1
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Fansher D, Besna JN, Fendri A, Pelletier JN. Choose Your Own Adventure: A Comprehensive Database of Reactions Catalyzed by Cytochrome P450 BM3 Variants. ACS Catal 2024; 14:5560-5592. [PMID: 38660610 PMCID: PMC11036407 DOI: 10.1021/acscatal.4c00086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 03/11/2024] [Accepted: 03/12/2024] [Indexed: 04/26/2024]
Abstract
Cytochrome P450 BM3 monooxygenase is the topic of extensive research as many researchers have evolved this enzyme to generate a variety of products. However, the abundance of information on increasingly diversified variants of P450 BM3 that catalyze a broad array of chemistry is not in a format that enables easy extraction and interpretation. We present a database that categorizes variants by their catalyzed reactions and includes details about substrates to provide reaction context. This database of >1500 P450 BM3 variants is downloadable and machine-readable and includes instructions to maximize ease of gathering information. The database allows rapid identification of commonly reported substitutions, aiding researchers who are unfamiliar with the enzyme in identifying starting points for enzyme engineering. For those actively engaged in engineering P450 BM3, the database, along with this review, provides a powerful and user-friendly platform to understand, predict, and identify the attributes of P450 BM3 variants, encouraging the further engineering of this enzyme.
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Affiliation(s)
- Douglas
J. Fansher
- Chemistry
Department, Université de Montréal, Montreal, QC, Canada H2V 0B3
- PROTEO,
The Québec Network for Research on Protein Function, Engineering,
and Applications, 201
Av. du Président-Kennedy, Montréal, QC, Canada H2X 3Y7
- CGCC,
Center in Green Chemistry and Catalysis, Montreal, QC, Canada H2V 0B3
| | - Jonathan N. Besna
- PROTEO,
The Québec Network for Research on Protein Function, Engineering,
and Applications, 201
Av. du Président-Kennedy, Montréal, QC, Canada H2X 3Y7
- CGCC,
Center in Green Chemistry and Catalysis, Montreal, QC, Canada H2V 0B3
- Department
of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC, Canada H3T 1J4
| | - Ali Fendri
- Chemistry
Department, Université de Montréal, Montreal, QC, Canada H2V 0B3
- PROTEO,
The Québec Network for Research on Protein Function, Engineering,
and Applications, 201
Av. du Président-Kennedy, Montréal, QC, Canada H2X 3Y7
- CGCC,
Center in Green Chemistry and Catalysis, Montreal, QC, Canada H2V 0B3
| | - Joelle N. Pelletier
- Chemistry
Department, Université de Montréal, Montreal, QC, Canada H2V 0B3
- PROTEO,
The Québec Network for Research on Protein Function, Engineering,
and Applications, 201
Av. du Président-Kennedy, Montréal, QC, Canada H2X 3Y7
- CGCC,
Center in Green Chemistry and Catalysis, Montreal, QC, Canada H2V 0B3
- Department
of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC, Canada H3T 1J4
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2
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Yu H, Zhang X, Acevedo-Rocha CG, Li A, Reetz MT. Protein engineering using mutability landscapes: Controlling site-selectivity of P450-catalyzed steroid hydroxylation. Methods Enzymol 2023; 693:191-229. [PMID: 37977731 DOI: 10.1016/bs.mie.2023.09.002] [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] [Indexed: 11/19/2023]
Abstract
Directed evolution and rational design have been used widely in engineering enzymes for their application in synthetic organic chemistry and biotechnology. With stereoselectivity playing a crucial role in catalysis for the synthesis of valuable chemical and pharmaceutical compounds, rational design has not achieved such wide success in this specific area compared to directed evolution. Nevertheless, one bottleneck of directed evolution is the laborious screening efforts and the observed trade-offs in catalytic profiles. This has motivated researchers to develop more efficient protein engineering methods. As a prime approach, mutability landscaping avoids such trade-offs by providing more information of sequence-function relationships. Here, we describe an application of this efficient protein engineering method to improve the regio-/stereoselectivity and activity of P450BM3 for steroid hydroxylation, while keeping the mutagenesis libraries small so that they will require only minimal screening.
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Affiliation(s)
- Huili Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, School of life science, Hubei University, Wuhan, P.R. China
| | - Xiaodong Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, School of life science, Hubei University, Wuhan, P.R. China
| | - Carlos G Acevedo-Rocha
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Aitao Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, School of life science, Hubei University, Wuhan, P.R. China.
| | - Manfred T Reetz
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1, Muelheim, Germany; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin, P. R. China.
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3
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Ashworth MA, Bombino E, de Jong RM, Wijma HJ, Janssen DB, McLean KJ, Munro AW. Computation-Aided Engineering of Cytochrome P450 for the Production of Pravastatin. ACS Catal 2022; 12:15028-15044. [PMID: 36570080 PMCID: PMC9764288 DOI: 10.1021/acscatal.2c03974] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 10/22/2022] [Indexed: 11/29/2022]
Abstract
CYP105AS1 is a cytochrome P450 from Amycolatopsis orientalis that catalyzes monooxygenation of compactin to 6-epi-pravastatin. For fermentative production of the cholesterol-lowering drug pravastatin, the stereoselectivity of the enzyme needs to be inverted, which has been partially achieved by error-prone PCR mutagenesis and screening. In the current study, we report further optimization of the stereoselectivity by a computationally aided approach. Using the CoupledMoves protocol of Rosetta, a virtual library of mutants was designed to bind compactin in a pro-pravastatin orientation. By examining the frequency of occurrence of beneficial substitutions and rational inspection of their interactions, a small set of eight mutants was predicted to show the desired selectivity and these variants were tested experimentally. The best CYP105AS1 variant gave >99% stereoselective hydroxylation of compactin to pravastatin, with complete elimination of the unwanted 6-epi-pravastatin diastereomer. The enzyme-substrate complexes were also examined by ultrashort molecular dynamics simulations of 50 × 100 ps and 5 × 22 ns, which revealed that the frequency of occurrence of near-attack conformations agreed with the experimentally observed stereoselectivity. These results show that a combination of computational methods and rational inspection could improve CYP105AS1 stereoselectivity beyond what was obtained by directed evolution. Moreover, the work lays out a general in silico framework for specificity engineering of enzymes of known structure.
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Affiliation(s)
- Mark A. Ashworth
- Manchester
Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Elvira Bombino
- Department
of Biochemistry, Groningen Biomolecular Sciences and Biotechnology
Institute, University of Groningen, Nijenborgh 4, Groningen 9747 AG, Netherlands
| | - René M. de Jong
- DSM
Food & Beverage, Alexander Fleminglaan 1, 2613 AX Delft, the Netherlands
| | - Hein J. Wijma
- Department
of Biochemistry, Groningen Biomolecular Sciences and Biotechnology
Institute, University of Groningen, Nijenborgh 4, Groningen 9747 AG, Netherlands
| | - Dick B. Janssen
- Department
of Biochemistry, Groningen Biomolecular Sciences and Biotechnology
Institute, University of Groningen, Nijenborgh 4, Groningen 9747 AG, Netherlands,
| | - Kirsty J. McLean
- Manchester
Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester M1 7DN, United Kingdom,Department
of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield HD1 3DH, United Kingdom
| | - Andrew W. Munro
- Manchester
Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester M1 7DN, United Kingdom
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4
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Zhang K, Yu A, Chu X, Li F, Liu J, Liu L, Bai W, He C, Wang X. Biocatalytic Enantioselective β‐Hydroxylation of Unactivated C−H Bonds in Aliphatic Carboxylic Acids. Angew Chem Int Ed Engl 2022; 61:e202204290. [DOI: 10.1002/anie.202204290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Kun Zhang
- College of Bioscience and Biotechnology Yangzhou University Yangzhou Jiangsu 225009 China
| | - Aiqin Yu
- College of Bioscience and Biotechnology Yangzhou University Yangzhou Jiangsu 225009 China
| | - Xuan Chu
- School of Life Science Economic and Technology Development Zone Anhui University Hefei Anhui 230601 China
| | - Fudong Li
- MOE Key Laboratory for Cellular Dynamics School of Life Sciences Division of Life Sciences and Medicine University of Science and Technology of China Hefei Anhui 230027 China
| | - Juan Liu
- Testing Center Yangzhou University Yangzhou Jiangsu 225009 China
| | - Lin Liu
- School of Life Science Economic and Technology Development Zone Anhui University Hefei Anhui 230601 China
| | - Wen‐Ju Bai
- Department of Chemistry Stanford University Stanford CA 94305 USA
| | - Chao He
- School of Life Science Economic and Technology Development Zone Anhui University Hefei Anhui 230601 China
| | - Xiqing Wang
- College of Bioscience and Biotechnology Yangzhou University Yangzhou Jiangsu 225009 China
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5
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Zhu R, Liu Y, Yang Y, Min Q, Li H, Chen L. Cytochrome P450 Monooxygenases Catalyse Steroid Nucleus Hydroxylation with Regio‐ and Stereo‐selectivity. Adv Synth Catal 2022. [DOI: 10.1002/adsc.202200210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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6
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van Vugt-Lussenburg BMA, Capinha L, Reinen J, Rooseboom M, Kranendonk M, Onderwater RCA, Jennings P. " Commandeuring" Xenobiotic Metabolism: Advances in Understanding Xenobiotic Metabolism. Chem Res Toxicol 2022; 35:1184-1201. [PMID: 35768066 PMCID: PMC9297329 DOI: 10.1021/acs.chemrestox.2c00067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
The understanding
of how exogenous chemicals (xenobiotics) are
metabolized, distributed, and eliminated is critical to determine
the impact of the chemical and its metabolites to the (human) organism.
This is part of the research and educational discipline ADMET (absorption,
distribution, metabolism, elimination, and toxicity). Here, we review
the work of Jan Commandeur and colleagues who have not only made a
significant impact in understanding of phase I and phase II metabolism
of several important compounds but also contributed greatly to the
development of experimental techniques for the study of xenobiotic
metabolism. Jan Commandeur’s work has covered a broad area
of research, such as the development of online screening methodologies,
the use of a combination of enzyme mutagenesis and molecular modeling
for structure–activity relationship (SAR) studies, and the
development of novel probe substrates. This work is the bedrock of
current activities and brings the field closer to personalized (cohort-based)
pharmacology, toxicology, and hazard/risk assessment.
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Affiliation(s)
| | - Liliana Capinha
- Division of Computational and Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute of Molecular and Life Sciences (AIMMs), Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Jelle Reinen
- Charles River Den Bosch, Hambakenwetering 7, 5203 DL Hertogenbosch, The Netherlands
| | - Martijn Rooseboom
- Shell Global Solutions International B.V., 1030 BN The Hague, The Netherlands
| | - Michel Kranendonk
- Center for Toxicogenomics and Human Health (ToxOmics), NOVA Medical School/Faculty of Medical Sciences, Universidade NOVA de Lisboa, Campo dos Mártires da Pátria 130, 1169-056 Lisboa, Portugal
| | | | - Paul Jennings
- Division of Computational and Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute of Molecular and Life Sciences (AIMMs), Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
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7
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Zhang K, Yu A, Chu X, Li F, Liu J, Liu L, Bai W, He C, Wang X. Biocatalytic Enantioselective β‐Hydroxylation of Unactivated C−H Bonds in Aliphatic Carboxylic Acids. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202204290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Kun Zhang
- College of Bioscience and Biotechnology Yangzhou University Yangzhou Jiangsu 225009 China
| | - Aiqin Yu
- College of Bioscience and Biotechnology Yangzhou University Yangzhou Jiangsu 225009 China
| | - Xuan Chu
- School of Life Science Economic and Technology Development Zone Anhui University Hefei Anhui 230601 China
| | - Fudong Li
- MOE Key Laboratory for Cellular Dynamics School of Life Sciences Division of Life Sciences and Medicine University of Science and Technology of China Hefei Anhui 230027 China
| | - Juan Liu
- Testing Center Yangzhou University Yangzhou Jiangsu 225009 China
| | - Lin Liu
- School of Life Science Economic and Technology Development Zone Anhui University Hefei Anhui 230601 China
| | - Wen‐Ju Bai
- Department of Chemistry Stanford University Stanford CA 94305 USA
| | - Chao He
- School of Life Science Economic and Technology Development Zone Anhui University Hefei Anhui 230601 China
| | - Xiqing Wang
- College of Bioscience and Biotechnology Yangzhou University Yangzhou Jiangsu 225009 China
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8
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Reetz MT. Making Enzymes Suitable for Organic Chemistry by Rational Protein Design. Chembiochem 2022; 23:e202200049. [PMID: 35389556 PMCID: PMC9401064 DOI: 10.1002/cbic.202200049] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 04/07/2022] [Indexed: 11/25/2022]
Abstract
This review outlines recent developments in protein engineering of stereo‐ and regioselective enzymes, which are of prime interest in organic and pharmaceutical chemistry as well as biotechnology. The widespread application of enzymes was hampered for decades due to limited enantio‐, diastereo‐ and regioselectivity, which was the reason why most organic chemists were not interested in biocatalysis. This attitude began to change with the advent of semi‐rational directed evolution methods based on focused saturation mutagenesis at sites lining the binding pocket. Screening constitutes the labor‐intensive step (bottleneck), which is the reason why various research groups are continuing to develop techniques for the generation of small and smart mutant libraries. Rational enzyme design, traditionally an alternative to directed evolution, provides small collections of mutants which require minimal screening. This approach first focused on thermostabilization, and did not enter the field of stereoselectivity until later. Computational guides such as the Rosetta algorithms, HotSpot Wizard metric, and machine learning (ML) contribute significantly to decision making. The newest advancements show that semi‐rational directed evolution such as CAST/ISM and rational enzyme design no longer develop on separate tracks, instead, they have started to merge. Indeed, researchers utilizing the two approaches have learned from each other. Today, the toolbox of organic chemists includes enzymes, primarily because the possibility of controlling stereoselectivity by protein engineering has ensured reliability when facing synthetic challenges. This review was also written with the hope that undergraduate and graduate education will include enzymes more so than in the past.
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Affiliation(s)
- Manfred T Reetz
- Max-Planck-Institut fur Kohlenforschung, Biocatalysis, Kaiser-Wilhelm-Platz 1, 45470, Muelheim an der Ruhr, GERMANY
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9
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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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10
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Advances in enzymatic oxyfunctionalization of aliphatic compounds. Biotechnol Adv 2021; 51:107703. [PMID: 33545329 DOI: 10.1016/j.biotechadv.2021.107703] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 01/17/2021] [Accepted: 01/25/2021] [Indexed: 12/27/2022]
Abstract
Selective oxyfunctionalizations of aliphatic compounds are difficult chemical reactions, where enzymes can play an important role due to their stereo- and regio-selectivity and operation under mild reaction conditions. P450 monooxygenases are well-known biocatalysts that mediate oxyfunctionalization reactions in different living organisms (from bacteria to humans). Unspecific peroxygenases (UPOs), discovered in fungi, have arisen as "dream biocatalysts" of great biotechnological interest because they catalyze the oxyfunctionalization of aliphatic and aromatic compounds, avoiding the necessity of expensive cofactors and regeneration systems, and only depending on H2O2 for their catalysis. Here, we summarize recent advances in aliphatic oxyfunctionalization reactions by UPOs, as well as the molecular determinants of the enzyme structures responsible for their activities, emphasizing the differences found between well-known P450s and the novel fungal peroxygenases.
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11
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Li A, Acevedo‐Rocha CG, D'Amore L, Chen J, Peng Y, Garcia‐Borràs M, Gao C, Zhu J, Rickerby H, Osuna S, Zhou J, Reetz MT. Regio- and Stereoselective Steroid Hydroxylation at C7 by Cytochrome P450 Monooxygenase Mutants. Angew Chem Int Ed Engl 2020; 59:12499-12505. [PMID: 32243054 PMCID: PMC7384163 DOI: 10.1002/anie.202003139] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 03/31/2020] [Indexed: 01/08/2023]
Abstract
Steroidal C7β alcohols and their respective esters have shown significant promise as neuroprotective and anti-inflammatory agents to treat chronic neuronal damage like stroke, brain trauma, and cerebral ischemia. Since C7 is spatially far away from any functional groups that could direct C-H activation, these transformations are not readily accessible using modern synthetic organic techniques. Reported here are P450-BM3 mutants that catalyze the oxidative hydroxylation of six different steroids with pronounced C7 regioselectivities and β stereoselectivities, as well as high activities. These challenging transformations were achieved by a focused mutagenesis strategy and application of a novel technology for protein library construction based on DNA assembly and USER (Uracil-Specific Excision Reagent) cloning. Upscaling reactions enabled the purification of the respective steroidal alcohols in moderate to excellent yields. The high-resolution X-ray structure and molecular dynamics simulations of the best mutant unveil the origin of regio- and stereoselectivity.
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Affiliation(s)
- Aitao Li
- School of life scienceHubei UniversityState Key Laboratory of Biocatalysis and Enzyme Engineering#368 Youyi RoadWuhan430062P.R. China
| | | | - Lorenzo D'Amore
- Institut de Química Computacional i Catàlisi and Departament de QuímicaUniversitat de GironaCarrer Maria Aurèlia Capmany 6917003GironaCataloniaSpain
| | - Jinfeng Chen
- State Key Laboratory of Bio-organic and Natural Products ChemistryCenter for Excellence in Molecular SynthesisShanghai Institute of Organic ChemistryUniversity of Chinese Academy of SciencesShanghai200032P. R. China
| | - Yaqin Peng
- School of life scienceHubei UniversityState Key Laboratory of Biocatalysis and Enzyme Engineering#368 Youyi RoadWuhan430062P.R. China
| | - Marc Garcia‐Borràs
- Institut de Química Computacional i Catàlisi and Departament de QuímicaUniversitat de GironaCarrer Maria Aurèlia Capmany 6917003GironaCataloniaSpain
| | - Chenghua Gao
- School of life scienceHubei UniversityState Key Laboratory of Biocatalysis and Enzyme Engineering#368 Youyi RoadWuhan430062P.R. China
| | - Jinmei Zhu
- School of life scienceHubei UniversityState Key Laboratory of Biocatalysis and Enzyme Engineering#368 Youyi RoadWuhan430062P.R. China
| | - Harry Rickerby
- LabGeniusG.01-06 Cocoa Studios100 Drummond RdLondonSE16 4DGUK
| | - Sílvia Osuna
- Institut de Química Computacional i Catàlisi and Departament de QuímicaUniversitat de GironaCarrer Maria Aurèlia Capmany 6917003GironaCataloniaSpain
- ICREAPg. Lluís Companys 2308010BarcelonaSpain
| | - Jiahai Zhou
- State Key Laboratory of Bio-organic and Natural Products ChemistryCenter for Excellence in Molecular SynthesisShanghai Institute of Organic ChemistryUniversity of Chinese Academy of SciencesShanghai200032P. R. China
| | - Manfred T. Reetz
- Max-Planck-Institut für KohlenforschungKaiser-Wilhelm-Platz 145470MuelheimGermany
- Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences32 West 7th AvenueTianjin300308P. R. China
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12
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Chen W, Fisher MJ, Leung A, Cao Y, Wong LL. Oxidative Diversification of Steroids by Nature-Inspired Scanning Glycine Mutagenesis of P450BM3 (CYP102A1). ACS Catal 2020. [DOI: 10.1021/acscatal.0c02077] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Wenyu Chen
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford OX1 3QR, U.K
| | - Matthew J. Fisher
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford OX1 3QR, U.K
| | - Aaron Leung
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford OX1 3QR, U.K
| | - Yang Cao
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford OX1 3QR, U.K
- Oxford Suzhou Centre for Advanced Research, Ruo Shui Road, Suzhou Industrial Park, Jiangsu 215123, P.R. China
| | - Luet L. Wong
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford OX1 3QR, U.K
- Oxford Suzhou Centre for Advanced Research, Ruo Shui Road, Suzhou Industrial Park, Jiangsu 215123, P.R. China
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13
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Fessner ND, Srdič M, Weber H, Schmid C, Schönauer D, Schwaneberg U, Glieder A. Preparative‐Scale Production of Testosterone Metabolites by Human Liver Cytochrome P450 Enzyme 3A4. Adv Synth Catal 2020. [DOI: 10.1002/adsc.202000251] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Nico D. Fessner
- Institute of Molecular BiotechnologyGraz University of Technology, NAWI Graz Petersgasse 14/3 Austria
| | - Matic Srdič
- SeSaM-Biotech GmbH Aachen Germany
- Bisy GmbH Hofstaetten Austria
| | - Hansjörg Weber
- Institute of Organic ChemistryGraz University of Technology, NAWI Graz Austria
| | - Christian Schmid
- Institute of Molecular BiotechnologyGraz University of Technology, NAWI Graz Petersgasse 14/3 Austria
- Austrian Centre of Industrial Biotechnology (ACIB) Graz Austria
| | | | | | - Anton Glieder
- Institute of Molecular BiotechnologyGraz University of Technology, NAWI Graz Petersgasse 14/3 Austria
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14
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Li A, Acevedo‐Rocha CG, D'Amore L, Chen J, Peng Y, Garcia‐Borràs M, Gao C, Zhu J, Rickerby H, Osuna S, Zhou J, Reetz MT. Regio‐ and Stereoselective Steroid Hydroxylation at C7 by Cytochrome P450 Monooxygenase Mutants. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202003139] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Aitao Li
- School of life science Hubei University State Key Laboratory of Biocatalysis and Enzyme Engineering #368 Youyi Road Wuhan 430062 P.R. China
| | | | - Lorenzo D'Amore
- Institut de Química Computacional i Catàlisi and Departament de Química Universitat de Girona Carrer Maria Aurèlia Capmany 69 17003 Girona Catalonia Spain
| | - Jinfeng Chen
- State Key Laboratory of Bio-organic and Natural Products Chemistry Center for Excellence in Molecular Synthesis Shanghai Institute of Organic Chemistry University of Chinese Academy of Sciences Shanghai 200032 P. R. China
| | - Yaqin Peng
- School of life science Hubei University State Key Laboratory of Biocatalysis and Enzyme Engineering #368 Youyi Road Wuhan 430062 P.R. China
| | - Marc Garcia‐Borràs
- Institut de Química Computacional i Catàlisi and Departament de Química Universitat de Girona Carrer Maria Aurèlia Capmany 69 17003 Girona Catalonia Spain
| | - Chenghua Gao
- School of life science Hubei University State Key Laboratory of Biocatalysis and Enzyme Engineering #368 Youyi Road Wuhan 430062 P.R. China
| | - Jinmei Zhu
- School of life science Hubei University State Key Laboratory of Biocatalysis and Enzyme Engineering #368 Youyi Road Wuhan 430062 P.R. China
| | - Harry Rickerby
- LabGenius G.01-06 Cocoa Studios 100 Drummond Rd London SE16 4DG UK
| | - Sílvia Osuna
- Institut de Química Computacional i Catàlisi and Departament de Química Universitat de Girona Carrer Maria Aurèlia Capmany 69 17003 Girona Catalonia Spain
- ICREA Pg. Lluís Companys 23 08010 Barcelona Spain
| | - Jiahai Zhou
- State Key Laboratory of Bio-organic and Natural Products Chemistry Center for Excellence in Molecular Synthesis Shanghai Institute of Organic Chemistry University of Chinese Academy of Sciences Shanghai 200032 P. R. China
| | - Manfred T. Reetz
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 45470 Muelheim Germany
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 32 West 7th Avenue Tianjin 300308 P. R. China
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15
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Luirink RA, Verkade‐Vreeker MCA, Commandeur JNM, Geerke DP. A Modified Arrhenius Approach to Thermodynamically Study Regioselectivity in Cytochrome P450-Catalyzed Substrate Conversion. Chembiochem 2020; 21:1461-1472. [PMID: 31919943 PMCID: PMC7318578 DOI: 10.1002/cbic.201900751] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Indexed: 12/21/2022]
Abstract
The regio- (and stereo-)selectivity and specific activity of cytochrome P450s are determined by the accessibility of potential sites of metabolism (SOMs) of the bound substrate relative to the heme, and the activation barrier of the regioselective oxidation reaction(s). The accessibility of potential SOMs depends on the relative binding free energy (ΔΔGbind ) of the catalytically active substrate-binding poses, and the probability of the substrate to adopt a transition-state geometry. An established experimental method to measure activation energies of enzymatic reactions is the analysis of reaction rate constants at different temperatures and the construction of Arrhenius plots. This is a challenge for multistep P450-catalyzed processes that involve redox partners. We introduce a modified Arrhenius approach to overcome the limitations in studying P450 selectivity, which can be applied in multiproduct enzyme catalysis. Our approach gives combined information on relative activation energies, ΔΔGbind values, and collision entropies, yielding direct insight into the basis of selectivity in substrate conversion.
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Affiliation(s)
- Rosa A. Luirink
- AIMMS Division of Molecular ToxicologyVrije UniversiteitDe Boelelaan 11081081 HZAmsterdamThe Netherlands
| | | | - Jan N. M. Commandeur
- AIMMS Division of Molecular ToxicologyVrije UniversiteitDe Boelelaan 11081081 HZAmsterdamThe Netherlands
| | - Daan P. Geerke
- AIMMS Division of Molecular ToxicologyVrije UniversiteitDe Boelelaan 11081081 HZAmsterdamThe Netherlands
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16
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Qu G, Li A, Acevedo‐Rocha CG, Sun Z, Reetz MT. Die zentrale Rolle der Methodenentwicklung in der gerichteten Evolution selektiver Enzyme. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201901491] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Ge Qu
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 32 West 7th Avenue, Tianjin Airport Economic Area Tianjin 300308 China
| | - Aitao Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering Hubei Collaborative Innovation Center for Green Transformation of Bio-resources Hubei Key Laboratory of Industrial Biotechnology College of Life Sciences Hubei University 368 Youyi Road Wuchang Wuhan 430062 China
| | | | - Zhoutong Sun
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 32 West 7th Avenue, Tianjin Airport Economic Area Tianjin 300308 China
| | - Manfred T. Reetz
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 32 West 7th Avenue, Tianjin Airport Economic Area Tianjin 300308 China
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 45470 Mülheim Deutschland
- Department of Chemistry, Hans-Meerwein-Straße 4 Philipps-Universität 35032 Marburg Deutschland
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17
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Qu G, Li A, Acevedo‐Rocha CG, Sun Z, Reetz MT. The Crucial Role of Methodology Development in Directed Evolution of Selective Enzymes. Angew Chem Int Ed Engl 2020; 59:13204-13231. [PMID: 31267627 DOI: 10.1002/anie.201901491] [Citation(s) in RCA: 233] [Impact Index Per Article: 58.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Indexed: 12/14/2022]
Affiliation(s)
- Ge Qu
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 32 West 7th Avenue, Tianjin Airport Economic Area Tianjin 300308 China
| | - Aitao Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering Hubei Collaborative Innovation Center for Green Transformation of Bio-resources Hubei Key Laboratory of Industrial Biotechnology College of Life Sciences Hubei University 368 Youyi Road Wuchang Wuhan 430062 China
| | | | - Zhoutong Sun
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 32 West 7th Avenue, Tianjin Airport Economic Area Tianjin 300308 China
| | - Manfred T. Reetz
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 32 West 7th Avenue, Tianjin Airport Economic Area Tianjin 300308 China
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 45470 Mülheim Germany
- Department of Chemistry, Hans-Meerwein-Strasse 4 Philipps-University 35032 Marburg Germany
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18
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Zhang X, Peng Y, Zhao J, Li Q, Yu X, Acevedo-Rocha CG, Li A. Bacterial cytochrome P450-catalyzed regio- and stereoselective steroid hydroxylation enabled by directed evolution and rational design. BIORESOUR BIOPROCESS 2020. [DOI: 10.1186/s40643-019-0290-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
AbstractSteroids are the most widely marketed products by the pharmaceutical industry after antibiotics. Steroid hydroxylation is one of the most important functionalizations because their derivatives enable a higher biological activity compared to their less polar non-hydroxylated analogs. Bacterial cytochrome P450s constitute promising biocatalysts for steroid hydroxylation due to their high expression level in common workhorses like Escherichia coli. However, they often suffer from wrong or insufficient regio- and/or stereoselectivity, low activity, narrow substrate range as well as insufficient thermostability, which hampers their industrial application. Fortunately, these problems can be generally solved by protein engineering based on directed evolution and rational design. In this work, an overview of recent developments on the engineering of bacterial cytochrome P450s for steroid hydroxylation is presented.
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19
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Fessner ND. P450 Monooxygenases Enable Rapid Late-Stage Diversification of Natural Products via C-H Bond Activation. ChemCatChem 2019; 11:2226-2242. [PMID: 31423290 PMCID: PMC6686969 DOI: 10.1002/cctc.201801829] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Revised: 01/07/2019] [Indexed: 01/07/2023]
Abstract
The biological potency of natural products has been exploited for decades. Their inherent structural complexity and natural diversity might hold the key to efficiently address the urgent need for the development of novel pharmaceuticals. At the same time, it is that very complexity, which impedes necessary chemical modifications such as structural diversification, to improve the effectiveness of the drug. For this purpose, Cytochrome P450 enzymes, which possess unique abilities to activate inert sp3-hybridised C-H bonds in a late-stage fashion, offer an attractive synthetic tool. In this review the potential of cytochrome P450 enzymes in chemoenzymatic lead diversification is illustrated discussing studies reporting late-stage functionalisations of natural products and other high-value compounds. These enzymes were proven to extend the synthetic toolbox significantly by adding to the flexibility and efficacy of synthetic strategies of natural product chemists, and scientists of other related disciplines.
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Affiliation(s)
- Nico D. Fessner
- Institute of Molecular BiotechnologyGraz University of Technology, NAWI GrazPetersgasse 148010GrazAustria
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20
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Dangi B, Lee CW, Kim K, Park S, Yu E, Jeong C, Park H, Lee JH, Oh T. Characterization of two steroid hydroxylases from different
Streptomyces
spp. and their ligand‐bound and ‐unbound crystal structures. FEBS J 2018; 286:1683-1699. [DOI: 10.1111/febs.14729] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 11/20/2018] [Accepted: 12/09/2018] [Indexed: 01/04/2023]
Affiliation(s)
- Bikash Dangi
- Department of Life Science and Biochemical Engineering Sunmoon University Asansi Korea
| | - Chang Woo Lee
- Unit of Polar Genomics Korea Polar Research Institute Incheon Korea
- Department of Polar Sciences University of Science and Technology Incheon Korea
| | - Ki‐Hwa Kim
- Department of Life Science and Biochemical Engineering Sunmoon University Asansi Korea
| | - Sun‐Ha Park
- Unit of Polar Genomics Korea Polar Research Institute Incheon Korea
| | - Eun‐Ji Yu
- Department of Life Science and Biochemical Engineering Sunmoon University Asansi Korea
| | - Chang‐Sook Jeong
- Unit of Polar Genomics Korea Polar Research Institute Incheon Korea
- Department of Polar Sciences University of Science and Technology Incheon Korea
| | - Hyun Park
- Unit of Polar Genomics Korea Polar Research Institute Incheon Korea
- Department of Polar Sciences University of Science and Technology Incheon Korea
| | - Jun Hyuck Lee
- Unit of Polar Genomics Korea Polar Research Institute Incheon Korea
- Department of Polar Sciences University of Science and Technology Incheon Korea
| | - Tae‐Jin Oh
- Department of Life Science and Biochemical Engineering Sunmoon University Asansi Korea
- Genome‐based BioIT Convergence Institute Asansi Korea
- Department of Pharmaceutical Engineering and Biotechnology Sunmoon University Asansi Korea
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21
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Abstract
This chapter describes the asymmetric hydroxylation of steroids on laboratory preparative scale, using engineered variants of P450BM3 (CYP102A1) as enzyme catalyst. The following protocol covers the creation of an Escherichia coli BL21-Gold (DE3) expression strain, including necessary control experiments like plasmid preparation, test expression, and creation of storage cultures, to verify successful experimental access to recombinant expressed P450BM3 variants. The recombinant expressed P450BM3 variants are obtained as cleared cell lysate and used in a biotransformation setup to hydroxylate 2.8 mg and up to 15 mg testosterone in the presented protocol. Since P450BM3 depends on NADPH as an electron source for the reaction, a glucose and glucose dehydrogenate based recycling system is added to the reaction. The protocol further includes liquid-liquid extraction of hydroxytestosterone and directs the experimenter to compound purification via column chromatography.
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22
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Acevedo-Rocha CG, Gamble CG, Lonsdale R, Li A, Nett N, Hoebenreich S, Lingnau JB, Wirtz C, Fares C, Hinrichs H, Deege A, Mulholland AJ, Nov Y, Leys D, McLean KJ, Munro AW, Reetz MT. P450-Catalyzed Regio- and Diastereoselective Steroid Hydroxylation: Efficient Directed Evolution Enabled by Mutability Landscaping. ACS Catal 2018. [DOI: 10.1021/acscatal.8b00389] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Carlos G. Acevedo-Rocha
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany
- Department of Chemistry, Philipps-University, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
| | - Charles G. Gamble
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, U.K
| | - Richard Lonsdale
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany
- Department of Chemistry, Philipps-University, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
| | - Aitao Li
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany
- Department of Chemistry, Philipps-University, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University 368 Youyi Road, Wuchang Wuhan 430062, China
| | - Nathalie Nett
- Department of Chemistry, Philipps-University, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
| | - Sabrina Hoebenreich
- Department of Chemistry, Philipps-University, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
| | - Julia B. Lingnau
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany
| | - Cornelia Wirtz
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany
| | - Christophe Fares
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany
| | - Heike Hinrichs
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany
| | - Alfred Deege
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany
| | - Adrian J. Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
| | - Yuval Nov
- Department of Statistics, University of Haifa, Haifa 31905, Israel
| | - David Leys
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, U.K
| | - Kirsty J. McLean
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, U.K
| | - Andrew W. Munro
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, U.K
| | - Manfred T. Reetz
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany
- Department of Chemistry, Philipps-University, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
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23
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Kiebist J, Schmidtke K, Zimmermann J, Kellner H, Jehmlich N, Ullrich R, Zänder D, Hofrichter M, Scheibner K. A Peroxygenase from Chaetomium globosum Catalyzes the Selective Oxygenation of Testosterone. Chembiochem 2017; 18:563-569. [PMID: 28103392 PMCID: PMC5363369 DOI: 10.1002/cbic.201600677] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Indexed: 01/18/2023]
Abstract
Unspecific peroxygenases (UPO, EC 1.11.2.1) secreted by fungi open an efficient way to selectively oxyfunctionalize diverse organic substrates, including less-activated hydrocarbons, by transferring peroxide-borne oxygen. We investigated a cell-free approach to incorporate epoxy and hydroxyl functionalities directly into the bulky molecule testosterone by a novel unspecific peroxygenase (UPO) that is produced by the ascomycetous fungus Chaetomium globosum in a complex medium rich in carbon and nitrogen. Purification by fast protein liquid chromatography revealed two enzyme fractions with the same molecular mass (36 kDa) and with specific activity of 4.4 to 12 U mg-1 . Although the well-known UPOs of Agrocybe aegerita (AaeUPO) and Marasmius rotula (MroUPO) failed to convert testosterone in a comparative study, the UPO of C. globosum (CglUPO) accepted testosterone as substrate and converted it with total turnover number (TTN) of up to 7000 into two oxygenated products: the 4,5-epoxide of testosterone in β-configuration and 16α-hydroxytestosterone. The reaction performed on a 100 mg scale resulted in the formation of about 90 % of the epoxide and 10 % of the hydroxylation product, both of which could be isolated with purities above 96 %. Thus, CglUPO is a promising biocatalyst for the oxyfunctionalization of bulky steroids and it will be a useful tool for the synthesis of pharmaceutically relevant steroidal molecules.
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Affiliation(s)
- Jan Kiebist
- Faculty of Environment and Natural SciencesBrandenburg University of Technology Cottbus-SenftenbergUniversitätsplatz 101968SenftenbergGermany
| | - Kai‐Uwe Schmidtke
- Faculty of Environment and Natural SciencesBrandenburg University of Technology Cottbus-SenftenbergUniversitätsplatz 101968SenftenbergGermany
| | - Jörg Zimmermann
- Faculty of Environment and Natural SciencesBrandenburg University of Technology Cottbus-SenftenbergUniversitätsplatz 101968SenftenbergGermany
| | - Harald Kellner
- Department of Bio- and Environmental SciencesTU DresdenInternational Institute ZittauMarkt 2302763ZittauGermany
| | - Nico Jehmlich
- Department of Molecular Systems BiologyHelmholtz-Centre for Environmental ResearchUFZPermoserstrasse 1504318LeipzigGermany
| | - René Ullrich
- Department of Bio- and Environmental SciencesTU DresdenInternational Institute ZittauMarkt 2302763ZittauGermany
| | | | - Martin Hofrichter
- Department of Bio- and Environmental SciencesTU DresdenInternational Institute ZittauMarkt 2302763ZittauGermany
| | - Katrin Scheibner
- Faculty of Environment and Natural SciencesBrandenburg University of Technology Cottbus-SenftenbergUniversitätsplatz 101968SenftenbergGermany
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24
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Jóźwik IK, Kiss FM, Gricman Ł, Abdulmughni A, Brill E, Zapp J, Pleiss J, Bernhardt R, Thunnissen AMWH. Structural basis of steroid binding and oxidation by the cytochrome P450 CYP109E1 from Bacillus megaterium. FEBS J 2016; 283:4128-4148. [PMID: 27686671 PMCID: PMC5132081 DOI: 10.1111/febs.13911] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 09/15/2016] [Accepted: 09/27/2016] [Indexed: 01/08/2023]
Abstract
Cytochrome P450 monooxygenases (P450s) are attractive enzymes for the pharmaceutical industry, in particular, for applications in steroidal drug synthesis. Here, we report a comprehensive functional and structural characterization of CYP109E1, a novel steroid‐converting cytochrome P450 enzyme identified from the genome of Bacillus megaterium DSM319. In vitro and whole‐cell in vivo turnover experiments, combined with binding assays, revealed that CYP109E1 is able to hydroxylate testosterone at position 16β. Related steroids with bulky substituents at carbon C17, like corticosterone, bind to the enzyme without being converted. High‐resolution X‐ray structures were solved of a steroid‐free form of CYP109E1 and of complexes with testosterone and corticosterone. The structural analysis revealed a highly dynamic active site at the distal side of the heme, which is wide open in the absence of steroids, can bind four ordered corticosterone molecules simultaneously, and undergoes substantial narrowing upon binding of single steroid molecules. In the crystal structures, the single bound steroids adopt unproductive binding modes coordinating the heme‐iron with their C3‐keto oxygen. Molecular dynamics (MD) simulations suggest that the steroids may also bind in ~180° reversed orientations with the C16 carbon and C17‐substituents pointing toward the heme, leading to productive binding of testosterone explaining the observed regio‐ and stereoselectivity. The X‐ray structures and MD simulations further identify several residues with important roles in steroid binding and conversion, which could be confirmed by site‐directed mutagenesis. Taken together, our results provide unique insights into the CYP109E1 activity, substrate specificity, and regio/stereoselectivity. Database The atomic coordinates and structure factors have been deposited in the Protein Data Bank with accession codes 5L90 (steroid‐free CYP109E1), 5L91 (CYP109E1‐COR4), 5L94 (CYP109E1‐TES), and 5L92 (CYP109E1‐COR). Enzymes Cytochrome P450 monooxygenase CYP109E1, EC 1.14.14.1, UniProt ID: D5DKI8, Adrenodoxin reductase EC 1.18.1.6.
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Affiliation(s)
- Ilona K Jóźwik
- Laboratory of Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands
| | - Flora M Kiss
- Institute of Biochemistry, Saarland University, Saarbrücken, Germany
| | - Łukasz Gricman
- Institute of Technical Biochemistry, University of Stuttgart, Germany
| | - Ammar Abdulmughni
- Institute of Biochemistry, Saarland University, Saarbrücken, Germany
| | - Elisa Brill
- Institute of Biochemistry, Saarland University, Saarbrücken, Germany
| | - Josef Zapp
- Pharmaceutical Biology, Saarland University, Saarbrücken, Germany
| | - Juergen Pleiss
- Institute of Technical Biochemistry, University of Stuttgart, Germany
| | - Rita Bernhardt
- Institute of Biochemistry, Saarland University, Saarbrücken, Germany
| | - Andy-Mark W H Thunnissen
- Laboratory of Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands
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25
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Probing Steroidal Substrate Specificity of Cytochrome P450 BM3 Variants. Molecules 2016; 21:molecules21060760. [PMID: 27294908 PMCID: PMC6273762 DOI: 10.3390/molecules21060760] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 06/04/2016] [Accepted: 06/06/2016] [Indexed: 11/23/2022] Open
Abstract
M01A82W, M11A82W and M01A82WS72I are three cytochrome P450 BM3 (CYP102A1) variants. They can catalyze the hydroxylation of testosterone (TES) and norethisterone at different positions, thereby making them promising biocatalysts for steroid hydroxylation. With the aim of obtaining more hydroxylated steroid precursors it is necessary to probe the steroidal substrate diversity of these BM3 variants. Here, three purified BM3 variants were first incubated with eight steroids, including testosterone (TES), methyltestosterone (MT), cholesterol, β-sitosterol, dehydroepiandrosterone (DHEA), diosgenin, pregnenolone and ergosterol. The results indicated that the two 3-keto-Δ4-steroids TES and MT can be hydroxylated at various positions by the three BM3 mutants, respectively. On the contrary, the three enzymes displayed no any activity toward the remaining six 3-hydroxy-Δ5-steroids. This result indicates that the BM3 mutants prefer 3-keto-Δ4-steroids as hydroxylation substrates. To further verify this notion, five other substrates, including two 3-hydroxy-Δ5-steroids and three 3-keto-Δ4-steroids, were carefully selected to incubate with the three BM3 variants. The results indicated the three 3-keto-Δ4-steroids can be metabolized to form hydroxysteroids by the three BM3 variants. On the other hand, the two 3-hydroxy-Δ5-steroids cannot be hydroxylated at any position by the BM3 mutants. These results further support the above conclusion, therefore demonstrating the 3-keto-Δ4–steroid substrate preference of BM3 mutants, and laying a foundation for microbial production of more hydroxylated steroid intermediates using BM3 variants.
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26
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Application of a cocktail approach to screen cytochrome P450 BM3 libraries for metabolic activity and diversity. Anal Bioanal Chem 2016; 408:1425-43. [PMID: 26753974 PMCID: PMC4723632 DOI: 10.1007/s00216-015-9241-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Revised: 11/25/2015] [Accepted: 12/01/2015] [Indexed: 11/01/2022]
Abstract
In the present study, the validity of using a cocktail screening method in combination with a chemometrical data mining approach to evaluate metabolic activity and diversity of drug-metabolizing bacterial Cytochrome P450 (CYP) BM3 mutants was investigated. In addition, the concept of utilizing an in-house-developed library of CYP BM3 mutants as a unique biocatalytic synthetic tool to support medicinal chemistry was evaluated. Metabolic efficiency of the mutant library towards a selection of CYP model substrates, being amitriptyline (AMI), buspirone (BUS), coumarine (COU), dextromethorphan (DEX), diclofenac (DIC) and norethisterone (NET), was investigated. First, metabolic activity of a selection of CYP BM3 mutants was screened against AMI and BUS. Subsequently, for a single CYP BM3 mutant, the effect of co-administration of multiple drugs on the metabolic activity and diversity towards AMI and BUS was investigated. Finally, a cocktail of AMI, BUS, COU, DEX, DIC and NET was screened against the whole in-house CYP BM3 library. Different validated quantitative and qualitative (U)HPLC-MS/MS-based analytical methods were applied to screen for substrate depletion and targeted product formation, followed by a more in-depth screen for metabolic diversity. A chemometrical approach was used to mine all data to search for unique metabolic properties of the mutants and allow classification of the mutants. The latter would open the possibility of obtaining a more in-depth mechanistic understanding of the metabolites. The presented method is the first MS-based method to screen CYP BM3 mutant libraries for diversity in combination with a chemometrical approach to interpret results and visualize differences between the tested mutants.
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27
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Khatri Y, Ringle. M, Lisurek M, von Kries JP, Zapp J, Bernhardt R. Substrate Hunting for the Myxobacterial CYP260A1 Revealed New 1α-Hydroxylated Products from C-19 Steroids. Chembiochem 2015; 17:90-101. [DOI: 10.1002/cbic.201500420] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Indexed: 12/11/2022]
Affiliation(s)
- Yogan Khatri
- Universität des Saarlandes; Biochemie; Campus B2.2 66123 Saarbrücken Germany
| | - Michael Ringle.
- Universität des Saarlandes; Biochemie; Campus B2.2 66123 Saarbrücken Germany
| | - Michael Lisurek
- Forschungsinstitut für Molekulare Pharmakologie; Robert-Rössle-Strasse 10 13125 Berlin Germany
| | - Jens Peter von Kries
- Forschungsinstitut für Molekulare Pharmakologie; Robert-Rössle-Strasse 10 13125 Berlin Germany
| | - Josef Zapp
- Universität des Saarlandes; Pharmazeutische Biologie; Campus C2.2 66123 Saarbrücken Germany
| | - Rita Bernhardt
- Universität des Saarlandes; Biochemie; Campus B2.2 66123 Saarbrücken Germany
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28
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Reinen J, Vredenburg G, Klaering K, Vermeulen NP, Commandeur JN, Honing M, Vos JC. Selective whole-cell biosynthesis of the designer drug metabolites 15- or 16-betahydroxynorethisterone by engineered Cytochrome P450 BM3 mutants. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.molcatb.2015.08.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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29
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Acevedo-Rocha CG, Reetz MT, Nov Y. Economical analysis of saturation mutagenesis experiments. Sci Rep 2015; 5:10654. [PMID: 26190439 PMCID: PMC4507136 DOI: 10.1038/srep10654] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 04/20/2015] [Indexed: 11/15/2022] Open
Abstract
Saturation mutagenesis is a powerful technique for engineering proteins, metabolic pathways and genomes. In spite of its numerous applications, creating high-quality saturation mutagenesis libraries remains a challenge, as various experimental parameters influence in a complex manner the resulting diversity. We explore from the economical perspective various aspects of saturation mutagenesis library preparation: We introduce a cheaper and faster control for assessing library quality based on liquid media; analyze the role of primer purity and supplier in libraries with and without redundancy; compare library quality, yield, randomization efficiency, and annealing bias using traditional and emergent randomization schemes based on mixtures of mutagenic primers; and establish a methodology for choosing the most cost-effective randomization scheme given the screening costs and other experimental parameters. We show that by carefully considering these parameters, laboratory expenses can be significantly reduced.
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Affiliation(s)
- Carlos G Acevedo-Rocha
- 1] Department of Organic Synthesis, Max-Planck-Institut für Kohlenforschung, Mulheim, 45470, Germany [2] Department of Chemistry, Philipps-Universität Marburg, 35032, Germany [3] Prokaryotic Small RNA Biology Group, Max-Planck-Institut für terrestrische Mikrobiologie, Marburg, 35043, Germany [4] Landes-Offensive zur Entwicklung Wissenschafltich-ökonomischer Exzellenz (LOEWE) Centre for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, 35032, Germany
| | - Manfred T Reetz
- 1] Department of Organic Synthesis, Max-Planck-Institut für Kohlenforschung, Mulheim, 45470, Germany [2] Department of Chemistry, Philipps-Universität Marburg, 35032, Germany
| | - Yuval Nov
- Department of Statistics, University of Haifa, Haifa, 31905, Israel
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Ilie A, Lonsdale R, Agudo R, Reetz MT. A diastereoselective P450-catalyzed epoxidation reaction: anti versus syn reactivity. Tetrahedron Lett 2015. [DOI: 10.1016/j.tetlet.2015.03.076] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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31
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Janocha S, Schmitz D, Bernhardt R. Terpene hydroxylation with microbial cytochrome P450 monooxygenases. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2015; 148:215-50. [PMID: 25682070 DOI: 10.1007/10_2014_296] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Terpenoids comprise a highly diverse group of natural products. In addition to their basic carbon skeleton, they differ from one another in their functional groups. Functional groups attached to the carbon skeleton are the basis of the terpenoids' diverse properties. Further modifications of terpene olefins include the introduction of acyl-, aryl-, or sugar moieties and usually start with oxidations catalyzed by cytochrome P450 monooxygenases (P450s, CYPs). P450s are ubiquitously distributed throughout nature, involved in essential biological pathways such as terpenoid biosynthesis as well as the tailoring of terpenoids and other natural products. Their ability to introduce oxygen into nonactivated C-H bonds is unique and makes P450s very attractive for applications in biotechnology. Especially in the field of terpene oxidation, biotransformation methods emerge as an attractive alternative to classical chemical synthesis. For this reason, microbial P450s depict a highly interesting target for protein engineering approaches in order to increase selectivity and activity, respectively. Microbial P450s have been described to convert industrial and pharmaceutically interesting terpenoids such as ionones, limone, valencene, resin acids, and triterpenes (including steroids) as well as vitamin D3. Highly selective and active mutants have been evolved by applying classical site-directed mutagenesis as well as directed evolution of proteins. As P450s usually depend on electron transfer proteins, mutagenesis has also been applied to improve the interactions between P450s and their respective redox partners. This chapter provides an overview of terpenoid hydroxylation reactions catalyzed by bacterial P450s and highlights the achievements made by protein engineering to establish productive hydroxylation processes.
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Affiliation(s)
- Simon Janocha
- Department of Biochemistry, Saarland University, Campus B2 2, 66123, Saarbruecken, Germany
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Ilie A, Agudo R, Roiban GD, Reetz MT. P450-catalyzed regio- and stereoselective oxidative hydroxylation of disubstituted cyclohexanes: creation of three centers of chirality in a single CH-activation event. Tetrahedron 2015. [DOI: 10.1016/j.tet.2014.11.067] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Roiban GD, Reetz MT. Expanding the toolbox of organic chemists: directed evolution of P450 monooxygenases as catalysts in regio- and stereoselective oxidative hydroxylation. Chem Commun (Camb) 2015; 51:2208-24. [DOI: 10.1039/c4cc09218j] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Cytochrome P450 enzymes (CYPs) have been used for more than six decades as catalysts for the CH-activating oxidative hydroxylation of organic compounds with formation of added-value products.
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Affiliation(s)
| | - Manfred T. Reetz
- Department of Chemistry
- Philipps-Universität Marburg
- 35032 Marburg
- Germany
- Max-Planck-Institut für Kohlenforschung
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Venkataraman H, te Poele EM, Rosłoniec KZ, Vermeulen N, Commandeur JNM, van der Geize R, Dijkhuizen L. Biosynthesis of a steroid metabolite by an engineered Rhodococcus erythropolis strain expressing a mutant cytochrome P450 BM3 enzyme. Appl Microbiol Biotechnol 2014; 99:4713-21. [DOI: 10.1007/s00253-014-6281-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 11/19/2014] [Accepted: 11/29/2014] [Indexed: 12/01/2022]
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Application of engineered cytochrome P450 mutants as biocatalysts for the synthesis of benzylic and aromatic metabolites of fenamic acid NSAIDs. Bioorg Med Chem 2014; 22:5613-20. [DOI: 10.1016/j.bmc.2014.06.022] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Revised: 06/09/2014] [Accepted: 06/11/2014] [Indexed: 11/19/2022]
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36
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Human P450-like oxidation of diverse proton pump inhibitor drugs by ‘gatekeeper’ mutants of flavocytochrome P450 BM3. Biochem J 2014; 460:247-59. [DOI: 10.1042/bj20140030] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Structurally destabilizing and conformation altering ‘gatekeeper’ mutants of the biotechnologically important flavocytochrome P450 BM3 mono-oxygenase were shown to catalyse oxidation of several proton pump inhibitor drugs, and to generate products identical to those formed by major human drug metabolizing P450s.
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Roiban GD, Agudo R, Reetz MT. Cytochrome P450 Catalyzed Oxidative Hydroxylation of Achiral Organic Compounds with Simultaneous Creation of Two Chirality Centers in a Single CH Activation Step. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201310892] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Roiban GD, Agudo R, Reetz MT. Cytochrome P450 catalyzed oxidative hydroxylation of achiral organic compounds with simultaneous creation of two chirality centers in a single C-H activation step. Angew Chem Int Ed Engl 2014; 53:8659-63. [PMID: 24590553 DOI: 10.1002/anie.201310892] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 01/22/2014] [Indexed: 11/08/2022]
Abstract
Regio- and stereoselective oxidative hydroxylation of achiral or chiral organic compounds mediated by synthetic reagents, catalysts, or enzymes generally leads to the formation of one new chiral center that appears in the respective enantiomeric or diastereomeric alcohols. By contrast, when subjecting appropriate achiral compounds to this type of C-H activation, the simultaneous creation of two chiral centers with a defined relative and absolute configuration may result, provided that control of the regio-, diastereo-, and enantioselectivity is ensured. The present study demonstrates that such control is possible by using wild type or mutant forms of the monooxygenase cytochrome P450 BM3 as catalysts in the oxidative hydroxylation of methylcyclohexane and seven other monosubstituted cyclohexane derivatives.
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Affiliation(s)
- Gheorghe-Doru Roiban
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr (Germany); Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Strasse, 35032 Marburg (Germany)
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Roiban GD, Agudo R, Ilie A, Lonsdale R, Reetz MT. CH-activating oxidative hydroxylation of 1-tetralones and related compounds with high regio- and stereoselectivity. Chem Commun (Camb) 2014; 50:14310-3. [DOI: 10.1039/c4cc04925j] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Mutants of P450-BM3 evolved by directed evolution are excellent catalysts in the CH-activating oxidative hydroxylation of 1-tetralone derivatives and of indanone, with unusually high regio- and enantioselectivity being observed.
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Affiliation(s)
- Gheorghe-Doru Roiban
- Max-Planck-Institut für Kohlenforschung
- 45470 Mülheim/Ruhr, Germany
- Fachbereich Chemie
- Philipps-Universität
- Hans-Meerwein-Strasse
| | - Rubén Agudo
- Max-Planck-Institut für Kohlenforschung
- 45470 Mülheim/Ruhr, Germany
- Fachbereich Chemie
- Philipps-Universität
- Hans-Meerwein-Strasse
| | - Adriana Ilie
- Max-Planck-Institut für Kohlenforschung
- 45470 Mülheim/Ruhr, Germany
- Fachbereich Chemie
- Philipps-Universität
- Hans-Meerwein-Strasse
| | - Richard Lonsdale
- Max-Planck-Institut für Kohlenforschung
- 45470 Mülheim/Ruhr, Germany
- Fachbereich Chemie
- Philipps-Universität
- Hans-Meerwein-Strasse
| | - Manfred T. Reetz
- Max-Planck-Institut für Kohlenforschung
- 45470 Mülheim/Ruhr, Germany
- Fachbereich Chemie
- Philipps-Universität
- Hans-Meerwein-Strasse
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40
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Reconstitution of the interplay between cytochrome P450 and human glutathione S-transferases in clozapine metabolism in yeast. Toxicol Lett 2013; 222:247-56. [DOI: 10.1016/j.toxlet.2013.07.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Revised: 07/22/2013] [Accepted: 07/24/2013] [Indexed: 01/10/2023]
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41
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Butler CF, Peet C, Mason AE, Voice MW, Leys D, Munro AW. Key mutations alter the cytochrome P450 BM3 conformational landscape and remove inherent substrate bias. J Biol Chem 2013; 288:25387-25399. [PMID: 23828198 DOI: 10.1074/jbc.m113.479717] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cytochrome P450 monooxygenases (P450s) have enormous potential in the production of oxychemicals, due to their unparalleled regio- and stereoselectivity. The Bacillus megaterium P450 BM3 enzyme is a key model system, with several mutants (many distant from the active site) reported to alter substrate selectivity. It has the highest reported monooxygenase activity of the P450 enzymes, and this catalytic efficiency has inspired protein engineering to enable its exploitation for biotechnologically relevant oxidations with structurally diverse substrates. However, a structural rationale is lacking to explain how these mutations have such effects in the absence of direct change to the active site architecture. Here, we provide the first crystal structures of BM3 mutants in complex with a human drug substrate, the proton pump inhibitor omeprazole. Supported by solution data, these structures reveal how mutation alters the conformational landscape and decreases the free energy barrier for transition to the substrate-bound state. Our data point to the importance of such "gatekeeper" mutations in enabling major changes in substrate recognition. We further demonstrate that these mutants catalyze the same 5-hydroxylation reaction as performed by human CYP2C19, the major human omeprazole-metabolizing P450 enzyme.
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Affiliation(s)
- Christopher F Butler
- From the Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom and
| | - Caroline Peet
- Cypex Ltd., 6 Tom McDonald Avenue, Dundee DD2 1NH, Scotland, United Kingdom
| | - Amy E Mason
- From the Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom and
| | - Michael W Voice
- Cypex Ltd., 6 Tom McDonald Avenue, Dundee DD2 1NH, Scotland, United Kingdom
| | - David Leys
- From the Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom and
| | - Andrew W Munro
- From the Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom and.
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42
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Stereo- and regioselectivity in the P450-catalyzed oxidative tandem difunctionalization of 1-methylcyclohexene. Tetrahedron 2013. [DOI: 10.1016/j.tet.2013.04.132] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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43
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44
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Di Nardo G, Gilardi G. Optimization of the bacterial cytochrome P450 BM3 system for the production of human drug metabolites. Int J Mol Sci 2012; 13:15901-24. [PMID: 23443101 PMCID: PMC3546669 DOI: 10.3390/ijms131215901] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Revised: 11/01/2012] [Accepted: 11/13/2012] [Indexed: 12/28/2022] Open
Abstract
Drug metabolism in human liver is a process involving many different enzymes. Among them, a number of cytochromes P450 isoforms catalyze the oxidation of most of the drugs commercially available. Each P450 isoform acts on more than one drug, and one drug may be oxidized by more than one enzyme. As a result, multiple products may be obtained from the same drug, and as the metabolites can be biologically active and may cause adverse drug reactions (ADRs), the metabolic profile of a new drug has to be known before this can be commercialized. Therefore, the metabolites of a certain drug must be identified, synthesized and tested for toxicity. Their synthesis must be in sufficient quantities to be used for metabolic tests. This review focuses on the progresses done in the field of the optimization of a bacterial self-sufficient and efficient cytochrome P450, P450 BM3 from Bacillus megaterium, used for the production of metabolites of human enzymes. The progress made in the improvement of its catalytic performance towards drugs, the substitution of the costly NADPH cofactor and its immobilization and scale-up of the process for industrial application are reported.
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Affiliation(s)
- Giovanna Di Nardo
- Department of Life Sciences and Systems Biology, University of Torino, via Accademia Albertina 13, 10123 Torino, Italy; E-Mail:
| | - Gianfranco Gilardi
- Department of Life Sciences and Systems Biology, University of Torino, via Accademia Albertina 13, 10123 Torino, Italy; E-Mail:
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45
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Zhang K, Shafer BM, Demars MD, Stern HA, Fasan R. Controlled oxidation of remote sp3 C-H bonds in artemisinin via P450 catalysts with fine-tuned regio- and stereoselectivity. J Am Chem Soc 2012; 134:18695-704. [PMID: 23121379 PMCID: PMC3498520 DOI: 10.1021/ja3073462] [Citation(s) in RCA: 148] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Indexed: 01/20/2023]
Abstract
The selective oxyfunctionalization of isolated sp(3) C-H bonds in complex molecules represents a formidable challenge in organic chemistry. Here, we describe a rational, systematic strategy to expedite the development of P450 oxidation catalysts with refined regio- and stereoselectivity for the hydroxylation of remote, unactivated C-H sites in a complex scaffold. Using artemisinin as model substrate, we demonstrate how a three-tier strategy involving first-sphere active site mutagenesis, high-throughput P450 fingerprinting, and fingerprint-driven P450 reactivity predictions enabled the rapid evolution of three efficient biocatalysts for the selective hydroxylation of a primary and a secondary C-H site (with both S and R stereoselectivity) in a relevant yet previously inaccessible region of this complex natural product. The evolved P450 variants could be applied to provide direct access to the desired hydroxylated derivatives at preparative scales (0.4 g) and in high isolated yields (>90%), thereby enabling further elaboration of this molecule. As an example, enantiopure C7-fluorinated derivatives of the clinical antimalarial drugs artesunate and artemether, in which a major metabolically sensitive site is protected by means of a C-H to C-F substitution, were afforded via P450-mediated chemoenzymatic synthesis.
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Affiliation(s)
- Kaidong Zhang
- Department of Chemistry,
University of Rochester, Rochester,
New York 14627, United States
| | - Brian M. Shafer
- Department of Chemistry,
University of Rochester, Rochester,
New York 14627, United States
| | - Matthew D. Demars
- Department of Chemistry,
University of Rochester, Rochester,
New York 14627, United States
| | - Harry A. Stern
- Department of Chemistry,
University of Rochester, Rochester,
New York 14627, United States
| | - Rudi Fasan
- Department of Chemistry,
University of Rochester, Rochester,
New York 14627, United States
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Venkataraman H, Beer SBAD, Geerke DP, Vermeulen NPE, Commandeur JNM. Regio- and Stereoselective Hydroxylation of Optically Active α-Ionone Enantiomers by Engineered Cytochrome P450 BM3 Mutants. Adv Synth Catal 2012. [DOI: 10.1002/adsc.201200067] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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47
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Agudo R, Roiban GD, Reetz MT. Achieving regio- and enantioselectivity of P450-catalyzed oxidative CH activation of small functionalized molecules by structure-guided directed evolution. Chembiochem 2012; 13:1465-73. [PMID: 22711296 DOI: 10.1002/cbic.201200244] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Indexed: 11/08/2022]
Abstract
Directed evolution of the monooxygenase P450-BM3 utilizing iterative saturation mutagenesis at and near the binding site enables a high degree of both regio- and enantioselectivity in the oxidative hydroxylation of cyclohexene-1-carboxylic acid methyl ester. Wild-type P450-BM3 is 84% regioselective for the allylic 3-position with 34% enantioselectivity in favor of the R alcohol. Mutants enabling R selectivity (>95% ee) or S selectivity (>95% ee) were evolved, while reducing other oxidation products and thus maximizing regioselectivity to >93%. Control of the substrate-to-enzyme ratio is necessary for obtaining optimal and reproducible enantioselectivities, an observation which is important in future protein engineering of these mono-oxygenases. An E. coli strain capable of NADPH regeneration was also engineered, simplifying directed evolution of P450 enzymes in general. These synthetic results set the stage for subsequent stereoselective and stereospecific chemical transformations to form more complex compounds, thereby illustrating the viability of combining genetically altered enzymes as catalysts in organic chemistry with traditional chemical methods.
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Affiliation(s)
- Rubén Agudo
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
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