretation. We present a database that categorizes variants by their catalyzed reactions and includes details about substrates to provide reaction context. This database of >1500 P450 BM3 variants is downloadable and machine-readable and includes instructions to maximize ease of gathering information. The database allows rapid identification of commonly reported substitutions, aiding researchers who are unfamiliar with the enzyme in identifying starting points for enzyme engineering. For those actively engaged in engineering P450 BM3, the database, along with this review, provides a powerful and user-friendly platform to understand, predict, and identify the attributes of P450 BM3 variants, encouraging the further engineering of this enzyme.
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Affiliation(s)
- Douglas
J. Fansher
- Chemistry
Department, Université de Montréal, Montreal, QC, Canada H2V 0B3
- PROTEO,
The Québec Network for Research on Protein Function, Engineering,
and Applications, 201
Av. du Président-Kennedy, Montréal, QC, Canada H2X 3Y7
- CGCC,
Center in Green Chemistry and Catalysis, Montreal, QC, Canada H2V 0B3
| | - Jonathan N. Besna
- PROTEO,
The Québec Network for Research on Protein Function, Engineering,
and Applications, 201
Av. du Président-Kennedy, Montréal, QC, Canada H2X 3Y7
- CGCC,
Center in Green Chemistry and Catalysis, Montreal, QC, Canada H2V 0B3
- Department
of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC, Canada H3T 1J4
| | - Ali Fendri
- Chemistry
Department, Université de Montréal, Montreal, QC, Canada H2V 0B3
- PROTEO,
The Québec Network for Research on Protein Function, Engineering,
and Applications, 201
Av. du Président-Kennedy, Montréal, QC, Canada H2X 3Y7
- CGCC,
Center in Green Chemistry and Catalysis, Montreal, QC, Canada H2V 0B3
| | - Joelle N. Pelletier
- Chemistry
Department, Université de Montréal, Montreal, QC, Canada H2V 0B3
- PROTEO,
The Québec Network for Research on Protein Function, Engineering,
and Applications, 201
Av. du Président-Kennedy, Montréal, QC, Canada H2X 3Y7
- CGCC,
Center in Green Chemistry and Catalysis, Montreal, QC, Canada H2V 0B3
- Department
of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC, Canada H3T 1J4
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2
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Huang S, Deng WH, Liao RZ, He C. Repurposing a Nitric Oxide Transport Hemoprotein Nitrophorin 2 for Olefin Cyclopropanation. ACS Catal 2022. [DOI: 10.1021/acscatal.2c03515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Shunzhi Huang
- School of Chemistry and Chemical Engineering, South China University of Technology, 510640 Guangzhou, China
| | - Wen-Hao Deng
- School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, 430074 Wuhan, China
| | - Rong-Zhen Liao
- School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, 430074 Wuhan, China
| | - Chunmao He
- School of Chemistry and Chemical Engineering, South China University of Technology, 510640 Guangzhou, China
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3
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Thomson RES, D'Cunha SA, Hayes MA, Gillam EMJ. Use of engineered cytochromes P450 for accelerating drug discovery and development. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2022; 95:195-252. [PMID: 35953156 DOI: 10.1016/bs.apha.2022.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Numerous steps in drug development, including the generation of authentic metabolites and late-stage functionalization of candidates, necessitate the modification of often complex molecules, such as natural products. While it can be challenging to make the required regio- and stereoselective alterations to a molecule using purely chemical catalysis, enzymes can introduce changes to complex molecules with a high degree of stereo- and regioselectivity. Cytochrome P450 enzymes are biocatalysts of unequalled versatility, capable of regio- and stereoselective functionalization of unactivated CH bonds by monooxygenation. Collectively they catalyze over 60 different biotransformations on structurally and functionally diverse organic molecules, including natural products, drugs, steroids, organic acids and other lipophilic molecules. This catalytic versatility and substrate range makes them likely candidates for application as potential biocatalysts for industrial chemistry. However, several aspects of the P450 catalytic cycle and other characteristics have limited their implementation to date in industry, including: their lability at elevated temperature, in the presence of solvents, and over lengthy incubation times; the typically low efficiency with which they metabolize non-natural substrates; and their lack of specificity for a single metabolic pathway. Protein engineering by rational design or directed evolution provides a way to engineer P450s for industrial use. Here we review the progress made to date toward engineering the properties of P450s, especially eukaryotic forms, for industrial application, and including the recent expansion of their catalytic repertoire to include non-natural reactions.
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Affiliation(s)
- Raine E S Thomson
- School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Stephlina A D'Cunha
- School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Martin A Hayes
- Compound Synthesis and Management, Discovery Sciences, BioPharmaceuticals R&D AstraZeneca, Mölndal, Sweden
| | - Elizabeth M J Gillam
- School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia.
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4
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Roelfes G. Repurposed and artificial heme enzymes for cyclopropanation reactions. J Inorg Biochem 2021; 222:111523. [PMID: 34217039 DOI: 10.1016/j.jinorgbio.2021.111523] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 06/10/2021] [Accepted: 06/16/2021] [Indexed: 10/21/2022]
Abstract
Heme enzymes are some of the most versatile catalysts in nature. In recent years it has been found that they can also catalyze reactions for which there are no equivalents in nature. This development has been driven by the abiological catalytic reactivity reported for bio-inspired and biomimetic iron porphyrin complexes. This review focuss es on heme enzymes for catalysis of cyclopropanation reactions. The two most important approaches used to create enzymes for cyclopropanation are repurposing of heme enzymes and the various strategies used to improve these enzymes such as mutagenesis and heme replacement, and artificial heme enzymes. These strategies are introduced and compared. Moreover, lessons learned with regard to mechanism and design principles are discussed.
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Affiliation(s)
- Gerard Roelfes
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, the Netherlands.
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5
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Affiliation(s)
- Vasco F. Batista
- LAQV-REQUIMTE and Department of Chemistry, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - Diana C. G. A. Pinto
- LAQV-REQUIMTE and Department of Chemistry, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - Artur M. S. Silva
- LAQV-REQUIMTE and Department of Chemistry, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
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6
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Zetzsche LE, Narayan ARH. Broadening the scope of biocatalytic C-C bond formation. Nat Rev Chem 2020; 4:334-346. [PMID: 34430708 PMCID: PMC8382263 DOI: 10.1038/s41570-020-0191-2] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/28/2020] [Indexed: 12/18/2022]
Abstract
The impeccable control over chemo-, site-, and stereoselectivity possible in enzymatic reactions has led to a surge in the development of new biocatalytic methods. Despite carbon-carbon (C-C) bonds providing the central framework for organic molecules, development of biocatalytic methods for their formation has been largely confined to the use of a select few lyases over the last several decades, limiting the types of C-C bond-forming transformations possible through biocatalytic methods. This Review provides an update on the suite of enzymes available for highly selective biocatalytic C-C bond formation. Examples will be discussed in reference to the (1) native activity of enzymes, (2) alteration of activity through protein or substrate engineering for broader applicability, and (3) utility of the biocatalyst for abiotic synthesis.
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Affiliation(s)
- Lara E. Zetzsche
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Alison R. H. Narayan
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
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7
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Lall MS, Bassyouni A, Bradow J, Brown M, Bundesmann M, Chen J, Ciszewski G, Hagen AE, Hyek D, Jenkinson S, Liu B, Obach RS, Pan S, Reilly U, Sach N, Smaltz DJ, Spracklin DK, Starr J, Wagenaar M, Walker GS. Late-Stage Lead Diversification Coupled with Quantitative Nuclear Magnetic Resonance Spectroscopy to Identify New Structure–Activity Relationship Vectors at Nanomole-Scale Synthesis: Application to Loratadine, a Human Histamine H1 Receptor Inverse Agonist. J Med Chem 2020; 63:7268-7292. [DOI: 10.1021/acs.jmedchem.0c00483] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Manjinder S. Lall
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Asser Bassyouni
- Pfizer Worldwide Research and Development, Science Center Drive, San Diego, California 92121, United States
| | - James Bradow
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Maria Brown
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Mark Bundesmann
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Jinshan Chen
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Gregory Ciszewski
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Anne E. Hagen
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Dennis Hyek
- Spectrix Analytical Services, LLC, 410 Sackett Point Road, Bldg 20, North Haven, Connecticut 06473, United States
| | - Stephen Jenkinson
- Pfizer Worldwide Research and Development, Science Center Drive, San Diego, California 92121, United States
| | - Bo Liu
- Spectrix Analytical Services, LLC, 410 Sackett Point Road, Bldg 20, North Haven, Connecticut 06473, United States
| | - R. Scott Obach
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Senliang Pan
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Usa Reilly
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Neal Sach
- Pfizer Worldwide Research and Development, Science Center Drive, San Diego, California 92121, United States
| | - Daniel J. Smaltz
- Pfizer Worldwide Research and Development, 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Douglas K. Spracklin
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Jeremy Starr
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Melissa Wagenaar
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Gregory S. Walker
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
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8
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Stenner R, Anderson JLR. Chemoselective N−H insertion catalyzed by ade novocarbene transferase. Biotechnol Appl Biochem 2020; 67:527-535. [DOI: 10.1002/bab.1924] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 03/18/2020] [Indexed: 12/31/2022]
Affiliation(s)
- Richard Stenner
- School of Biochemistry University of Bristol Bristol UK
- Bristol Centre for Functional Nanomaterials HH Wills Physics Laboratory, University of Bristol Bristol UK
| | - John Leslie Ross Anderson
- School of Biochemistry University of Bristol Bristol UK
- BrisSynBio Synthetic Biology Research Centre University of Bristol Bristol UK
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9
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Abstract
While the bottom-up design of enzymes appears to be an intractably complex problem, a minimal approach that combines elementary, de novo-designed proteins with intrinsically reactive cofactors offers a simple means to rapidly access sophisticated catalytic mechanisms. Not only is this method proven in the reproduction of powerful oxidative chemistry of the natural peroxidase enzymes, but we show here that it extends to the efficient, abiological—and often asymmetric—formation of strained cyclopropane rings, nitrogen–carbon and carbon–carbon bonds, and the ring expansion of a simple cyclic molecule to form a precursor for NAD+, a fundamentally important biological cofactor. That the enzyme also functions in vivo paves the way for its incorporation into engineered biosynthetic pathways within living organisms. By constructing an in vivo-assembled, catalytically proficient peroxidase, C45, we have recently demonstrated the catalytic potential of simple, de novo-designed heme proteins. Here, we show that C45’s enzymatic activity extends to the efficient and stereoselective intermolecular transfer of carbenes to olefins, heterocycles, aldehydes, and amines. Not only is this a report of carbene transferase activity in a completely de novo protein, but also of enzyme-catalyzed ring expansion of aromatic heterocycles via carbene transfer by any enzyme.
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10
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Liu Y, You T, Wang HX, Tang Z, Zhou CY, Che CM. Iron- and cobalt-catalyzed C(sp3)–H bond functionalization reactions and their application in organic synthesis. Chem Soc Rev 2020; 49:5310-5358. [DOI: 10.1039/d0cs00340a] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
This review highlights the developments in iron and cobalt catalyzed C(sp3)–H bond functionalization reactions with emphasis on their applications in organic synthesis, i.e. natural products and pharmaceuticals synthesis and/or modification.
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Affiliation(s)
- Yungen Liu
- Department of Chemistry
- Southern University of Science and Technology
- Shenzhen
- P. R. China
| | - Tingjie You
- Department of Chemistry
- State Key Laboratory of Synthetic Chemistry
- The University of Hong Kong
- Hong Kong
- P. R. China
| | - Hai-Xu Wang
- Department of Chemistry
- State Key Laboratory of Synthetic Chemistry
- The University of Hong Kong
- Hong Kong
- P. R. China
| | - Zhou Tang
- Department of Chemistry
- State Key Laboratory of Synthetic Chemistry
- The University of Hong Kong
- Hong Kong
- P. R. China
| | - Cong-Ying Zhou
- Department of Chemistry
- State Key Laboratory of Synthetic Chemistry
- The University of Hong Kong
- Hong Kong
- P. R. China
| | - Chi-Ming Che
- Department of Chemistry
- Southern University of Science and Technology
- Shenzhen
- P. R. China
- Department of Chemistry
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11
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Abstract
On the occasion of Professor Frances H. Arnold's recent acceptance of the 2018 Nobel Prize in Chemistry, we honor her numerous contributions to the fields of directed evolution and biocatalysis. Arnold pioneered the development of directed evolution methods for engineering enzymes as biocatalysts. Her highly interdisciplinary research has provided a ground not only for understanding the mechanisms of enzyme evolution but also for developing commercially viable enzyme biocatalysts and biocatalytic processes. In this Account, we highlight some of her notable contributions in the past three decades in the development of foundational directed evolution methods and their applications in the design and engineering of enzymes with desired functions for biocatalysis. Her work has created a paradigm shift in the broad catalysis field.
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Affiliation(s)
- Rudi Fasan
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - S. B. Jennifer Kan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Huimin Zhao
- Departments of Chemical and Biomolecular Engineering, Chemistry, and Biochemistry, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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12
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Gober JG, Rydeen AE, Schwochert TD, Gibson-O'Grady EJ, Brustad EM. Enhancing cytochrome P450-mediated non-natural cyclopropanation by mutation of a conserved second-shell residue. Biotechnol Bioeng 2018; 115:1416-1426. [DOI: 10.1002/bit.26571] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 02/13/2018] [Indexed: 12/15/2022]
Affiliation(s)
- Joshua G. Gober
- Department of Chemistry; University of North Carolina at Chapel Hill; Chapel Hill North Carolina
| | - Amy E. Rydeen
- Department of Chemistry; University of North Carolina at Chapel Hill; Chapel Hill North Carolina
| | - Timothy D. Schwochert
- Department of Chemistry; University of North Carolina at Chapel Hill; Chapel Hill North Carolina
| | - Evan J. Gibson-O'Grady
- Department of Chemistry; University of North Carolina at Chapel Hill; Chapel Hill North Carolina
| | - Eric M. Brustad
- Department of Chemistry; University of North Carolina at Chapel Hill; Chapel Hill North Carolina
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13
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Brandenberg OF, Prier CK, Chen K, Knight AM, Wu Z, Arnold FH. Stereoselective Enzymatic Synthesis of Heteroatom-Substituted Cyclopropanes. ACS Catal 2018. [DOI: 10.1021/acscatal.7b04423] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Oliver F. Brandenberg
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Christopher K. Prier
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Kai Chen
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Anders M. Knight
- Division of Biology and Bioengineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Zachary Wu
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Frances H. Arnold
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
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14
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Oohora K, Meichin H, Zhao L, Wolf MW, Nakayama A, Hasegawa JY, Lehnert N, Hayashi T. Catalytic Cyclopropanation by Myoglobin Reconstituted with Iron Porphycene: Acceleration of Catalysis due to Rapid Formation of the Carbene Species. J Am Chem Soc 2017; 139:17265-17268. [DOI: 10.1021/jacs.7b10154] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Koji Oohora
- Department
of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita 565-0871, Japan
- Frontier
Research Base for Global Young Researchers, Graduate School of Engineering, Osaka University, Suita 565-0871, Japan
- PRESTO, Japan Science and Technology Agency (JST), Kawaguchi 332-0012, Japan
| | - Hiroyuki Meichin
- Department
of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita 565-0871, Japan
| | - Liming Zhao
- Institute
for Catalysis, Hokkaido University, Sapporo 001-0021, Japan
| | - Matthew W. Wolf
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Akira Nakayama
- PRESTO, Japan Science and Technology Agency (JST), Kawaguchi 332-0012, Japan
- Institute
for Catalysis, Hokkaido University, Sapporo 001-0021, Japan
| | - Jun-ya Hasegawa
- Institute
for Catalysis, Hokkaido University, Sapporo 001-0021, Japan
| | - Nicolai Lehnert
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Takashi Hayashi
- Department
of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita 565-0871, Japan
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15
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16
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17
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Gober JG, Brustad EM. Non-natural carbenoid and nitrenoid insertion reactions catalyzed by heme proteins. Curr Opin Chem Biol 2016; 35:124-132. [PMID: 27697701 DOI: 10.1016/j.cbpa.2016.09.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Accepted: 09/12/2016] [Indexed: 01/08/2023]
Abstract
Despite increasing interest in using enzymes as tools for synthesis, many reactions discovered through the creativity of synthetic chemists remain beyond the scope of biocatalysis. This vacancy in the field has compelled researchers to develop strategies to adapt protein scaffolds for new reactivity. Heme proteins have recently been shown to activate synthetic precursors to generate reactive metallocarbenoid and metallonitrenoid species that enable the biosynthetic construction of novel C-C, C-N, and other bonds using mechanisms not previously explored by Nature. By interrogating heme proteins with synthetic, non-natural reagents, scientists are merging the reaction space traditionally dominated by organocatalysis and transition metal catalysis with the mild reaction conditions, selectivity, and adaptability imparted by native protein scaffolds.
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Affiliation(s)
- Joshua G Gober
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Eric M Brustad
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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18
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Renata H, Lewis RD, Sweredoski MJ, Moradian A, Hess S, Wang ZJ, Arnold FH. Identification of Mechanism-Based Inactivation in P450-Catalyzed Cyclopropanation Facilitates Engineering of Improved Enzymes. J Am Chem Soc 2016; 138:12527-33. [PMID: 27573353 DOI: 10.1021/jacs.6b06823] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Following the recent discovery that heme proteins can catalyze the cyclopropanation of styrenyl olefins with high efficiency and selectivity, interest in developing new enzymes for a variety of non-natural carbene transfer reactions has burgeoned. The fact that diazo compounds and other carbene precursors are known mechanism-based inhibitors of P450s, however, led us to investigate if they also interfere with this new enzyme function. We present evidence for two inactivation pathways that are operative during cytochrome P450-catalyzed cyclopropanation. Using a combination of UV-vis, mass spectrometry, and proteomic analyses, we show that the heme cofactor and several nucleophilic side chains undergo covalent modification by ethyl diazoacetate (EDA). Substitution of two of the affected residues with less-nucleophilic amino acids led to a more than twofold improvement in cyclopropanation performance (total TTN). Elucidating the inactivation pathways of heme protein-based carbene transfer catalysts should aid in the optimization of this new biocatalytic function.
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Affiliation(s)
- Hans Renata
- Division of Chemistry and Chemical Engineering, MC 210-41, and ‡Proteome Exploration Laboratory, Division of Biology and Biological Engineering, Beckman Institute, MC 139-74, California Institute of Technology , 1200 E California Blvd, Pasadena, California 91125, United States
| | - Russell D Lewis
- Division of Chemistry and Chemical Engineering, MC 210-41, and ‡Proteome Exploration Laboratory, Division of Biology and Biological Engineering, Beckman Institute, MC 139-74, California Institute of Technology , 1200 E California Blvd, Pasadena, California 91125, United States
| | - Michael J Sweredoski
- Division of Chemistry and Chemical Engineering, MC 210-41, and ‡Proteome Exploration Laboratory, Division of Biology and Biological Engineering, Beckman Institute, MC 139-74, California Institute of Technology , 1200 E California Blvd, Pasadena, California 91125, United States
| | - Annie Moradian
- Division of Chemistry and Chemical Engineering, MC 210-41, and ‡Proteome Exploration Laboratory, Division of Biology and Biological Engineering, Beckman Institute, MC 139-74, California Institute of Technology , 1200 E California Blvd, Pasadena, California 91125, United States
| | - Sonja Hess
- Division of Chemistry and Chemical Engineering, MC 210-41, and ‡Proteome Exploration Laboratory, Division of Biology and Biological Engineering, Beckman Institute, MC 139-74, California Institute of Technology , 1200 E California Blvd, Pasadena, California 91125, United States
| | - Z Jane Wang
- Division of Chemistry and Chemical Engineering, MC 210-41, and ‡Proteome Exploration Laboratory, Division of Biology and Biological Engineering, Beckman Institute, MC 139-74, California Institute of Technology , 1200 E California Blvd, Pasadena, California 91125, United States
| | - Frances H Arnold
- Division of Chemistry and Chemical Engineering, MC 210-41, and ‡Proteome Exploration Laboratory, Division of Biology and Biological Engineering, Beckman Institute, MC 139-74, California Institute of Technology , 1200 E California Blvd, Pasadena, California 91125, United States
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19
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Murciano-Calles J, Romney DK, Brinkmann-Chen S, Buller AR, Arnold FH. A Panel of TrpB Biocatalysts Derived from Tryptophan Synthase through the Transfer of Mutations that Mimic Allosteric Activation. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201606242] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Javier Murciano-Calles
- Division of Chemistry and Chemical Engineering; California Institute of Technology; Pasadena CA 91125 USA
| | - David K. Romney
- Division of Chemistry and Chemical Engineering; California Institute of Technology; Pasadena CA 91125 USA
| | - Sabine Brinkmann-Chen
- Division of Chemistry and Chemical Engineering; California Institute of Technology; Pasadena CA 91125 USA
| | - Andrew R. Buller
- Division of Chemistry and Chemical Engineering; California Institute of Technology; Pasadena CA 91125 USA
| | - Frances H. Arnold
- Division of Chemistry and Chemical Engineering; California Institute of Technology; Pasadena CA 91125 USA
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20
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Murciano-Calles J, Romney DK, Brinkmann-Chen S, Buller AR, Arnold FH. A Panel of TrpB Biocatalysts Derived from Tryptophan Synthase through the Transfer of Mutations that Mimic Allosteric Activation. Angew Chem Int Ed Engl 2016; 55:11577-81. [PMID: 27510733 DOI: 10.1002/anie.201606242] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Indexed: 11/05/2022]
Abstract
Naturally occurring enzyme homologues often display highly divergent activity with non-natural substrates. Exploiting this diversity with enzymes engineered for new or altered function, however, is laborious because the engineering must be replicated for each homologue. A small set of mutations of the tryptophan synthase β-subunit (TrpB) from Pyrococcus furiosus, which mimics the activation afforded by binding of the α-subunit, was demonstrated to have a similar activating effect in different TrpB homologues with as little as 57 % sequence identity. Kinetic and spectroscopic analyses indicate that the mutations function through the same mechanism: mimicry of α-subunit binding. From these enzymes, we identified a new TrpB catalyst that displays a remarkably broad activity profile in the synthesis of 5-substituted tryptophans. This demonstrates that allosteric activation can be recapitulated throughout a protein family to explore natural sequence diversity for desirable biocatalytic transformations.
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Affiliation(s)
- Javier Murciano-Calles
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - David K Romney
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Sabine Brinkmann-Chen
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Andrew R Buller
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Frances H Arnold
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA.
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21
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The chemistry of the carbon-transition metal double and triple bond: Annual survey covering the year 2014. Coord Chem Rev 2016. [DOI: 10.1016/j.ccr.2015.09.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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22
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Affiliation(s)
- David L. Hughes
- Cidara Therapeutics, Inc., 6310
Nancy Ridge Drive, Suite 101, San Diego, California 92121, United States
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23
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Molina-Espeja P, Viña-Gonzalez J, Gomez-Fernandez BJ, Martin-Diaz J, Garcia-Ruiz E, Alcalde M. Beyond the outer limits of nature by directed evolution. Biotechnol Adv 2016; 34:754-767. [PMID: 27064127 DOI: 10.1016/j.biotechadv.2016.03.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 03/22/2016] [Accepted: 03/27/2016] [Indexed: 01/19/2023]
Abstract
For more than thirty years, biotechnology has borne witness to the power of directed evolution in designing molecules of industrial relevance. While scientists all over the world discuss the future of molecular evolution, dozens of laboratory-designed products are being released with improved characteristics in terms of turnover rates, substrate scope, catalytic promiscuity or stability. In this review we aim to present the most recent advances in this fascinating research field that are allowing us to surpass the limits of nature and apply newly gained attributes to a range of applications, from gene therapy to novel green processes. The use of directed evolution in non-natural environments, the generation of catalytic promiscuity for non-natural reactions, the insertion of unnatural amino acids into proteins or the creation of unnatural DNA, is described comprehensively, together with the potential applications in bioremediation, biomedicine and in the generation of new bionanomaterials. These successful case studies show us that the limits of directed evolution will be defined by our own imagination, and in some cases, stretching beyond that.
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Affiliation(s)
- Patricia Molina-Espeja
- Department of Biocatalysis, Institute of Catalysis, CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Javier Viña-Gonzalez
- Department of Biocatalysis, Institute of Catalysis, CSIC, Cantoblanco, 28049 Madrid, Spain
| | | | - Javier Martin-Diaz
- Department of Biocatalysis, Institute of Catalysis, CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Eva Garcia-Ruiz
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 South Mathews Ave, Urbana, IL 61801, USA; Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 600 South Mathews Ave, Urbana, IL 61801, USA
| | - Miguel Alcalde
- Department of Biocatalysis, Institute of Catalysis, CSIC, Cantoblanco, 28049 Madrid, Spain.
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24
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King JR, Edgar S, Qiao K, Stephanopoulos G. Accessing Nature's diversity through metabolic engineering and synthetic biology. F1000Res 2016; 5. [PMID: 27081481 PMCID: PMC4813638 DOI: 10.12688/f1000research.7311.1] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/21/2016] [Indexed: 12/31/2022] Open
Abstract
In this perspective, we highlight recent examples and trends in metabolic engineering and synthetic biology that demonstrate the synthetic potential of enzyme and pathway engineering for natural product discovery. In doing so, we introduce natural paradigms of secondary metabolism whereby simple carbon substrates are combined into complex molecules through “scaffold diversification”, and subsequent “derivatization” of these scaffolds is used to synthesize distinct complex natural products. We provide examples in which modern pathway engineering efforts including combinatorial biosynthesis and biological retrosynthesis can be coupled to directed enzyme evolution and rational enzyme engineering to allow access to the “privileged” chemical space of natural products in industry-proven microbes. Finally, we forecast the potential to produce natural product-like discovery platforms in biological systems that are amenable to single-step discovery, validation, and synthesis for streamlined discovery and production of biologically active agents.
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Affiliation(s)
- Jason R King
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Steven Edgar
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kangjian Qiao
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Gregory Stephanopoulos
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
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25
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Hyster TK, Ward TR. Genetische Optimierung von Metalloenzymen: Weiterentwicklung von Enzymen für nichtnatürliche Reaktionen. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201508816] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Todd K. Hyster
- Department of Chemistry; Princeton University; Princeton NJ 08544 USA
| | - Thomas R. Ward
- Departement Chemie; Universität Basel; Spitalstrasse 51 CH-4056 Basel Schweiz
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26
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Hyster TK, Ward TR. Genetic Optimization of Metalloenzymes: Enhancing Enzymes for Non-Natural Reactions. Angew Chem Int Ed Engl 2016; 55:7344-57. [PMID: 26971363 DOI: 10.1002/anie.201508816] [Citation(s) in RCA: 119] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2015] [Indexed: 12/30/2022]
Abstract
Artificial metalloenzymes have received increasing attention over the last decade as a possible solution to unaddressed challenges in synthetic organic chemistry. Whereas traditional transition-metal catalysts typically only take advantage of the first coordination sphere to control reactivity and selectivity, artificial metalloenzymes can modulate both the first and second coordination spheres. This difference can manifest itself in reactivity profiles that can be truly unique to artificial metalloenzymes. This Review summarizes attempts to modulate the second coordination sphere of artificial metalloenzymes by using genetic modifications of the protein sequence. In doing so, successful attempts and creative solutions to address the challenges encountered are highlighted.
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Affiliation(s)
- Todd K Hyster
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA.
| | - Thomas R Ward
- Department of Chemistry, University of Basel, Spitalstrasse 51, CH-4056, Basel, Switzerland.
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27
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Gober JG, Rydeen AE, Gibson-O'Grady EJ, Leuthaeuser JB, Fetrow JS, Brustad EM. Mutating a Highly Conserved Residue in Diverse Cytochrome P450s Facilitates Diastereoselective Olefin Cyclopropanation. Chembiochem 2016; 17:394-7. [PMID: 26690878 PMCID: PMC5241096 DOI: 10.1002/cbic.201500624] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Indexed: 11/07/2022]
Abstract
Cytochrome P450s and other heme-containing proteins have recently been shown to have promiscuous activity for the cyclopropanation of olefins using diazoacetate reagents. Despite the progress made thus far, engineering selective catalysts for all possible stereoisomers for the cyclopropanation reaction remains a considerable challenge. Previous investigations of a model P450 (P450BM3 ) revealed that mutation of a conserved active site threonine (Thr268) to alanine transformed the enzyme into a highly active and selective cyclopropanation catalyst. By incorporating this mutation into a diverse panel of P450 scaffolds, we were able to quickly identify enantioselective catalysts for all possible diastereomers in the model reaction of styrene with ethyl diazoacetate. Some alanine variants exhibited selectivities that were markedly different from the wild-type enzyme, with a few possessing moderate to high diastereoselectivity and enantioselectivities up to 97 % for synthetically challenging cis-cyclopropane diastereomers.
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Affiliation(s)
- Joshua G Gober
- Department of Chemistry, University of North Carolina at Chapel Hill, 125 South Rd CB 3290, Chapel Hill, NC, 27599-3290, USA
| | - Amy E Rydeen
- Department of Chemistry, University of North Carolina at Chapel Hill, 125 South Rd CB 3290, Chapel Hill, NC, 27599-3290, USA
| | - Evan J Gibson-O'Grady
- Department of Chemistry, University of North Carolina at Chapel Hill, 125 South Rd CB 3290, Chapel Hill, NC, 27599-3290, USA
| | - Janelle B Leuthaeuser
- Department of Molecular Genetics and Genomics, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC, 27157, USA
| | - Jacquelyn S Fetrow
- Department of Chemistry, Gottwald Center for the Sciences, University of Richmond, 28 Westhampton Way, Richmond, VA, 23173, USA
| | - Eric M Brustad
- Department of Chemistry, University of North Carolina at Chapel Hill, 125 South Rd CB 3290, Chapel Hill, NC, 27599-3290, USA.
- Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
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28
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McIntosh JA, Heel T, Buller AR, Chio L, Arnold FH. Structural Adaptability Facilitates Histidine Heme Ligation in a Cytochrome P450. J Am Chem Soc 2015; 137:13861-5. [PMID: 26299431 PMCID: PMC4635421 DOI: 10.1021/jacs.5b07107] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Indexed: 11/29/2022]
Abstract
Almost all known members of the cytochrome P450 (CYP) superfamily conserve a key cysteine residue that coordinates the heme iron. Although mutation of this residue abolishes monooxygenase activity, recent work has shown that mutation to either serine or histidine unlocks non-natural carbene- and nitrene-transfer activities. Here we present the first crystal structure of a histidine-ligated P450. The T213A/C317H variant of the thermostable CYP119 from Sulfolobus acidocaldarius maintains heme iron coordination through the introduced ligand, an interaction that is accompanied by large changes in the overall protein structure. We also find that the axial cysteine C317 may be substituted with any other amino acid without abrogating folding and heme cofactor incorporation. Several of the axial mutants display unusual spectral features, suggesting that they have active sites with unique steric and electronic properties. These novel, highly stable enzyme active sites will be fruitful starting points for investigations of non-natural P450 catalysis and mechanisms.
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Affiliation(s)
- John A. McIntosh
- Division of Chemistry and
Chemical Engineering 210-41, California
Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Thomas Heel
- Division of Chemistry and
Chemical Engineering 210-41, California
Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Andrew R. Buller
- Division of Chemistry and
Chemical Engineering 210-41, California
Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Linda Chio
- Division of Chemistry and
Chemical Engineering 210-41, California
Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Frances H. Arnold
- Division of Chemistry and
Chemical Engineering 210-41, California
Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
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29
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Prier CK, Arnold FH. Chemomimetic biocatalysis: exploiting the synthetic potential of cofactor-dependent enzymes to create new catalysts. J Am Chem Soc 2015; 137:13992-4006. [PMID: 26502343 DOI: 10.1021/jacs.5b09348] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Despite the astonishing breadth of enzymes in nature, no enzymes are known for many of the valuable catalytic transformations discovered by chemists. Recent work in enzyme design and evolution, however, gives us good reason to think that this will change. We describe a chemomimetic biocatalysis approach that draws from small-molecule catalysis and synthetic chemistry, enzymology, and molecular evolution to discover or create enzymes with non-natural reactivities. We illustrate how cofactor-dependent enzymes can be exploited to promote reactions first established with related chemical catalysts. The cofactors can be biological, or they can be non-biological to further expand catalytic possibilities. The ability of enzymes to amplify and precisely control the reactivity of their cofactors together with the ability to optimize non-natural reactivity by directed evolution promises to yield exceptional catalysts for challenging transformations that have no biological counterparts.
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Affiliation(s)
- Christopher K Prier
- Division of Chemistry and Chemical Engineering, California Institute of Technology , 1200 East California Boulevard, MC 210-41, Pasadena, California 91125, United States
| | - Frances H Arnold
- Division of Chemistry and Chemical Engineering, California Institute of Technology , 1200 East California Boulevard, MC 210-41, Pasadena, California 91125, United States
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30
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Abstract
Artificial metalloenzymes (ArMs) formed by incorporating synthetic metal catalysts into protein scaffolds have the potential to impart to chemical reactions selectivity that would be difficult to achieve using metal catalysts alone. In this work, we covalently link an alkyne-substituted dirhodium catalyst to a prolyl oligopeptidase containing a genetically encoded L-4-azidophenylalanine residue to create an ArM that catalyses olefin cyclopropanation. Scaffold mutagenesis is then used to improve the enantioselectivity of this reaction, and cyclopropanation of a range of styrenes and donor-acceptor carbene precursors were accepted. The ArM reduces the formation of byproducts, including those resulting from the reaction of dirhodium-carbene intermediates with water. This shows that an ArM can improve the substrate specificity of a catalyst and, for the first time, the water tolerance of a metal-catalysed reaction. Given the diversity of reactions catalysed by dirhodium complexes, we anticipate that dirhodium ArMs will provide many unique opportunities for selective catalysis.
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31
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Abstract
AbstractI describe how we direct the evolution of non-natural enzyme activities, using chemical intuition and information on structure and mechanism to guide us to the most promising reaction/enzyme systems. With synthetic reagents to generate new reactive intermediates and just a few amino acid substitutions to tune the active site, a cytochrome P450 can catalyze a variety of carbene and nitrene transfer reactions. The cyclopropanation, N–H insertion, C–H amination, sulfimidation, and aziridination reactions now demonstrated are all well known in chemical catalysis but have no counterparts in nature. The new enzymes are fully genetically encoded, assemble and function inside of cells, and can be optimized for different substrates, activities, and selectivities. We are learning how to use nature's innovation mechanisms to marry some of the synthetic chemists’ favorite transformations with the exquisite selectivity and tunability of enzymes.
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32
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33
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Farwell C, Zhang RK, McIntosh JA, Hyster TK, Arnold FH. Enantioselective Enzyme-Catalyzed Aziridination Enabled by Active-Site Evolution of a Cytochrome P450. ACS CENTRAL SCIENCE 2015; 1:89-93. [PMID: 26405689 PMCID: PMC4571169 DOI: 10.1021/acscentsci.5b00056] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Indexed: 05/21/2023]
Abstract
One of the greatest challenges in protein design is creating new enzymes, something evolution does all the time, starting from existing ones. Borrowing from nature's evolutionary strategy, we have engineered a bacterial cytochrome P450 to catalyze highly enantioselective intermolecular aziridination, a synthetically useful reaction that has no natural biological counterpart. The new enzyme is fully genetically encoded, functions in vitro or in whole cells, and can be optimized rapidly to exhibit high enantioselectivity (up to 99% ee) and productivity (up to 1,000 catalytic turnovers) for intermolecular aziridination, demonstrated here with tosyl azide and substituted styrenes. This new aziridination activity highlights the remarkable ability of a natural enzyme to adapt and take on new functions. Once discovered in an evolvable enzyme, this non-natural activity was improved and its selectivity tuned through an evolutionary process of accumulating beneficial mutations.
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34
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Wallace S, Balskus EP. Interfacing Microbial Styrene Production with a Biocompatible Cyclopropanation Reaction. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201502185] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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35
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Wallace S, Balskus EP. Interfacing microbial styrene production with a biocompatible cyclopropanation reaction. Angew Chem Int Ed Engl 2015; 54:7106-9. [PMID: 25925138 DOI: 10.1002/anie.201502185] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Indexed: 01/04/2023]
Abstract
The introduction of new reactivity into living organisms is a major challenge in synthetic biology. Despite an increasing interest in both the development of small-molecule catalysts that are compatible with aqueous media and the engineering of enzymes to perform new chemistry in vitro, the integration of non-native reactivity into metabolic pathways for small-molecule production has been underexplored. Herein we report a biocompatible iron(III) phthalocyanine catalyst capable of efficient olefin cyclopropanation in the presence of a living microorganism. By interfacing this catalyst with E. coli engineered to produce styrene, we synthesized non-natural phenyl cyclopropanes directly from D-glucose in single-vessel fermentations. This process is the first example of the combination of nonbiological carbene-transfer reactivity with cellular metabolism for small-molecule production.
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Affiliation(s)
- Stephen Wallace
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138 (USA) http://scholar.harvard.edu/balskus
| | - Emily P Balskus
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138 (USA) http://scholar.harvard.edu/balskus.
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36
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Renata H, Wang ZJ, Arnold FH. Expanding the enzyme universe: accessing non-natural reactions by mechanism-guided directed evolution. Angew Chem Int Ed Engl 2015; 54:3351-67. [PMID: 25649694 PMCID: PMC4404643 DOI: 10.1002/anie.201409470] [Citation(s) in RCA: 360] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Indexed: 11/10/2022]
Abstract
High selectivity and exquisite control over the outcome of reactions entice chemists to use biocatalysts in organic synthesis. However, many useful reactions are not accessible because they are not in nature's known repertoire. In this Review, we outline an evolutionary approach to engineering enzymes to catalyze reactions not found in nature. We begin with examples of how nature has discovered new catalytic functions and how such evolutionary progression has been recapitulated in the laboratory starting from extant enzymes. We then examine non-native enzyme activities that have been exploited for chemical synthesis, with an emphasis on reactions that do not have natural counterparts. Non-natural activities can be improved by directed evolution, thus mimicking the process used by nature to create new catalysts. Finally, we describe the discovery of non-native catalytic functions that may provide future opportunities for the expansion of the enzyme universe.
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Affiliation(s)
- Hans Renata
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd. MC 210-41, Pasadena, CA 91125 (USA)
| | - Z. Jane Wang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd. MC 210-41, Pasadena, CA 91125 (USA)
| | - Frances H. Arnold
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd. MC 210-41, Pasadena, CA 91125 (USA)
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37
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Renata H, Wang ZJ, Arnold FH. Ausdehnung des Enzym-Universums: Zugang zu nicht-natürlichen Reaktionen durch mechanismusgeleitete, gerichtete Evolution. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201409470] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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38
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Sreenilayam G, Fasan R. Myoglobin-catalyzed intermolecular carbene N-H insertion with arylamine substrates. Chem Commun (Camb) 2015; 51:1532-4. [PMID: 25504318 PMCID: PMC4282819 DOI: 10.1039/c4cc08753d] [Citation(s) in RCA: 138] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Engineered variants of the heme-containing protein myoglobin can efficiently catalyze the insertion of α-diazo esters into the N-H bond of arylamines, featuring a combination of high chemoselectivity, elevated turnover numbers, and broad substrate scope.
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39
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Hyster TK, Farwell CC, Buller AR, McIntosh JA, Arnold FH. Enzyme-controlled nitrogen-atom transfer enables regiodivergent C-H amination. J Am Chem Soc 2014; 136:15505-8. [PMID: 25325618 PMCID: PMC4227740 DOI: 10.1021/ja509308v] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2014] [Indexed: 12/18/2022]
Abstract
We recently demonstrated that variants of cytochrome P450BM3 (CYP102A1) catalyze the insertion of nitrogen species into benzylic C-H bonds to form new C-N bonds. An outstanding challenge in the field of C-H amination is catalyst-controlled regioselectivity. Here, we report two engineered variants of P450BM3 that provide divergent regioselectivity for C-H amination-one favoring amination of benzylic C-H bonds and the other favoring homo-benzylic C-H bonds. The two variants provide nearly identical kinetic isotope effect values (2.8-3.0), suggesting that C-H abstraction is rate-limiting. The 2.66-Å crystal structure of the most active enzyme suggests that the engineered active site can preorganize the substrate for reactivity. We hypothesize that the enzyme controls regioselectivity through localization of a single C-H bond close to the iron nitrenoid.
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Affiliation(s)
- Todd K. Hyster
- Division of Chemistry and
Chemical Engineering 210-41, California
Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Christopher C. Farwell
- Division of Chemistry and
Chemical Engineering 210-41, California
Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Andrew R. Buller
- Division of Chemistry and
Chemical Engineering 210-41, California
Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - John A. McIntosh
- Division of Chemistry and
Chemical Engineering 210-41, California
Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Frances H. Arnold
- Division of Chemistry and
Chemical Engineering 210-41, California
Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
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