1
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Fansher DJ, Besna JN, Pelletier JN. Indigo production identifies hotspots in cytochrome P450 BM3 for diversifying aromatic hydroxylation. Faraday Discuss 2024. [PMID: 38993060 DOI: 10.1039/d4fd00017j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2024]
Abstract
Evolution of P450 BM3 is a topic of extensive research, but screening the various substrate/reaction combinations remains a time-consuming process. Indigo production has the potential to serve as a simple high-throughput method for reaction screening, as bacterial colonies expressing indigo (+) variants can be visually identified via their blue phenotype. Indigo (+) single variants, indigo (-) single variants and a combinatorial library, containing mutations that enable the blue phenotype, were screened for their ability to hydroxylate a panel of 12 aromatic compounds using the 4-aminoantipyrine colorimetric assay. Recombination of indigo (+) single variants to create a multiple-variant library is a particularly useful strategy, as all top performing P450 BM3 variants with high hydroxylation activity were either indigo (+) single variants or contained multiple substitutions. Furthermore, active variants, as determined using the 4-AAP assay, were further characterized and several variants were identified that gave more than 90% conversion with 1,3-dichlorobenzene and predominantly formed 2,6-dichlorophenol; other variants showed significant substrate selectivity. This supports the hypothesis that substitution at positions that enable the indigo (+) phenotype, or hotspot residues, is a general mechanism for increasing aromatic hydroxylation activity. Overall, this research demonstrates that indigo (+) single variants, identified via colorimetric colony-based screening, may be recombined to generate a multiply-substituted variant library containing many variants with high aromatic hydroxylation activity. The combination of colony-based screening and other screening assays greatly accelerates enzyme engineering, as readily-identified indigo (+) single variants can be recombined to create a library of active multiple variants without extensive screening of single variants.
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Affiliation(s)
- Douglas J Fansher
- Chemistry Department, Université de Montréal, Montreal, QC, Canada.
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Quebec, QC, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montreal, QC, Canada
| | - Jonathan N Besna
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Quebec, QC, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montreal, QC, Canada
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC, Canada
| | - Joelle N Pelletier
- Chemistry Department, Université de Montréal, Montreal, QC, Canada.
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Quebec, QC, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montreal, QC, Canada
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC, Canada
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2
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Soler J, Gergel S, Hammer SC, Garcia-Borràs M. Molecular Basis for Chemoselectivity Control in Oxidations of Internal Aryl-Alkenes Catalyzed by Laboratory Evolved P450s. Chembiochem 2024; 25:e202400066. [PMID: 38567500 DOI: 10.1002/cbic.202400066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 03/28/2024] [Accepted: 04/03/2024] [Indexed: 04/04/2024]
Abstract
P450 enzymes naturally perform selective hydroxylations and epoxidations of unfunctionalized hydrocarbon substrates, among other reactions. The adaptation of P450 enzymes to a particular oxidative reaction involving alkenes is of great interest for the design of new synthetically useful biocatalysts. However, the mechanism that these enzymes utilize to precisely modulate the chemoselectivity and distinguishing between competing alkene double bond epoxidations and allylic C-H hydroxylations is sometimes not clear, which hampers the rational design of specific biocatalysts. In a previous work, a P450 from Labrenzia aggregata (P450LA1) was engineered in the laboratory using directed evolution to catalyze the direct oxidation of trans-β-methylstyrene to phenylacetone. The final variant, KS, was able to overcome the intrinsic preference for alkene epoxidation to directly generate a ketone product via the formation of a highly reactive carbocation intermediate. Here, additional library screening along this evolutionary lineage permitted to serendipitously detect a mutation that overcomes epoxidation and carbonyl formation by exhibiting a large selectivity of 94 % towards allylic C-H hydroxylation. A multiscalar computational methodology was applied to reveal the molecular basis towards this hydroxylation preference. Enzyme modelling suggests that introduction of a bulky substitution dramatically changes the accessible conformations of the substrate in the active site, thus modifying the enzymatic selectivity towards terminal hydroxylation and avoiding the competing epoxidation pathway, which is sterically hindered.
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Affiliation(s)
- Jordi Soler
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Carrer Maria Aurèlia Capmany 69, 17003, Girona, Catalonia, Spain
| | - Sebastian Gergel
- Organic Chemistry and Biocatalysis, Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Stephan C Hammer
- Organic Chemistry and Biocatalysis, Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Marc Garcia-Borràs
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Carrer Maria Aurèlia Capmany 69, 17003, Girona, Catalonia, Spain
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3
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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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4
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Kim JH, Park CM, Jeong HC, Jeong GH, Cha GS, Lee S, Yun CH. Production of Mono-Hydroxylated Derivatives of Terpinen-4-ol by Bacterial CYP102A1 Enzymes. J Microbiol Biotechnol 2024; 34:725-734. [PMID: 38044690 PMCID: PMC11016761 DOI: 10.4014/jmb.2310.10018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 12/05/2023]
Abstract
CYP102A1 from Bacillus megaterium is an important enzyme in biotechnology, because engineered CYP102A1 enzymes can react with diverse substrates and produce human cytochrome P450-like metabolites. Therefore, CYP102A1 can be applied to drug metabolite production. Terpinen-4-ol is a cyclic monoterpene and the primary component of essential tea tree oil. Terpinen-4-ol was known for therapeutic effects, including antibacterial, antifungal, antiviral, and anti-inflammatory. Because terpenes are natural compounds, examining novel terpenes and investigating the therapeutic effects of terpenes represent responses to social demands for eco-friendly compounds. In this study, we investigated the catalytic activity of engineered CYP102A1 on terpinen-4-ol. Among CYP102A1 mutants tested here, the R47L/F81I/F87V/E143G/L188Q/N213S/E267V mutant showed the highest activity to terpinen-4-ol. Two major metabolites of terpinen-4-ol were generated by engineered CYP102A1. Characterization of major metabolites was confirmed by liquid chromatography-mass spectrometry (LC-MS), gas chromatography-MS, and nuclear magnetic resonance spectroscopy (NMR). Based on the LC-MS results, the difference in mass-to-charge ratio of an ion (m/z) between terpinen-4-ol and its major metabolites was 16. One major metabolite was defined as 1,4-dihydroxy-p-menth-2-ene by NMR. Given these results, we speculate that another major metabolite is also a mono-hydroxylated product. Taken together, we suggest that CYP102A1 can be applied to make novel terpene derivatives.
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Affiliation(s)
- Jeong-Hoon Kim
- School of Biological Sciences and Biotechnology, Graduate School, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Chan Mi Park
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Hae Chan Jeong
- School of Biological Sciences and Biotechnology, Graduate School, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Gyeong Han Jeong
- Research Division for Biotechnology, Advanced Radiation Technology Institute (ARTI), Korea Atomic Energy Research Institute (KAERI), Jeongeup 56212, Republic of Korea
| | - Gun Su Cha
- Namhae Garlic Research Institute, Namhae 52430, Republic of Korea
| | - Sungbeom Lee
- Research Division for Biotechnology, Advanced Radiation Technology Institute (ARTI), Korea Atomic Energy Research Institute (KAERI), Jeongeup 56212, Republic of Korea
- Department of Radiation Science and Technology, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Chul-Ho Yun
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Republic of Korea
- Institute of Synthetic Biology for Carbon Neutralization, Chonnam National University, Gwangju 61186, Republic of Korea
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5
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Abstract
The ability to site-selectively modify equivalent functional groups in a molecule has the potential to streamline syntheses and increase product yields by lowering step counts. Enzymes catalyze site-selective transformations throughout primary and secondary metabolism, but leveraging this capability for non-native substrates and reactions requires a detailed understanding of the potential and limitations of enzyme catalysis and how these bounds can be extended by protein engineering. In this review, we discuss representative examples of site-selective enzyme catalysis involving functional group manipulation and C-H bond functionalization. We include illustrative examples of native catalysis, but our focus is on cases involving non-native substrates and reactions often using engineered enzymes. We then discuss the use of these enzymes for chemoenzymatic transformations and target-oriented synthesis and conclude with a survey of tools and techniques that could expand the scope of non-native site-selective enzyme catalysis.
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Affiliation(s)
- Dibyendu Mondal
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Harrison M Snodgrass
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Christian A Gomez
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Jared C Lewis
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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6
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Call A, Capocasa G, Palone A, Vicens L, Aparicio E, Choukairi Afailal N, Siakavaras N, López Saló ME, Bietti M, Costas M. Highly Enantioselective Catalytic Lactonization at Nonactivated Primary and Secondary γ-C-H Bonds. J Am Chem Soc 2023; 145:18094-18103. [PMID: 37540636 PMCID: PMC10507665 DOI: 10.1021/jacs.3c06231] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Indexed: 08/06/2023]
Abstract
Chiral oxygenated aliphatic moieties are recurrent in biological and pharmaceutically relevant molecules and constitute one of the most versatile types of functionalities for further elaboration. Herein we report a protocol for straightforward and general access to chiral γ-lactones via enantioselective oxidation of strong nonactivated primary and secondary C(sp3)-H bonds in readily available carboxylic acids. The key enabling aspect is the use of robust sterically encumbered manganese catalysts that provide outstanding enantioselectivities (up to >99.9%) and yields (up to 96%) employing hydrogen peroxide as the oxidant. The resulting γ-lactones are of immediate interest for the preparation of inter alia natural products and recyclable polymeric materials.
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Affiliation(s)
- Arnau Call
- Institut
de Química Computacional i Catàlisi (IQCC) and Departament
de Química, Universitat de Girona, Campus Montilivi, Girona E-17071, Catalonia, Spain
| | - Giorgio Capocasa
- Institut
de Química Computacional i Catàlisi (IQCC) and Departament
de Química, Universitat de Girona, Campus Montilivi, Girona E-17071, Catalonia, Spain
| | - Andrea Palone
- Institut
de Química Computacional i Catàlisi (IQCC) and Departament
de Química, Universitat de Girona, Campus Montilivi, Girona E-17071, Catalonia, Spain
| | - Laia Vicens
- Institut
de Química Computacional i Catàlisi (IQCC) and Departament
de Química, Universitat de Girona, Campus Montilivi, Girona E-17071, Catalonia, Spain
| | - Eric Aparicio
- Institut
de Química Computacional i Catàlisi (IQCC) and Departament
de Química, Universitat de Girona, Campus Montilivi, Girona E-17071, Catalonia, Spain
| | - Najoua Choukairi Afailal
- Institut
de Química Computacional i Catàlisi (IQCC) and Departament
de Química, Universitat de Girona, Campus Montilivi, Girona E-17071, Catalonia, Spain
| | - Nikos Siakavaras
- Institut
de Química Computacional i Catàlisi (IQCC) and Departament
de Química, Universitat de Girona, Campus Montilivi, Girona E-17071, Catalonia, Spain
| | - Maria Eugènia López Saló
- Institut
de Química Computacional i Catàlisi (IQCC) and Departament
de Química, Universitat de Girona, Campus Montilivi, Girona E-17071, Catalonia, Spain
| | - Massimo Bietti
- Dipartimento
di Scienze e Tecnologie Chimiche, Università
“Tor Vergata”, Via della Ricerca Scientifica, 1 I-00133 Rome, Italy
| | - Miquel Costas
- Institut
de Química Computacional i Catàlisi (IQCC) and Departament
de Química, Universitat de Girona, Campus Montilivi, Girona E-17071, Catalonia, Spain
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7
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Palone A, Casadevall G, Ruiz-Barragan S, Call A, Osuna S, Bietti M, Costas M. C-H Bonds as Functional Groups: Simultaneous Generation of Multiple Stereocenters by Enantioselective Hydroxylation at Unactivated Tertiary C-H Bonds. J Am Chem Soc 2023; 145:15742-15753. [PMID: 37431886 PMCID: PMC10651061 DOI: 10.1021/jacs.2c10148] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Indexed: 07/12/2023]
Abstract
Enantioselective C-H oxidation is a standing chemical challenge foreseen as a powerful tool to transform readily available organic molecules into precious oxygenated building blocks. Here, we describe a catalytic enantioselective hydroxylation of tertiary C-H bonds in cyclohexane scaffolds with H2O2, an evolved manganese catalyst that provides structural complementary to the substrate similarly to the lock-and-key recognition operating in enzymatic active sites. Theoretical calculations unveil that enantioselectivity is governed by the precise fitting of the substrate scaffold into the catalytic site, through a network of complementary weak non-covalent interactions. Stereoretentive C(sp3)-H hydroxylation results in a single-step generation of multiple stereogenic centers (up to 4) that can be orthogonally manipulated by conventional methods providing rapid access, from a single precursor to a variety of chiral scaffolds.
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Affiliation(s)
- Andrea Palone
- Institut
de Química Computacional i Catàlisi (IQCC) and Departament
de Química, Universitat de Girona, Campus Montilivi, Girona, Catalonia E-17071, Spain
- Dipartimento
di Scienze e Tecnologie Chimiche, Università
“Tor Vergata”, Via della Ricerca Scientifica, 1, I-00133 Rome, Italy
| | - Guillem Casadevall
- Institut
de Química Computacional i Catàlisi (IQCC) and Departament
de Química, Universitat de Girona, Campus Montilivi, Girona, Catalonia E-17071, Spain
| | - Sergi Ruiz-Barragan
- Institut
de Química Computacional i Catàlisi (IQCC) and Departament
de Química, Universitat de Girona, Campus Montilivi, Girona, Catalonia E-17071, Spain
| | - Arnau Call
- Institut
de Química Computacional i Catàlisi (IQCC) and Departament
de Química, Universitat de Girona, Campus Montilivi, Girona, Catalonia E-17071, Spain
| | - Sílvia Osuna
- Institut
de Química Computacional i Catàlisi (IQCC) and Departament
de Química, Universitat de Girona, Campus Montilivi, Girona, Catalonia E-17071, Spain
- ICREA, Pg. Lluís Companys 23, Barcelona 08010, Spain
| | - Massimo Bietti
- Dipartimento
di Scienze e Tecnologie Chimiche, Università
“Tor Vergata”, Via della Ricerca Scientifica, 1, I-00133 Rome, Italy
| | - Miquel Costas
- Institut
de Química Computacional i Catàlisi (IQCC) and Departament
de Química, Universitat de Girona, Campus Montilivi, Girona, Catalonia E-17071, Spain
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8
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Chai J, Guo G, McSweeney SM, Shanklin J, Liu Q. Structural basis for enzymatic terminal C-H bond functionalization of alkanes. Nat Struct Mol Biol 2023; 30:521-526. [PMID: 36997762 PMCID: PMC10113152 DOI: 10.1038/s41594-023-00958-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 03/01/2023] [Indexed: 04/01/2023]
Abstract
Alkane monooxygenase (AlkB) is a widely occurring integral membrane metalloenzyme that catalyzes the initial step in the functionalization of recalcitrant alkanes with high terminal selectivity. AlkB enables diverse microorganisms to use alkanes as their sole carbon and energy source. Here we present the 48.6-kDa cryo-electron microscopy structure of a natural fusion from Fontimonas thermophila between AlkB and its electron donor AlkG at 2.76 Å resolution. The AlkB portion contains six transmembrane helices with an alkane entry tunnel within its transmembrane domain. A dodecane substrate is oriented by hydrophobic tunnel-lining residues to present a terminal C-H bond toward a diiron active site. AlkG, an [Fe-4S] rubredoxin, docks via electrostatic interactions and sequentially transfers electrons to the diiron center. The archetypal structural complex presented reveals the basis for terminal C-H selectivity and functionalization within this broadly distributed evolutionary class of enzymes.
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Affiliation(s)
- Jin Chai
- Biology Department, Brookhaven National Laboratory, Upton, NY, USA
| | - Gongrui Guo
- Biology Department, Brookhaven National Laboratory, Upton, NY, USA
- NSLS-II, Brookhaven National Laboratory, Upton, NY, USA
| | | | - John Shanklin
- Biology Department, Brookhaven National Laboratory, Upton, NY, USA.
| | - Qun Liu
- Biology Department, Brookhaven National Laboratory, Upton, NY, USA.
- NSLS-II, Brookhaven National Laboratory, Upton, NY, USA.
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9
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Pogrányi B, Mielke T, Díaz-Rodríguez A, Cartwright J, Unsworth WP, Grogan G. Preparative-Scale Biocatalytic Oxygenation of N-Heterocycles with a Lyophilized Peroxygenase Catalyst. Angew Chem Int Ed Engl 2023; 62:e202214759. [PMID: 36453718 PMCID: PMC10107140 DOI: 10.1002/anie.202214759] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/17/2022] [Accepted: 11/30/2022] [Indexed: 12/02/2022]
Abstract
A lyophilized preparation of an unspecific peroxygenase variant from Agrocybe aegerita (rAaeUPO-PaDa-I-H) is a highly effective catalyst for the oxygenation of a diverse range of N-heterocyclic compounds. Scalable biocatalytic oxygenations (27 preparative examples, ca. 100 mg scale) have been developed across a wide range of substrates, including alkyl pyridines, bicyclic N-heterocycles and indoles. H2 O2 is the only stoichiometric oxidant needed, without auxiliary electron transport proteins, which is key to the practicality of the method. Reaction outcomes can be altered depending on whether hydrogen peroxide was delivered by syringe pump or through in situ generation using an alcohol oxidase from Pichia pastoris (PpAOX) and methanol as a co-substrate. Good synthetic yields (up to 84 %), regioselectivity and enantioselectivity (up to 99 % ee) were observed in some cases, highlighting the promise of UPOs as practical, versatile and scalable oxygenation biocatalysts.
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Affiliation(s)
- Balázs Pogrányi
- Department of Chemistry, University of York, Heslington York, YO10 5DD, UK
| | - Tamara Mielke
- Department of Chemistry, University of York, Heslington York, YO10 5DD, UK
| | - Alba Díaz-Rodríguez
- GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
| | - Jared Cartwright
- Department of Biology, University of York, Heslington York, YO10 5DD, UK
| | - William P Unsworth
- Department of Chemistry, University of York, Heslington York, YO10 5DD, UK
| | - Gideon Grogan
- Department of Chemistry, University of York, Heslington York, YO10 5DD, UK
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10
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Abstract
The P450 superfamily comprises some of the most powerful and versatile enzymes for the site-selective oxidation of small molecules. One of the main drawbacks for the applications of the P450s in biotechnology is that the majority of these enzymes is multicomponent in nature and requires the presence of suitable redox partners to support their functions. Nevertheless, the discovery of several self-sufficient P450s, namely those from Classes VII and VIII, has served as an inspiration for fusion approaches to generate chimeric P450 systems that are self-sufficient. In this Perspective, we highlight the domain organizations of the Class VII and Class VIII P450 systems, summarize recent case studies in the engineering of catalytically self-sufficient P450s based on these systems, and outline outstanding challenges in the field, along with several emerging technologies as potential solutions.
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Affiliation(s)
- Hans Renata
- Department of Chemistry, BioScience Research Collaborative, Rice University, Houston, TX, 77005
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11
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Robinson WXQ, Mielke T, Melling B, Cuetos A, Parkin A, Unsworth WP, Cartwright J, Grogan G. Comparing the Catalytic and Structural Characteristics of a 'Short' Unspecific Peroxygenase (UPO) Expressed in Pichia pastoris and Escherichia coli. Chembiochem 2023; 24:e202200558. [PMID: 36374006 PMCID: PMC10098773 DOI: 10.1002/cbic.202200558] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 11/14/2022] [Indexed: 11/16/2022]
Abstract
Unspecific peroxygenases (UPOs) have emerged as valuable tools for the oxygenation of non-activated carbon atoms, as they exhibit high turnovers, good stability and depend only on hydrogen peroxide as the external oxidant for activity. However, the isolation of UPOs from their natural fungal sources remains a barrier to wider application. We have cloned the gene encoding an 'artificial' peroxygenase (artUPO), close in sequence to the 'short' UPO from Marasmius rotula (MroUPO), and expressed it in both the yeast Pichia pastoris and E. coli to compare the catalytic and structural characteristics of the enzymes produced in each system. Catalytic efficiency for the UPO substrate 5-nitro-1,3-benzodioxole (NBD) was largely the same for both enzymes, and the structures also revealed few differences apart from the expected glycosylation of the yeast enzyme. However, the glycosylated enzyme displayed greater stability, as determined by nano differential scanning fluorimetry (nano-DSF) measurements. Interestingly, while artUPO hydroxylated ethylbenzene derivatives to give the (R)-alcohols, also given by a variant of the 'long' UPO from Agrocybe aegerita (AaeUPO), it gave the opposite (S)-series of sulfoxide products from a range of sulfide substrates, broadening the scope for application of the enzymes. The structures of artUPO reveal substantial differences to that of AaeUPO, and provide a platform for investigating the distinctive activity of this and related'short' UPOs.
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Affiliation(s)
- Wendy X Q Robinson
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - Tamara Mielke
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - Benjamin Melling
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - Anibal Cuetos
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - Alison Parkin
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - William P Unsworth
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - Jared Cartwright
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK
| | - Gideon Grogan
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
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12
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Cheng S, Li Q, Cheng X, Lin Y, Gong L. Recent Advances in Asymmetric Transformations of Unactivated Alkanes and Cycloalkanes through Direct C–H Functionalization. CHINESE J CHEM 2022. [DOI: 10.1002/cjoc.202200435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Shiyan Cheng
- Key Laboratory of Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering Xiamen University Xiamen Fujian 361005 China
| | - Qianyu Li
- Key Laboratory of Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering Xiamen University Xiamen Fujian 361005 China
| | - Xiuliang Cheng
- Key Laboratory of Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering Xiamen University Xiamen Fujian 361005 China
| | - Yu‐Mei Lin
- Key Laboratory of Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering Xiamen University Xiamen Fujian 361005 China
| | - Lei Gong
- Key Laboratory of Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering Xiamen University Xiamen Fujian 361005 China
- Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen 361005 China
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13
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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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14
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Van Stappen C, Deng Y, Liu Y, Heidari H, Wang JX, Zhou Y, Ledray AP, Lu Y. Designing Artificial Metalloenzymes by Tuning of the Environment beyond the Primary Coordination Sphere. Chem Rev 2022; 122:11974-12045. [PMID: 35816578 DOI: 10.1021/acs.chemrev.2c00106] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Metalloenzymes catalyze a variety of reactions using a limited number of natural amino acids and metallocofactors. Therefore, the environment beyond the primary coordination sphere must play an important role in both conferring and tuning their phenomenal catalytic properties, enabling active sites with otherwise similar primary coordination environments to perform a diverse array of biological functions. However, since the interactions beyond the primary coordination sphere are numerous and weak, it has been difficult to pinpoint structural features responsible for the tuning of activities of native enzymes. Designing artificial metalloenzymes (ArMs) offers an excellent basis to elucidate the roles of these interactions and to further develop practical biological catalysts. In this review, we highlight how the secondary coordination spheres of ArMs influence metal binding and catalysis, with particular focus on the use of native protein scaffolds as templates for the design of ArMs by either rational design aided by computational modeling, directed evolution, or a combination of both approaches. In describing successes in designing heme, nonheme Fe, and Cu metalloenzymes, heteronuclear metalloenzymes containing heme, and those ArMs containing other metal centers (including those with non-native metal ions and metallocofactors), we have summarized insights gained on how careful controls of the interactions in the secondary coordination sphere, including hydrophobic and hydrogen bonding interactions, allow the generation and tuning of these respective systems to approach, rival, and, in a few cases, exceed those of native enzymes. We have also provided an outlook on the remaining challenges in the field and future directions that will allow for a deeper understanding of the secondary coordination sphere a deeper understanding of the secondary coordintion sphere to be gained, and in turn to guide the design of a broader and more efficient variety of ArMs.
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Affiliation(s)
- Casey Van Stappen
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yunling Deng
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yiwei Liu
- Department of Chemistry, University of Illinois, Urbana-Champaign, 505 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Hirbod Heidari
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Jing-Xiang Wang
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yu Zhou
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Aaron P Ledray
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yi Lu
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States.,Department of Chemistry, University of Illinois, Urbana-Champaign, 505 South Mathews Avenue, Urbana, Illinois 61801, United States
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15
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Mahor D, Cong Z, Weissenborn MJ, Hollmann F, Zhang W. Valorization of Small Alkanes by Biocatalytic Oxyfunctionalization. CHEMSUSCHEM 2022; 15:e202101116. [PMID: 34288540 DOI: 10.1002/cssc.202101116] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/18/2021] [Indexed: 06/13/2023]
Abstract
The oxidation of alkanes into valuable chemical products is a vital reaction in organic synthesis. This reaction, however, is challenging, owing to the inertness of C-H bonds. Transition metal catalysts for C-H functionalization are frequently explored. Despite chemical alternatives, nature has also evolved powerful oxidative enzymes (e. g., methane monooxygenases, cytochrome P450 oxygenases, peroxygenases) that are capable of transforming C-H bonds under very mild conditions, with only the use of molecular oxygen or hydrogen peroxide as electron acceptors. Although progress in alkane oxidation has been reviewed extensively, little attention has been paid to small alkane oxidation. The latter holds great potential for the manufacture of chemicals. This Minireview provides a concise overview of the most relevant enzyme classes capable of small alkanes (C<6 ) oxyfunctionalization, describes the essentials of the catalytic mechanisms, and critically outlines the current state-of-the-art in preparative applications.
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Affiliation(s)
- Durga Mahor
- National Innovation Center for Synthetic Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, P. R. China
- Indian Institute of Science Education and Research Berhampur, Odisha, 760010, India
| | - Zhiqi Cong
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology Chinese Academy of Sciences, Qingdao, Shandong, 266101, P. R. China
| | - Martin J Weissenborn
- Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Saale), Germany
| | - Frank Hollmann
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ, Delft, The Netherlands
| | - Wuyuan Zhang
- National Innovation Center for Synthetic Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, P. R. China
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16
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Worakaensai S, Kluaiphanngam S, Wet-Osot S, Charoenwattanasatien R, Ngivprom U, Duangkamol C, Kamkaew A, Lai RY. Design of a surrogate for high throughput screening of fatty aldehyde reductase engineering. Chem Commun (Camb) 2021; 57:13373-13376. [PMID: 34821892 DOI: 10.1039/d1cc05472d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We designed and synthesized a fatty aldehyde surrogate containing a formyl thioester group, which can be reduced by fatty aldehyde reductase (FALR) with stoichiometric formaldehyde generation. It can be rapidly visualized and quantified using the Purpald assay. We demonstrated its successful application in the high throughput screening of FALR engineering.
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Affiliation(s)
- Suphanida Worakaensai
- School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima, 30000 Thailand.
| | - Surayut Kluaiphanngam
- School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima, 30000 Thailand.
| | - Sirawit Wet-Osot
- School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima, 30000 Thailand.
| | - Ratana Charoenwattanasatien
- Synchrotron Light Research Institute (Public Organization), 111 University Avenue, Nakhon Ratchasima, 30000 Thailand.,Center for Biomolecular Structure, Function and Application, Suranaree University of Technology, Nakhon Ratchasima, 30000 Thailand
| | - Utumporn Ngivprom
- School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima, 30000 Thailand.
| | - Chuthamat Duangkamol
- School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima, 30000 Thailand.
| | - Anyanee Kamkaew
- School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima, 30000 Thailand.
| | - Rung-Yi Lai
- School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima, 30000 Thailand. .,Center for Biomolecular Structure, Function and Application, Suranaree University of Technology, Nakhon Ratchasima, 30000 Thailand
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17
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A Promiscuous Bacterial P450: The Unparalleled Diversity of BM3 in Pharmaceutical Metabolism. Int J Mol Sci 2021; 22:ijms222111380. [PMID: 34768811 PMCID: PMC8583553 DOI: 10.3390/ijms222111380] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/12/2021] [Accepted: 10/12/2021] [Indexed: 11/16/2022] Open
Abstract
CYP102A1 (BM3) is a catalytically self-sufficient flavocytochrome fusion protein isolated from Bacillus megaterium, which displays similar metabolic capabilities to many drug-metabolizing human P450 isoforms. BM3's high catalytic efficiency, ease of production and malleable active site makes the enzyme a desirable tool in the production of small molecule metabolites, especially for compounds that exhibit drug-like chemical properties. The engineering of select key residues within the BM3 active site vastly expands the catalytic repertoire, generating variants which can perform a range of modifications. This provides an attractive alternative route to the production of valuable compounds that are often laborious to synthesize via traditional organic means. Extensive studies have been conducted with the aim of engineering BM3 to expand metabolite production towards a comprehensive range of drug-like compounds, with many key examples found both in the literature and in the wider industrial bioproduction setting of desirable oxy-metabolite production by both wild-type BM3 and related variants. This review covers the past and current research on the engineering of BM3 to produce drug metabolites and highlights its crucial role in the future of biosynthetic pharmaceutical production.
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18
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Costas M. Site and Enantioselective Aliphatic C-H Oxidation with Bioinspired Chiral Complexes. CHEM REC 2021; 21:4000-4014. [PMID: 34609780 DOI: 10.1002/tcr.202100227] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/17/2021] [Accepted: 09/17/2021] [Indexed: 12/12/2022]
Abstract
Selective oxidation of aliphatic C-H bonds stands as an unsolved problem in organic synthesis, with the potential to offer novel paths for preparing molecules of biological interest. The quest for reagents that can perform this class of reactions finds oxygenases and their mechanisms of action as inspiration motifs. Among the numerous families of synthetic catalysts that have been explored, complexes with linear tetraazadentate ligands combining two aliphatic amines and two aromatic amine heterocycles display a structural versatility proven instrumental in the design of C-H oxidation reactions showing site and enantioselectivities, not accessible by conventional oxidants. This manuscript makes a review of recent advances in the field.
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Affiliation(s)
- Miquel Costas
- Department of Chemistry and Institut de Química Computacional I Catàlisi (IQCC), Universitat de Girona Facultat de Ciències, Campus de Montilivi, 17003, Girona, Spain
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19
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Wu X, Chen Y, Wang X, Wei W, Liang Y. Origin of Site Selectivity in Toluene Hydroxylation by Cytochrome P450 Enzymes. J Org Chem 2021; 86:13768-13773. [PMID: 34533309 DOI: 10.1021/acs.joc.1c01295] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Computational studies are utilized to reveal factors that determine the site selectivity in toluene hydroxylation by cytochrome P450 enzymes (CYPs). The DFT-computed inherent barriers suggest that the priority of product formation is in the order of benzyl alcohol > ortho- ≈ para- > meta-cresol. However, the specific size and shape of the cavities at the active sites of different CYPs dramatically affect the binding orientation of toluene, and thus, the site selectivity can be reordered.
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Affiliation(s)
- Xuan Wu
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023,China
| | - Yu Chen
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023,China
| | - Xin Wang
- Henan-Macquarie University Joint Centre for Biomedical Innovation, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Wanqing Wei
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023,China
| | - Yong Liang
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023,China
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20
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Late-stage C–H functionalization offers new opportunities in drug discovery. Nat Rev Chem 2021; 5:522-545. [PMID: 37117588 DOI: 10.1038/s41570-021-00300-6] [Citation(s) in RCA: 261] [Impact Index Per Article: 87.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/02/2021] [Indexed: 12/24/2022]
Abstract
Over the past decade, the landscape of molecular synthesis has gained major impetus by the introduction of late-stage functionalization (LSF) methodologies. C-H functionalization approaches, particularly, set the stage for new retrosynthetic disconnections, while leading to improvements in resource economy. A variety of innovative techniques have been successfully applied to the C-H diversification of pharmaceuticals, and these key developments have enabled medicinal chemists to integrate LSF strategies in their drug discovery programmes. This Review highlights the significant advances achieved in the late-stage C-H functionalization of drugs and drug-like compounds, and showcases how the implementation of these modern strategies allows increased efficiency in the drug discovery process. Representative examples are examined and classified by mechanistic patterns involving directed or innate C-H functionalization, as well as emerging reaction manifolds, such as electrosynthesis and biocatalysis, among others. Structurally complex bioactive entities beyond small molecules are also covered, including diversification in the new modalities sphere. The challenges and limitations of current LSF methods are critically assessed, and avenues for future improvements of this rapidly expanding field are discussed. We, hereby, aim to provide a toolbox for chemists in academia as well as industrial practitioners, and introduce guiding principles for the application of LSF strategies to access new molecules of interest.
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21
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Affiliation(s)
- Judith Münch
- Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle, Saale, Germany
| | - Pascal Püllmann
- Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle, Saale, Germany
| | - Wuyuan Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West seventh Avenue, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, 32 West seventh Avenue, Tianjin 300308, China
| | - Martin J. Weissenborn
- Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle, Saale, Germany
- Institute of Chemistry, MartinLuther-University Halle-Wittenberg, Kurt-Mothes-Strasse 2, 06120, Halle, Saale, Germany
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22
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Yang Y, Arnold FH. Navigating the Unnatural Reaction Space: Directed Evolution of Heme Proteins for Selective Carbene and Nitrene Transfer. Acc Chem Res 2021; 54:1209-1225. [PMID: 33491448 PMCID: PMC7931446 DOI: 10.1021/acs.accounts.0c00591] [Citation(s) in RCA: 119] [Impact Index Per Article: 39.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
Despite the astonishing diversity of naturally
occurring biocatalytic
processes, enzymes do not catalyze many of the transformations favored
by synthetic chemists. Either nature does not care about the specific
products, or if she does, she has adopted a different synthetic strategy.
In many cases, the appropriate reagents used by synthetic chemists
are not readily accessible to biological systems. Here, we discuss
our efforts to expand the catalytic repertoire of enzymes to encompass
powerful reactions previously known only in small-molecule catalysis:
formation and transfer of reactive carbene and nitrene intermediates
leading to a broad range of products, including products with bonds
not known in biology. In light of the structural similarity of iron
carbene (Fe=C(R1)(R2)) and iron nitrene
(Fe=NR) to the iron oxo (Fe=O) intermediate involved
in cytochrome P450-catalyzed oxidation, we have used synthetic carbene
and nitrene precursors that biological systems have not encountered
and repurposed P450s to catalyze reactions that are not known in the
natural world. The resulting protein catalysts are fully genetically
encoded and function in intact microbial cells or cell-free lysates,
where their performance can be improved and optimized by directed
evolution. By leveraging the catalytic promiscuity of P450 enzymes,
we evolved a range of carbene and nitrene transferases exhibiting
excellent activity toward these new-to-nature reactions. Since our
initial report in 2012, a number of other heme proteins including
myoglobins, protoglobins, and cytochromes c have
also been found and engineered to promote unnatural carbene and nitrene
transfer. Due to the altered active-site environments, these heme
proteins often displayed complementary activities and selectivities
to P450s. Using wild-type and engineered heme proteins, we and
others have
described a range of selective carbene transfer reactions, including
cyclopropanation, cyclopropenation, Si–H insertion, B–H
insertion, and C–H insertion. Similarly, a variety of asymmetric
nitrene transfer processes including aziridination, sulfide imidation,
C–H amidation, and, most recently, C–H amination have
been demonstrated. The scopes of these biocatalytic carbene and nitrene
transfer reactions are often complementary to the state-of-the-art
processes based on small-molecule transition-metal catalysts, making
engineered biocatalysts a valuable addition to the synthetic chemist’s
toolbox. Moreover, enabled by the exquisite regio- and stereocontrol
imposed by the enzyme catalyst, this biocatalytic platform provides
an exciting opportunity to address challenging problems in modern
synthetic chemistry and selective catalysis, including ones that have
eluded synthetic chemists for decades.
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Affiliation(s)
- Yang Yang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 210-41, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Frances H. Arnold
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 210-41, 1200 East California Boulevard, Pasadena, California 91125, United States
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23
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Rapp LR, Marques SM, Zukic E, Rowlinson B, Sharma M, Grogan G, Damborsky J, Hauer B. Substrate Anchoring and Flexibility Reduction in CYP153A M.aq Leads to Highly Improved Efficiency toward Octanoic Acid. ACS Catal 2021. [DOI: 10.1021/acscatal.0c05193] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lea R. Rapp
- Institute of Biochemistry and Technical Biochemistry, Department of Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Sérgio M. Marques
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
- International Centre for Clinical Research, St. Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Erna Zukic
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, U.K
| | - Benjamin Rowlinson
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, U.K
| | - Mahima Sharma
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, U.K
| | - Gideon Grogan
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, U.K
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
- International Centre for Clinical Research, St. Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Bernhard Hauer
- Institute of Biochemistry and Technical Biochemistry, Department of Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
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25
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Ebrecht AC, Aschenbrenner JC, Smit MS, Opperman DJ. Biocatalytic synthesis of non-vicinal aliphatic diols. Org Biomol Chem 2021; 19:439-445. [PMID: 33331366 DOI: 10.1039/d0ob02086a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Biocatalysts are receiving increased attention in the field of selective oxyfunctionalization of C-H bonds, with cytochrome P450 monooxygenases (CYP450s), and the related peroxygenases, leading the field. Here we report on the substrate promiscuity of CYP505A30, previously characterized as a fatty acid hydroxylase. In addition to its regioselective oxyfunctionalization of saturated fatty acids (ω-1 - ω-3 hydroxylation), primary fatty alcohols are also accepted with similar regioselectivities. Moreover, alkanes such as n-octane and n-decane are also readily accepted, allowing for the production of non-vicinal diols through sequential oxygenation.
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Affiliation(s)
- Ana C Ebrecht
- Department of Biotechnology, University of the Free State, 205 Nelson Mandela Drive, Bloemfontein, 9300, South Africa.
| | - Jasmin C Aschenbrenner
- Department of Biotechnology, University of the Free State, 205 Nelson Mandela Drive, Bloemfontein, 9300, South Africa. and South African DST-NRF Centre of Excellence in Catalysis, c*change, South Africa
| | - Martha S Smit
- Department of Biotechnology, University of the Free State, 205 Nelson Mandela Drive, Bloemfontein, 9300, South Africa. and South African DST-NRF Centre of Excellence in Catalysis, c*change, South Africa
| | - Diederik J Opperman
- Department of Biotechnology, University of the Free State, 205 Nelson Mandela Drive, Bloemfontein, 9300, South Africa.
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26
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Aschenbrenner JC, Ebrecht AC, Tolmie C, Smit MS, Opperman DJ. Structure of the fungal hydroxylase, CYP505A30, and rational transfer of mutation data from CYP102A1 to alter regioselectivity. Catal Sci Technol 2021. [DOI: 10.1039/d1cy01348c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Regioselective oxyfunctionalisation of n-alkanes and production of non-vicinal diols by evolved CYP505A30 through rational transfer of knowledge between protein scaffolds.
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Affiliation(s)
- Jasmin C. Aschenbrenner
- Department of Microbiology and Biochemistry, University of the Free State, 205 Nelson Mandela Drive, Bloemfontein, 9300, South Africa
- South African DST-NRF Centre of Excellence in Catalysis, c*change, University of Cape Town, South Africa
| | - Ana C. Ebrecht
- Department of Microbiology and Biochemistry, University of the Free State, 205 Nelson Mandela Drive, Bloemfontein, 9300, South Africa
| | - Carmien Tolmie
- Department of Microbiology and Biochemistry, University of the Free State, 205 Nelson Mandela Drive, Bloemfontein, 9300, South Africa
| | - Martha S. Smit
- Department of Microbiology and Biochemistry, University of the Free State, 205 Nelson Mandela Drive, Bloemfontein, 9300, South Africa
- South African DST-NRF Centre of Excellence in Catalysis, c*change, University of Cape Town, South Africa
| | - Diederik J. Opperman
- Department of Microbiology and Biochemistry, University of the Free State, 205 Nelson Mandela Drive, Bloemfontein, 9300, South Africa
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27
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28
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Wang Z, Jian Y, Han Y, Fu Z, Lu D, Wu J, Liu Z. Recent progress in enzymatic functionalization of carbon-hydrogen bonds for the green synthesis of chemicals. Chin J Chem Eng 2020. [DOI: 10.1016/j.cjche.2020.06.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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29
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Finnigan JD, Young C, Cook DJ, Charnock SJ, Black GW. Cytochromes P450 (P450s): A review of the class system with a focus on prokaryotic P450s. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020; 122:289-320. [PMID: 32951814 DOI: 10.1016/bs.apcsb.2020.06.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Cytochromes P450 (P450s) are a large superfamily of heme-containing monooxygenases. P450s are found in all Kingdoms of life and exhibit incredible diversity, both at sequence level and also on a biochemical basis. In the majority of cases, P450s can be assigned into one of ten classes based on their associated redox partners, domain architecture and cellular localization. Prokaryotic P450s now represent a large diverse collection of annotated/known enzymes, of which many have great potential biocatalytic potential. The self-sufficient P450 classes (Class VII/VIII) have been explored significantly over the past decade, with many annotated and biochemically characterized members. It is clear that the prokaryotic P450 world is expanding rapidly, as the number of published genomes and metagenome studies increases, and more P450 families are identified and annotated (CYP families).
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Affiliation(s)
| | - Carl Young
- Prozomix Limited, Haltwhistle, Northumberland, United Kingdom
| | - Darren J Cook
- Prozomix Limited, Haltwhistle, Northumberland, United Kingdom
| | | | - Gary W Black
- Hub for Biotechnology in the Built Environment, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
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30
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Abstract
Nowadays, biocatalysts have received much more attention in chemistry regarding their potential to enable high efficiency, high yield, and eco-friendly processes for a myriad of applications. Nature’s vast repository of catalysts has inspired synthetic chemists. Furthermore, the revolutionary technologies in bioengineering have provided the fast discovery and evolution of enzymes that empower chemical synthesis. This article attempts to deliver a comprehensive overview of the last two decades of investigation into enzymatic reactions and highlights the effective performance progress of bio-enzymes exploited in organic synthesis. Based on the types of enzymatic reactions and enzyme commission (E.C.) numbers, the enzymes discussed in the article are classified into oxidoreductases, transferases, hydrolases, and lyases. These applications should provide us with some insight into enzyme design strategies and molecular mechanisms.
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31
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Serrano-Plana J, Rumo C, Rebelein JG, Peterson RL, Barnet M, Ward TR. Enantioselective Hydroxylation of Benzylic C(sp 3)-H Bonds by an Artificial Iron Hydroxylase Based on the Biotin-Streptavidin Technology. J Am Chem Soc 2020; 142:10617-10623. [PMID: 32450689 PMCID: PMC7332155 DOI: 10.1021/jacs.0c02788] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
The selective hydroxylation of C–H
bonds is of great interest
to the synthetic community. Both homogeneous catalysts and enzymes
offer complementary means to tackle this challenge. Herein, we show
that biotinylated Fe(TAML)-complexes (TAML = Tetra Amido Macrocyclic
Ligand) can be used as cofactors for incorporation into streptavidin
to assemble artificial hydroxylases. Chemo-genetic optimization of
both cofactor and streptavidin allowed optimizing the performance
of the hydroxylase. Using H2O2 as oxidant, up
to ∼300 turnovers for the oxidation of benzylic C–H
bonds were obtained. Upgrading the ee was achieved by kinetic resolution
of the resulting benzylic alcohol to afford up to >98% ee for (R)-tetralol. X-ray analysis of artificial hydroxylases highlights
critical details of the second coordination sphere around the Fe(TAML)
cofactor.
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Affiliation(s)
- Joan Serrano-Plana
- Department of Chemistry, University of Basel, BPR1096, Mattenstrasse 24a, CH-4058 Basel, Switzerland
| | - Corentin Rumo
- Department of Chemistry, University of Basel, BPR1096, Mattenstrasse 24a, CH-4058 Basel, Switzerland
| | - Johannes G Rebelein
- Department of Chemistry, University of Basel, BPR1096, Mattenstrasse 24a, CH-4058 Basel, Switzerland
| | - Ryan L Peterson
- Department of Chemistry, University of Basel, BPR1096, Mattenstrasse 24a, CH-4058 Basel, Switzerland.,Department of Chemistry and Biochemistry, Texas State University, 78666 Texas, United States
| | - Maxime Barnet
- Department of Chemistry, University of Basel, BPR1096, Mattenstrasse 24a, CH-4058 Basel, Switzerland
| | - Thomas R Ward
- Department of Chemistry, University of Basel, BPR1096, Mattenstrasse 24a, CH-4058 Basel, Switzerland
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32
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Watanabe Y, Aiba Y, Ariyasu S, Abe S. Molecular Design and Regulation of Metalloenzyme Activities through Two Novel Approaches: Ferritin and P450s. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2020. [DOI: 10.1246/bcsj.20190305] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Yoshihito Watanabe
- Research Center for Materials Science, Nagoya University, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Yuichiro Aiba
- Department of Chemistry, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Shinya Ariyasu
- Department of Chemistry, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Satoshi Abe
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Nagatsuda-cho, Yokohama, Kanagawa, Japan
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33
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Collins CH, Cirino PC. Commemorating Frances Arnold. AIChE J 2020. [DOI: 10.1002/aic.16924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Cynthia H. Collins
- Department of Chemical and Biological EngineeringRensselaer Polytechnic Institute Troy New York
| | - Patrick C. Cirino
- Department of Chemical & Biomolecular EngineeringUniversity of Houston Houston Texas
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34
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Sarkar MR, Bell SG. Complementary and selective oxidation of hydrocarbon derivatives by two cytochrome P450 enzymes of the same family. Catal Sci Technol 2020. [DOI: 10.1039/d0cy01040e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The cytochrome P450 enzymes CYP101B1 and CYP101C1, from a Novosphingobium bacterium, can efficiently hydroxylate hydrocarbon derivatives containing a carbonyl moiety. Cyclic ketones (C9 to C15) were oxidised with contrasting yet high selectivity.
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Affiliation(s)
| | - Stephen G. Bell
- Department of Chemistry
- University of Adelaide
- Adelaide
- Australia
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35
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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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36
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Kanoh N, Kawamata-Asano A, Suzuki K, Takahashi Y, Miyazawa T, Nakamura T, Moriya T, Hirano H, Osada H, Iwabuchi Y, Takahashi S. An integrated screening system for the selection of exemplary substrates for natural and engineered cytochrome P450s. Sci Rep 2019; 9:18023. [PMID: 31792277 PMCID: PMC6888865 DOI: 10.1038/s41598-019-54473-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 11/14/2019] [Indexed: 11/26/2022] Open
Abstract
Information about substrate and product selectivity is critical for understanding the function of cytochrome P450 monooxygenases. In addition, comprehensive understanding of changes in substrate selectivity of P450 upon amino acid mutation would enable the design and creation of engineered P450s with desired selectivities. Therefore, systematic methods for obtaining such information are required. Herein, we developed an integrated P450 substrate screening system for the selection of “exemplary” substrates for a P450 of interest. The established screening system accurately selected the known exemplary substrates and also identified previously unknown exemplary substrates for microbial-derived P450s from a library containing sp3-rich synthetic small molecules. Synthetically potent transformations were also found by analyzing the reactions and oxidation products. The screening system was applied to analyze the substrate selectivity of the P450 BM3 mutants F87A and F87A/A330W, which acquired an ability to hydroxylate non-natural substrate steroids regio- and stereoselectively by two amino acid mutations. The distinct transition of exemplary substrates due to each single amino acid mutation was revealed, demonstrating the utility of the established system.
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Affiliation(s)
- Naoki Kanoh
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan. .,Institute of Medicinal Chemistry, Hoshi University, 2-4-1 Ebara, Shinagawa-ku, Tokyo, 142-8501, Japan.
| | - Ayano Kawamata-Asano
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| | - Kana Suzuki
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| | - Yusuke Takahashi
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| | - Takeshi Miyazawa
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Takemichi Nakamura
- Molecular Structure Characterization Unit, Technology Platform Division, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Takashi Moriya
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| | - Hiroyuki Hirano
- Chemical Resource Development Research Unit, Technology Platform Division, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Hiroyuki Osada
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.,Chemical Resource Development Research Unit, Technology Platform Division, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Yoshiharu Iwabuchi
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| | - Shunji Takahashi
- Natural Product Biosynthesis Research Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
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37
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Rousseau O, Ebert MCCJC, Quaglia D, Fendri A, Parisien AH, Besna JN, Iyathurai S, Pelletier JN. Indigo Formation and Rapid NADPH Consumption Provide Robust Prediction of Raspberry Ketone Synthesis by Engineered Cytochrome P450 BM3. ChemCatChem 2019. [DOI: 10.1002/cctc.201901974] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Olivier Rousseau
- Department of ChemistryUniversité de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
- Center for Green Chemistry and Catalysis (CGCC)Université de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
- PROTEOThe Québec Network for Research on Protein Function Engineering and Applications Québec QC−G1V 0A6 Canada
| | - Maximilian C. C. J. C. Ebert
- Center for Green Chemistry and Catalysis (CGCC)Université de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
- PROTEOThe Québec Network for Research on Protein Function Engineering and Applications Québec QC−G1V 0A6 Canada
- Department of BiochemistryUniversité de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
| | - Daniela Quaglia
- Department of ChemistryUniversité de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
- Center for Green Chemistry and Catalysis (CGCC)Université de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
- PROTEOThe Québec Network for Research on Protein Function Engineering and Applications Québec QC−G1V 0A6 Canada
| | - Ali Fendri
- Department of ChemistryUniversité de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
- Center for Green Chemistry and Catalysis (CGCC)Université de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
- PROTEOThe Québec Network for Research on Protein Function Engineering and Applications Québec QC−G1V 0A6 Canada
| | - Adem H. Parisien
- Center for Green Chemistry and Catalysis (CGCC)Université de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
- PROTEOThe Québec Network for Research on Protein Function Engineering and Applications Québec QC−G1V 0A6 Canada
- Department of BiochemistryUniversité de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
| | - Jonathan N. Besna
- Center for Green Chemistry and Catalysis (CGCC)Université de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
- PROTEOThe Québec Network for Research on Protein Function Engineering and Applications Québec QC−G1V 0A6 Canada
- Department of BiochemistryUniversité de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
| | - Saathanan Iyathurai
- Center for Green Chemistry and Catalysis (CGCC)Université de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
- PROTEOThe Québec Network for Research on Protein Function Engineering and Applications Québec QC−G1V 0A6 Canada
- Department of BiochemistryUniversité de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
| | - Joelle N. Pelletier
- Department of ChemistryUniversité de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
- Center for Green Chemistry and Catalysis (CGCC)Université de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
- PROTEOThe Québec Network for Research on Protein Function Engineering and Applications Québec QC−G1V 0A6 Canada
- Department of BiochemistryUniversité de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
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38
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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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39
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de Rond T, Gao J, Zargar A, de Raad M, Cunha J, Northen TR, Keasling JD. A High-Throughput Mass Spectrometric Enzyme Activity Assay Enabling the Discovery of Cytochrome P450 Biocatalysts. Angew Chem Int Ed Engl 2019; 58:10114-10119. [PMID: 31140688 PMCID: PMC6640108 DOI: 10.1002/anie.201901782] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 04/29/2019] [Indexed: 12/21/2022]
Abstract
Assaying for enzymatic activity is a persistent bottleneck in biocatalyst and drug development. Existing high-throughput assays for enzyme activity tend to be applicable only to a narrow range of biochemical transformations, whereas universal enzyme characterization methods usually require chromatography to determine substrate turnover, greatly diminishing throughput. We present an enzyme activity assay that allows the high-throughput mass-spectrometric detection of enzyme activity in complex matrices without the need for a chromatographic step. This technology, which we call probing enzymes with click-assisted NIMS (PECAN), can detect the activity of medically and biocatalytically significant cytochrome P450s in cell lysate, microsomes, and bacteria. Using this approach, a cytochrome P450BM3 mutant library was successfully screened for the ability to catalyze the oxidation of the sesquiterpene valencene.
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Affiliation(s)
- Tristan de Rond
- College of Chemistry, University of California, Berkeley, Berkeley, CA 94270 (USA); Joint Bioenergy Institute (JBEI), Lawrence Berkeley National Laboratory, Emeryville, CA 94608 (USA); Current Affiliation: Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92037 (USA)
| | - Jian Gao
- Department of Energy Joint Genome Institute (DOE JGI), Lawrence Berkeley National Laboratory
| | - Amin Zargar
- Joint Bioenergy Institute (JBEI), Lawrence Berkeley National Laboratory, Emeryville, CA 94608 (USA)
| | - Markus de Raad
- Department of Energy Joint Genome Institute (DOE JGI), Lawrence Berkeley National Laboratory; Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory
| | - Jack Cunha
- Joint Bioenergy Institute (JBEI), Lawrence Berkeley National Laboratory, Emeryville, CA 94608 (USA)
| | - Trent R. Northen
- Joint Bioenergy Institute (JBEI), Lawrence Berkeley National Laboratory, Emeryville, CA 94608 (USA); Department of Energy Joint Genome Institute (DOE JGI), Lawrence Berkeley National Laboratory; Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory
| | - Jay D. Keasling
- College of Chemistry, University of California, Berkeley, Berkeley, CA 94270 (USA); Joint Bioenergy Institute (JBEI), Lawrence Berkeley National Laboratory, Emeryville, CA 94608 (USA); Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory; Center for Biosustainability, Danish Technical University, Lyngby, Denmark; Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes of Advanced Technology, Shenzhen, China
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40
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Chen J, Kong F, Ma N, Zhao P, Liu C, Wang X, Cong Z. Peroxide-Driven Hydroxylation of Small Alkanes Catalyzed by an Artificial P450BM3 Peroxygenase System. ACS Catal 2019. [DOI: 10.1021/acscatal.9b02507] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Jie Chen
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fanhui Kong
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
| | - Nana Ma
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Panxia Zhao
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chuanfei Liu
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
| | - Xiling Wang
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
| | - Zhiqi Cong
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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41
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Li Y, Wong LL. Multi‐Functional Oxidase Activity of CYP102A1 (P450BM3) in the Oxidation of Quinolines and Tetrahydroquinolines. Angew Chem Int Ed Engl 2019; 58:9551-9555. [DOI: 10.1002/anie.201904157] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 05/13/2019] [Indexed: 11/06/2022]
Affiliation(s)
- Yushu Li
- Department of ChemistryUniversity of OxfordInorganic Chemistry Laboratory South Parks Road Oxford OX1 3QR UK
| | - Luet L. Wong
- Department of ChemistryUniversity of OxfordInorganic Chemistry Laboratory South Parks Road Oxford OX1 3QR UK
- Oxford Suzhou Centre for Advanced Research Ruo Shui Road, Suzhou Industrial Park Jiangsu 215123 P. R. China
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42
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de Rond T, Gao J, Zargar A, de Raad M, Cunha J, Northen TR, Keasling JD. A High‐Throughput Mass Spectrometric Enzyme Activity Assay Enabling the Discovery of Cytochrome P450 Biocatalysts. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201901782] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Tristan de Rond
- College of Chemistry University of California, Berkeley Berkeley CA 94270 USA
- Joint Bioenergy Institute (JBEI) Lawrence Berkeley National Laboratory Emeryville CA 94608 USA
- Current address: Scripps Institution of Oceanography University of California, San Diego La Jolla CA 92037 USA
| | - Jian Gao
- Department of Energy Joint Genome Institute (DOE JGI) Lawrence Berkeley National Laboratory USA
| | - Amin Zargar
- Joint Bioenergy Institute (JBEI) Lawrence Berkeley National Laboratory Emeryville CA 94608 USA
| | - Markus de Raad
- Department of Energy Joint Genome Institute (DOE JGI) Lawrence Berkeley National Laboratory USA
- Environmental Genomics and Systems Biology Lawrence Berkeley National Laboratory USA
| | - Jack Cunha
- Joint Bioenergy Institute (JBEI) Lawrence Berkeley National Laboratory Emeryville CA 94608 USA
| | - Trent R. Northen
- Joint Bioenergy Institute (JBEI) Lawrence Berkeley National Laboratory Emeryville CA 94608 USA
- Department of Energy Joint Genome Institute (DOE JGI) Lawrence Berkeley National Laboratory USA
- Environmental Genomics and Systems Biology Lawrence Berkeley National Laboratory USA
| | - Jay D. Keasling
- College of Chemistry University of California, Berkeley Berkeley CA 94270 USA
- Joint Bioenergy Institute (JBEI) Lawrence Berkeley National Laboratory Emeryville CA 94608 USA
- Biological Systems and Engineering Division Lawrence Berkeley National Laboratory USA
- Center for Biosustainability Danish Technical University Lyngby Denmark
- Center for Synthetic Biochemistry Institute for Synthetic Biology Shenzhen Institutes of Advanced Technology Shenzhen China
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43
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Li Y, Wong LL. Multi‐Functional Oxidase Activity of CYP102A1 (P450BM3) in the Oxidation of Quinolines and Tetrahydroquinolines. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201904157] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Yushu Li
- Department of ChemistryUniversity of OxfordInorganic Chemistry Laboratory South Parks Road Oxford OX1 3QR UK
| | - Luet L. Wong
- Department of ChemistryUniversity of OxfordInorganic Chemistry Laboratory South Parks Road Oxford OX1 3QR UK
- Oxford Suzhou Centre for Advanced Research Ruo Shui Road, Suzhou Industrial Park Jiangsu 215123 P. R. China
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44
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Chang Z. The 2018 Nobel Prize in Chemistry: Engineering proteins (enzymes/peptide/antibodies) towards desired properties via the construction of random libraries. SCIENCE CHINA-LIFE SCIENCES 2019; 62:713-724. [PMID: 30931497 DOI: 10.1007/s11427-019-9498-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 02/01/2019] [Indexed: 10/27/2022]
Affiliation(s)
- Zengyi Chang
- School of Life Sciences, State Key Laboratory of Protein and Plant Engineering Research, Center for Protein Science, Center of History and Philosophy of Science, Peking University, Beijing, 100871, China.
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45
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Wrublewski DT. Analysis for Science Librarians of the 2018 Nobel Prize in Chemistry: Directed Evolution of Enzymes and Phage Display of Peptides and Antibodies. ACTA ACUST UNITED AC 2019. [DOI: 10.1080/0194262x.2019.1579159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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46
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Jeffreys LN, Poddar H, Golovanova M, Levy CW, Girvan HM, McLean KJ, Voice MW, Leys D, Munro AW. Novel insights into P450 BM3 interactions with FDA-approved antifungal azole drugs. Sci Rep 2019; 9:1577. [PMID: 30733479 PMCID: PMC6367340 DOI: 10.1038/s41598-018-37330-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 11/14/2018] [Indexed: 11/09/2022] Open
Abstract
Flavocytochrome P450 BM3 is a natural fusion protein constructed of cytochrome P450 and NADPH-cytochrome P450 reductase domains. P450 BM3 binds and oxidizes several mid- to long-chain fatty acids, typically hydroxylating these lipids at the ω-1, ω-2 and ω-3 positions. However, protein engineering has led to variants of this enzyme that are able to bind and oxidize diverse compounds, including steroids, terpenes and various human drugs. The wild-type P450 BM3 enzyme binds inefficiently to many azole antifungal drugs. However, we show that the BM3 A82F/F87V double mutant (DM) variant binds substantially tighter to numerous azole drugs than does the wild-type BM3, and that their binding occurs with more extensive heme spectral shifts indicative of complete binding of several azoles to the BM3 DM heme iron. We report here the first crystal structures of P450 BM3 bound to azole antifungal drugs - with the BM3 DM heme domain bound to the imidazole drugs clotrimazole and tioconazole, and to the triazole drugs fluconazole and voriconazole. This is the first report of any protein structure bound to the azole drug tioconazole, as well as the first example of voriconazole heme iron ligation through a pyrimidine nitrogen from its 5-fluoropyrimidine ring.
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Affiliation(s)
- Laura N Jeffreys
- Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Harshwardhan Poddar
- Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Marina Golovanova
- Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Colin W Levy
- Manchester Protein Structure Facility (MPSF), Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Hazel M Girvan
- Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Kirsty J McLean
- Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Michael W Voice
- Cypex Ltd., 6 Tom McDonald Avenue, Dundee DD2 1NH, Scotland, United Kingdom
| | - David Leys
- Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Andrew W Munro
- Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom.
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47
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One-step process for production of N-methylated amino acids from sugars and methylamine using recombinant Corynebacterium glutamicum as biocatalyst. Sci Rep 2018; 8:12895. [PMID: 30150644 PMCID: PMC6110843 DOI: 10.1038/s41598-018-31309-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 08/02/2018] [Indexed: 02/07/2023] Open
Abstract
N-methylated amino acids are found in Nature in various biological compounds. N-methylation of amino acids has been shown to improve pharmacokinetic properties of peptide drugs due to conformational changes, improved proteolytic stability and/or higher lipophilicity. Due to these characteristics N-methylated amino acids received increasing interest by the pharmaceutical industry. Syntheses of N-methylated amino acids by chemical and biocatalytic approaches are known, but often show incomplete stereoselectivity, low yields or expensive co-factor regeneration. So far a one-step fermentative process from sugars has not yet been described. Here, a one-step conversion of sugars and methylamine to the N-methylated amino acid N-methyl-l-alanine was developed. A whole-cell biocatalyst was derived from a pyruvate overproducing C. glutamicum strain by heterologous expression of the N-methyl-l-amino acid dehydrogenase gene from Pseudomonas putida. As proof-of-concept, N-methyl-l-alanine titers of 31.7 g L−1 with a yield of 0.71 g per g glucose were achieved in fed-batch cultivation. The C. glutamicum strain producing this imine reductase enzyme was engineered further to extend this green chemistry route to production of N-methyl-l-alanine from alternative feed stocks such as starch or the lignocellulosic sugars xylose and arabinose.
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48
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Milan M, Bietti M, Costas M. Enantioselective aliphatic C-H bond oxidation catalyzed by bioinspired complexes. Chem Commun (Camb) 2018; 54:9559-9570. [PMID: 30039814 DOI: 10.1039/c8cc03165g] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Enantioselective aliphatic C-H bond oxidation simultaneously installs functionality and chirality into hydrocarbon units, converting in a single step readily available, inexpensive and typically inert hydrocarbons into precious building blocks for organic synthesis. The reaction remains however an open problem eager for catalyst development and improvement. Metal complexes reproducing structural and reactivity aspects of oxygenases are emerging as promising homogeneous catalysts for this class of reactions. The present work reviews the current status of field, analyzing the difficulties of the reaction, discussing principles of catalyst design, and critically highlighting the limitations of the current state-of-the-art methodologies.
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Affiliation(s)
- Michela Milan
- QBIS Research Group, Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Campus Montilivi, Girona E-17071, Catalonia, Spain.
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49
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Efficient hydroxylation of cycloalkanes by co-addition of decoy molecules to variants of the cytochrome P450 CYP102A1. J Inorg Biochem 2018. [DOI: 10.1016/j.jinorgbio.2018.03.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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50
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Li RJ, Xu JH, Chen Q, Zhao J, Li AT, Yu HL. Enhancing the Catalytic Performance of a CYP116B Monooxygenase by Transdomain Combination Mutagenesis. ChemCatChem 2018. [DOI: 10.1002/cctc.201800054] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Ren-Jie Li
- Laboratory of Biocatalysis and Synthetic Biotechnology; State Key Laboratory of Bioreactor Engineering; East China University of Science and Technology; 130 Meilong Road Shanghai 200237 P.R. China
| | - Jian-He Xu
- Laboratory of Biocatalysis and Synthetic Biotechnology; State Key Laboratory of Bioreactor Engineering; East China University of Science and Technology; 130 Meilong Road Shanghai 200237 P.R. China
| | - Qi Chen
- Laboratory of Biocatalysis and Synthetic Biotechnology; State Key Laboratory of Bioreactor Engineering; East China University of Science and Technology; 130 Meilong Road Shanghai 200237 P.R. China
| | - Jing Zhao
- Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; Tianjin 300308 P.R. China
| | - Ai-Tao Li
- Hubei Collaborative Innovation Center for, Green Transformation of Bio-resources; Hubei Key Laboratory of Industrial Biotechnology; College of Life Sciences; Hubei University; Wuhan 430062 P.R. China
| | - Hui-Lei Yu
- Laboratory of Biocatalysis and Synthetic Biotechnology; State Key Laboratory of Bioreactor Engineering; East China University of Science and Technology; 130 Meilong Road Shanghai 200237 P.R. China
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