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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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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3
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Thomson RES, D'Cunha SA, Hayes MA, Gillam EMJ. Use of engineered cytochromes P450 for accelerating drug discovery and development. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2022; 95:195-252. [PMID: 35953156 DOI: 10.1016/bs.apha.2022.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Numerous steps in drug development, including the generation of authentic metabolites and late-stage functionalization of candidates, necessitate the modification of often complex molecules, such as natural products. While it can be challenging to make the required regio- and stereoselective alterations to a molecule using purely chemical catalysis, enzymes can introduce changes to complex molecules with a high degree of stereo- and regioselectivity. Cytochrome P450 enzymes are biocatalysts of unequalled versatility, capable of regio- and stereoselective functionalization of unactivated CH bonds by monooxygenation. Collectively they catalyze over 60 different biotransformations on structurally and functionally diverse organic molecules, including natural products, drugs, steroids, organic acids and other lipophilic molecules. This catalytic versatility and substrate range makes them likely candidates for application as potential biocatalysts for industrial chemistry. However, several aspects of the P450 catalytic cycle and other characteristics have limited their implementation to date in industry, including: their lability at elevated temperature, in the presence of solvents, and over lengthy incubation times; the typically low efficiency with which they metabolize non-natural substrates; and their lack of specificity for a single metabolic pathway. Protein engineering by rational design or directed evolution provides a way to engineer P450s for industrial use. Here we review the progress made to date toward engineering the properties of P450s, especially eukaryotic forms, for industrial application, and including the recent expansion of their catalytic repertoire to include non-natural reactions.
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Affiliation(s)
- Raine E S Thomson
- School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Stephlina A D'Cunha
- School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Martin A Hayes
- Compound Synthesis and Management, Discovery Sciences, BioPharmaceuticals R&D AstraZeneca, Mölndal, Sweden
| | - Elizabeth M J Gillam
- School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia.
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4
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Petitpoisson L, Pichette A, Alsarraf J. Towards better syntheses of partially methylated carbohydrates? Org Chem Front 2022. [DOI: 10.1039/d2qo00893a] [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 give an overview of the reported synthetic strategies towards partially methylated glycosides and discuss how better protocols could stem from catalytic site-selective transformations of carbohydrates and cleaner methylation reagents.
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Affiliation(s)
- Lucas Petitpoisson
- Centre de recherche sur la boréalie (CREB), Laboratoire d'analyse et de séparation des essences végétales (LASEVE), Université du Québec à Chicoutimi, 555 boulevard de l'Université, Chicoutimi G7H 2B1, Québec, Canada
| | - André Pichette
- Centre de recherche sur la boréalie (CREB), Laboratoire d'analyse et de séparation des essences végétales (LASEVE), Université du Québec à Chicoutimi, 555 boulevard de l'Université, Chicoutimi G7H 2B1, Québec, Canada
| | - Jérôme Alsarraf
- Centre de recherche sur la boréalie (CREB), Laboratoire d'analyse et de séparation des essences végétales (LASEVE), Université du Québec à Chicoutimi, 555 boulevard de l'Université, Chicoutimi G7H 2B1, Québec, Canada
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5
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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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6
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Donoso RA, Ruiz D, Gárate-Castro C, Villegas P, González-Pastor JE, de Lorenzo V, González B, Pérez-Pantoja D. Identification of a self-sufficient cytochrome P450 monooxygenase from Cupriavidus pinatubonensis JMP134 involved in 2-hydroxyphenylacetic acid catabolism, via homogentisate pathway. Microb Biotechnol 2021; 14:1944-1960. [PMID: 34156761 PMCID: PMC8449657 DOI: 10.1111/1751-7915.13865] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 05/24/2021] [Accepted: 05/26/2021] [Indexed: 11/28/2022] Open
Abstract
The self-sufficient cytochrome P450 RhF and its homologues belonging to the CYP116B subfamily have attracted considerable attention due to the potential for biotechnological applications based in their ability to catalyse an array of challenging oxidative reactions without requiring additional protein partners. In this work, we showed for the first time that a CYP116B self-sufficient cytochrome P450 encoded by the ohpA gene harboured by Cupriavidus pinatubonensis JMP134, a β-proteobacterium model for biodegradative pathways, catalyses the conversion of 2-hydroxyphenylacetic acid (2-HPA) into homogentisate. Mutational analysis and HPLC metabolite detection in strain JMP134 showed that 2-HPA is degraded through the well-known homogentisate pathway requiring a 2-HPA 5-hydroxylase activity provided by OhpA, which was additionally supported by heterologous expression and enzyme assays. The ohpA gene belongs to an operon including also ohpT, coding for a substrate-binding subunit of a putative transporter, whose expression is driven by an inducible promoter responsive to 2-HPA in presence of a predicted OhpR transcriptional regulator. OhpA homologues can be found in several genera belonging to Actinobacteria and α-, β- and γ-proteobacteria lineages indicating a widespread distribution of 2-HPA catabolism via homogentisate route. These results provide first time evidence for the natural function of members of the CYP116B self-sufficient oxygenases and represent a significant input to support novel kinetic and structural studies to develop cytochrome P450-based biocatalytic processes.
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Affiliation(s)
- Raúl A Donoso
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación (PIDi), Universidad Tecnológica Metropolitana, Santiago, Chile.,Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile
| | - Daniela Ruiz
- Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile.,Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, Santiago, Chile
| | - Carla Gárate-Castro
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación (PIDi), Universidad Tecnológica Metropolitana, Santiago, Chile.,Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile
| | - Pamela Villegas
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación (PIDi), Universidad Tecnológica Metropolitana, Santiago, Chile
| | - José Eduardo González-Pastor
- Laboratory of Molecular Adaptation, Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Madrid, Spain
| | - Víctor de Lorenzo
- Systems and Synthetic Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, Madrid, Spain
| | - Bernardo González
- Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile.,Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, Santiago, Chile
| | - Danilo Pérez-Pantoja
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación (PIDi), Universidad Tecnológica Metropolitana, Santiago, Chile
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7
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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: 127] [Impact Index Per Article: 42.3] [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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8
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Reilley DJ, Hennefarth MR, Alexandrova AN. The Case for Enzymatic Competitive Metal Affinity Methods. ACS Catal 2020; 10:2298-2307. [PMID: 34012720 PMCID: PMC8130888 DOI: 10.1021/acscatal.9b04831] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- David J Reilley
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, CA 90095-1569, USA
| | - Matthew R Hennefarth
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, CA 90095-1569, USA
| | - Anastassia N Alexandrova
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, CA 90095-1569, USA
- California NanoSystems Institute, University of California, Los Angeles, 570 Westwood Plaza, Los Angeles, California 90095-1569, USA
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9
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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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10
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Li Z, Jiang Y, Guengerich FP, Ma L, Li S, Zhang W. Engineering cytochrome P450 enzyme systems for biomedical and biotechnological applications. J Biol Chem 2020; 295:833-849. [PMID: 31811088 PMCID: PMC6970918 DOI: 10.1074/jbc.rev119.008758] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Cytochrome P450 enzymes (P450s) are broadly distributed among living organisms and play crucial roles in natural product biosynthesis, degradation of xenobiotics, steroid biosynthesis, and drug metabolism. P450s are considered as the most versatile biocatalysts in nature because of the vast variety of substrate structures and the types of reactions they catalyze. In particular, P450s can catalyze regio- and stereoselective oxidations of nonactivated C-H bonds in complex organic molecules under mild conditions, making P450s useful biocatalysts in the production of commodity pharmaceuticals, fine or bulk chemicals, bioremediation agents, flavors, and fragrances. Major efforts have been made in engineering improved P450 systems that overcome the inherent limitations of the native enzymes. In this review, we focus on recent progress of different strategies, including protein engineering, redox-partner engineering, substrate engineering, electron source engineering, and P450-mediated metabolic engineering, in efforts to more efficiently produce pharmaceuticals and other chemicals. We also discuss future opportunities for engineering and applications of the P450 systems.
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Affiliation(s)
- Zhong Li
- Shandong Provincial Key Laboratory of Synthetic Biology and CAS Key Laboratory of Biofuels at Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuanyuan Jiang
- Shandong Provincial Key Laboratory of Synthetic Biology and CAS Key Laboratory of Biofuels at Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - F Peter Guengerich
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146
| | - Li Ma
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Shengying Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 Shandong, China
| | - Wei Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 Shandong, China
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11
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12
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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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13
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Morrill LA, Susick RB, Chari JV, Garg NK. Total Synthesis as a Vehicle for Collaboration. J Am Chem Soc 2019; 141:12423-12443. [PMID: 31356068 DOI: 10.1021/jacs.9b05588] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
"Collaboration" is not the first word most would associate with the field of total synthesis. In fact, the spirit of total synthesis is all-too-often reputed as being more competitive, rather than collaborative, sometimes even within individual laboratories. However, recent studies in total synthesis have inspired a number of collaborative efforts that strategically blend synthetic methodology, biocatalysis, biosynthesis, computational chemistry, and drug discovery with complex molecule synthesis. This Perspective highlights select recent advances in these areas, including collaborative syntheses of chlorolissoclimide, nigelladine A, artemisinin, ingenol, hippolachnin A, communesin A, and citrinalin B. The legendary Woodward-Eschenmoser collaboration that led to the total synthesis of vitamin B12 is also discussed.
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Affiliation(s)
- Lucas A Morrill
- Department of Chemistry and Biochemistry , University of California , Los Angeles , California 90095 , United States
| | - Robert B Susick
- Department of Chemistry and Biochemistry , University of California , Los Angeles , California 90095 , United States
| | - Jason V Chari
- Department of Chemistry and Biochemistry , University of California , Los Angeles , California 90095 , United States
| | - Neil K Garg
- Department of Chemistry and Biochemistry , University of California , Los Angeles , California 90095 , United States
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14
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Dockrey SB, Suh CE, Benítez AR, Wymore T, Brooks CL, Narayan ARH. Positioning-Group-Enabled Biocatalytic Oxidative Dearomatization. ACS CENTRAL SCIENCE 2019; 5:1010-1016. [PMID: 31263760 PMCID: PMC6598382 DOI: 10.1021/acscentsci.9b00163] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Indexed: 05/21/2023]
Abstract
Biocatalysts have the potential to perform reactions with exceptional selectivity and high catalytic efficiency while utilizing safe and sustainable reagents. Despite these positive attributes, the utility of a biocatalyst can be limited by the breadth of substrates that can be accommodated in the active site in a reactive pose. Proven strategies exist for optimizing the performance of a biocatalyst toward unnatural substrates, including protein engineering; however, these methods can be time intensive and require specialized equipment that renders these approaches inaccessible to synthetic chemists. Strategies accessible to chemists for the expansion of a natural enzyme's substrate scope, while maintaining high levels of site- and stereoselectivity, remain elusive. Here, we employ a computationally guided substrate engineering strategy to expand the synthetic utility of a flavin-dependent monooxygenase. Specifically, experimental observations and computational modeling led to the identification of a critical interaction between the substrate and protein which is responsible for orienting the substrate in a pose productive for catalysis. The fundamental hypothesis for this positioning group strategy is supported by binding and kinetic assays as well as computational studies with a panel of compounds. Further, incorporation of this positioning group into substrates through a cleavable ester linkage transformed compounds not oxidized by the biocatalyst SorbC into substrates efficiently oxidatively dearomatized by the wild-type enzyme with the highest levels of site- and stereoselectivity known for this transformation.
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Affiliation(s)
- Summer
A. Baker Dockrey
- Department
of Chemistry, Life Sciences Institute, Program in Chemical Biology, and Department of
Biophysics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Carolyn E. Suh
- Department
of Chemistry, Life Sciences Institute, Program in Chemical Biology, and Department of
Biophysics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Attabey Rodríguez Benítez
- Department
of Chemistry, Life Sciences Institute, Program in Chemical Biology, and Department of
Biophysics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Troy Wymore
- Department
of Chemistry, Life Sciences Institute, Program in Chemical Biology, and Department of
Biophysics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Charles L. Brooks
- Department
of Chemistry, Life Sciences Institute, Program in Chemical Biology, and Department of
Biophysics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Alison R. H. Narayan
- Department
of Chemistry, Life Sciences Institute, Program in Chemical Biology, and Department of
Biophysics, University of Michigan, Ann Arbor, Michigan 48109, United States
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15
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Specificity and mechanism of carbohydrate demethylation by cytochrome P450 monooxygenases. Biochem J 2018; 475:3875-3886. [PMID: 30404923 PMCID: PMC6292453 DOI: 10.1042/bcj20180762] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 11/02/2018] [Accepted: 11/06/2018] [Indexed: 01/21/2023]
Abstract
Degradation of carbohydrates by bacteria represents a key step in energy metabolism that can be inhibited by methylated sugars. Removal of methyl groups, which is critical for further processing, poses a biocatalytic challenge because enzymes need to overcome a high energy barrier. Our structural and computational analysis revealed how a member of the cytochrome P450 family evolved to oxidize a carbohydrate ligand. Using structural biology, we ascertained the molecular determinants of substrate specificity and revealed a highly specialized active site complementary to the substrate chemistry. Invariance of the residues involved in substrate recognition across the subfamily suggests that they are critical for enzyme function and when mutated, the enzyme lost substrate recognition. The structure of a carbohydrate-active P450 adds mechanistic insight into monooxygenase action on a methylated monosaccharide and reveals the broad conservation of the active site machinery across the subfamily.
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16
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Abrams DJ, Provencher PA, Sorensen EJ. Recent applications of C-H functionalization in complex natural product synthesis. Chem Soc Rev 2018; 47:8925-8967. [PMID: 30426998 DOI: 10.1039/c8cs00716k] [Citation(s) in RCA: 385] [Impact Index Per Article: 64.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In this review, recent examples featuring C-H functionalization in the synthesis of complex natural products are discussed. A focus is given to the way in which C-H functionalization can influence the logical process of retrosynthesis, and the review is organized by the type and method of C-H functionalization.
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Affiliation(s)
- Dylan J Abrams
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA.
| | | | - Erik J Sorensen
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA.
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17
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Shen C, Shan T, Zhao W, Ou C, Li L, Liu X, Liu J, Yu B. Regio- and enantioselective O-demethylation of tetrahydroprotoberberines by cytochrome P450 enzyme system from Streptomyces griseus ATCC 13273. Appl Microbiol Biotechnol 2018; 103:761-776. [PMID: 30368581 DOI: 10.1007/s00253-018-9416-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 09/10/2018] [Accepted: 09/20/2018] [Indexed: 11/27/2022]
Abstract
Tetrahydroprotoberberines (THPBs), a class of naturally occurring isoquinoline alkaloids, contain substituent methoxyl or hydroxyl groups which play a significant role in the pharmacological properties of these molecules. In this study, we report a biocatalytic strategy for selective O-demethylation of THPBs. CYP105D1, a cytochrome P450 from Streptomyces griseus ATCC 13273, exhibited markedly regioselective demethylation of nonhydroxyl-THPBs and monohydroxyl-THPBs on the D-ring. A possible binding mode of THPBs with CYP105D1 was investigated by docking analysis, and the results revealed that the D-rings of THPBs were with the minimum distance to the heme iron. Tetrahydropalmatine was used as a model substrate and enantioselective demethylation was demonstrated. (S)-Tetrahydropalmatine was only demethylated at C-10, while (R)-tetrahydropalmatine was first demethylated at C-10 and then subsequently demethylated at C-9. The kcat/Km value for demethylation of (R)-tetrahydropalmatine by CYP105D1 was 3.7 times greater than that for demethylation of (S)-tetrahydropalmatine. Furthermore, selective demethylation of (S)-tetrahydropalmatine by the CYP105D1-based whole-cell system was demonstrated for the highly efficient production of (S)-corydalmine which has distinct pharmacological applications, such as providing relief from bone cancer pain and reducing morphine tolerance. Moreover, a homologous redox partner was identified to enhance the catalytic efficiency of the CYP105D1-based whole-cell system. This is the first enzymatic characterization of a cytochrome P450 that has regio- and enantioselective demethylation activity of THPBs for application purpose. The cytochrome P450 system could be a promising strategy for selective demethylation in the pharmaceutical industry.
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Affiliation(s)
- Chen Shen
- Jiangsu Key Laboratory of TCM Evaluation and Translational Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, Jiangsu, China
| | - Tianyue Shan
- Jiangsu Key Laboratory of TCM Evaluation and Translational Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, Jiangsu, China
| | - Wanli Zhao
- Jiangsu Key Laboratory of TCM Evaluation and Translational Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, Jiangsu, China
| | - Chenhui Ou
- Jiangsu Key Laboratory of TCM Evaluation and Translational Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, Jiangsu, China
| | - Li Li
- Jiangsu Key Laboratory of TCM Evaluation and Translational Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, Jiangsu, China
| | - Xiufeng Liu
- Jiangsu Key Laboratory of TCM Evaluation and Translational Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, Jiangsu, China.
| | - Jihua Liu
- Jiangsu Key Laboratory of TCM Evaluation and Translational Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, Jiangsu, China.
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, Jiangsu, China.
| | - Boyang Yu
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, Jiangsu, China
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18
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Reisky L, Büchsenschütz HC, Engel J, Song T, Schweder T, Hehemann JH, Bornscheuer UT. Oxidative demethylation of algal carbohydrates by cytochrome P450 monooxygenases. Nat Chem Biol 2018; 14:342-344. [PMID: 29459682 DOI: 10.1038/s41589-018-0005-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 12/20/2017] [Indexed: 01/22/2023]
Abstract
Sugar O-methylation shields algal polysaccharides against microbial hydrolytic enzymes. Here, we describe cytochrome P450 monooxygenases from marine bacteria that, together with appropriate redox-partner proteins, catalyze the oxidative demethylation of 6-O-methyl-D-galactose, which is an abundant monosaccharide of the algal polysaccharides agarose and porphyran. This previously unknown biological function extends the group of carbohydrate-active enzymes to include the class of cytochrome P450 monooxygenases.
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Affiliation(s)
- Lukas Reisky
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Hanna C Büchsenschütz
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Jennifer Engel
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Tao Song
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Thomas Schweder
- Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Jan-Hendrik Hehemann
- Max Planck Institute for Marine Microbiology, Bremen, Germany. .,University of Bremen, Center for Marine Environmental Sciences (MARUM), Bremen, Germany.
| | - Uwe T Bornscheuer
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, Greifswald, Germany.
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19
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Porter JL, Manning J, Sabatini S, Tavanti M, Turner NJ, Flitsch SL. Characterisation of CYP102A25 fromBacillus marmarensisand CYP102A26 fromPontibacillus halophilus: P450 Homologues of BM3 with Preference towards Hydroxylation of Medium-Chain Fatty Acids. Chembiochem 2018; 19:513-520. [DOI: 10.1002/cbic.201700598] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Indexed: 12/16/2022]
Affiliation(s)
- Joanne L. Porter
- School of Chemistry; Manchester Institute of Biotechnology; The University of Manchester; 131 Princess Street Manchester M1 7DN UK
| | - Jack Manning
- School of Chemistry; Manchester Institute of Biotechnology; The University of Manchester; 131 Princess Street Manchester M1 7DN UK
| | - Selina Sabatini
- School of Chemistry; Manchester Institute of Biotechnology; The University of Manchester; 131 Princess Street Manchester M1 7DN UK
| | - Michele Tavanti
- School of Chemistry; Manchester Institute of Biotechnology; The University of Manchester; 131 Princess Street Manchester M1 7DN UK
| | - Nicholas J. Turner
- School of Chemistry; Manchester Institute of Biotechnology; The University of Manchester; 131 Princess Street Manchester M1 7DN UK
| | - Sabine L. Flitsch
- School of Chemistry; Manchester Institute of Biotechnology; The University of Manchester; 131 Princess Street Manchester M1 7DN UK
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20
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King-Smith E, Zwick CR, Renata H. Applications of Oxygenases in the Chemoenzymatic Total Synthesis of Complex Natural Products. Biochemistry 2017; 57:403-412. [DOI: 10.1021/acs.biochem.7b00998] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Emma King-Smith
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Christian R. Zwick
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Hans Renata
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
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21
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Loskot SA, Romney DK, Arnold FH, Stoltz BM. Enantioselective Total Synthesis of Nigelladine A via Late-Stage C-H Oxidation Enabled by an Engineered P450 Enzyme. J Am Chem Soc 2017; 139:10196-10199. [PMID: 28721734 DOI: 10.1021/jacs.7b05196] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
An enantioselective total synthesis of the norditerpenoid alkaloid nigelladine A is described. Strategically, the synthesis relies on a late-stage C-H oxidation of an advanced intermediate. While traditional chemical methods failed to deliver the desired outcome, an engineered cytochrome P450 enzyme was employed to effect a chemo- and regioselective allylic C-H oxidation in the presence of four oxidizable positions. The enzyme variant was readily identified from a focused library of three enzymes, allowing for completion of the synthesis without the need for extensive screening.
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Affiliation(s)
- Steven A Loskot
- Division of Chemistry and Chemical Engineering, California Institute of Technology , Pasadena, California 91125, United States
| | - David K Romney
- Division of Chemistry and Chemical Engineering, California Institute of Technology , Pasadena, California 91125, United States
| | - Frances H Arnold
- Division of Chemistry and Chemical Engineering, California Institute of Technology , Pasadena, California 91125, United States
| | - Brian M Stoltz
- Division of Chemistry and Chemical Engineering, California Institute of Technology , Pasadena, California 91125, United States
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22
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Belsare KD, Andorfer MC, Cardenas FS, Chael JR, Park HJ, Lewis JC. A Simple Combinatorial Codon Mutagenesis Method for Targeted Protein Engineering. ACS Synth Biol 2017; 6:416-420. [PMID: 28033708 DOI: 10.1021/acssynbio.6b00297] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Directed evolution is a powerful tool for optimizing enzymes, and mutagenesis methods that improve enzyme library quality can significantly expedite the evolution process. Here, we report a simple method for targeted combinatorial codon mutagenesis (CCM). To demonstrate the utility of this method for protein engineering, CCM libraries were constructed for cytochrome P450BM3, pfu prolyl oligopeptidase, and the flavin-dependent halogenase RebH; 10-26 sites were targeted for codon mutagenesis in each of these enzymes, and libraries with a tunable average of 1-7 codon mutations per gene were generated. Each of these libraries provided improved enzymes for their respective transformations, which highlights the generality, simplicity, and tunability of CCM for targeted protein engineering.
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Affiliation(s)
- Ketaki D. Belsare
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Mary C. Andorfer
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Frida S. Cardenas
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Julia R. Chael
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Hyun June Park
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Jared C. Lewis
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
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23
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Zhao YT, Huang LB, Li Q, Li ZJ. A mild method for regioselective de-O-methylation of saccharides by Co2(CO)8/Et3SiH/CO system. Tetrahedron 2016. [DOI: 10.1016/j.tet.2016.07.081] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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24
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Durak LJ, Payne JT, Lewis JC. Late-Stage Diversification of Biologically Active Molecules via Chemoenzymatic C-H Functionalization. ACS Catal 2016; 6:1451-1454. [PMID: 27274902 PMCID: PMC4890977 DOI: 10.1021/acscatal.5b02558] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Engineered variants of rebeccamycin halogenase were used to selectively halogenate a number of biologically active aromatic compounds. Subsequent Pd-catalyzed cross-coupling reactions on the crude extracts of these reactions were used to install aryl, amine, and ether substituents at the halogenation site. This simple, chemoenzymatic method enables non-directed functionalization of C-H bonds on a range of substrates to provide access to derivatives that would be challenging or inefficient to prepare by other means.
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Affiliation(s)
- Landon J. Durak
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - James T. Payne
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Jared C. Lewis
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
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25
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Andorfer MC, Park HJ, Vergara-Coll J, Lewis JC. Directed Evolution of RebH for Catalyst-Controlled Halogenation of Indole C-H Bonds. Chem Sci 2016; 7:3720-3729. [PMID: 27347367 PMCID: PMC4917012 DOI: 10.1039/c5sc04680g] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
RebH variants capable of chlorinating substituted indoles ortho-, meta-, and para- to the indole nitrogen were evolved by directly screening for altered selectivity on deuterium-substituted probe substrates using mass spectrometry. This systematic approach allowed for rapid accumulation of beneficial mutations using simple adaptive walks and should prove generally useful for altering and optimizing the selectivity of C-H functionalization catalysts. Analysis of the beneficial mutations showed that structure-guided selection of active site residues for targeted mutagenesis can be complicated either by activity/selectivity tradeoffs that reduce the possibility of detecting such mutations or by epistatic effects that actually eliminate the benefits of a mutation in certain contexts. As a corollary to this finding, the precise manner in which the beneficial mutations identified led to the observed changes in RebH selectivity is not clear. Docking simulations suggest that tryptamine binds to these variants as tryptophan does to native halogenases, but structural studies will be required to confirm these models and shed light on how particular mutations impact tryptamine binding. Similar directed evolution efforts on other enzymes or artificial metalloenzymes could enable a wide range of C-H functionalization reactions.
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Affiliation(s)
- Mary C Andorfer
- Department of Chemistry, University of Chicago, Chicago, IL 60637
| | - Hyun June Park
- Department of Chemistry, University of Chicago, Chicago, IL 60637
| | | | - Jared C Lewis
- Department of Chemistry, University of Chicago, Chicago, IL 60637
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26
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Li RJ, Xu JH, Yin YC, Wirth N, Ren JM, Zeng BB, Yu HL. Rapid probing of the reactivity of P450 monooxygenases from the CYP116B subfamily using a substrate-based method. NEW J CHEM 2016. [DOI: 10.1039/c6nj00809g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Four types of O-methylated substrates were designed as probes for the detection of fingerprints of Type IV P450s.
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Affiliation(s)
- Ren-Jie Li
- State Key of Laboratory of Bioreactor Engineering
- East China University of Science and Technology
- Shanghai 200237
- P. R. China
| | - Jian-He Xu
- State Key of Laboratory of Bioreactor Engineering
- East China University of Science and Technology
- Shanghai 200237
- P. R. China
| | - Yue-Cai Yin
- State Key of Laboratory of Bioreactor Engineering
- East China University of Science and Technology
- Shanghai 200237
- P. R. China
| | - Nicolas Wirth
- State Key of Laboratory of Bioreactor Engineering
- East China University of Science and Technology
- Shanghai 200237
- P. R. China
| | - Jiang-Meng Ren
- Shanghai Key Laboratory of New Drug Design
- East China University of Science and Technology
- Shanghai 200237
- P. R. China
| | - Bu-Bing Zeng
- Shanghai Key Laboratory of New Drug Design
- East China University of Science and Technology
- Shanghai 200237
- P. R. China
| | - Hui-Lei Yu
- State Key of Laboratory of Bioreactor Engineering
- East China University of Science and Technology
- Shanghai 200237
- P. R. China
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27
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28
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Verma R, Schwaneberg U, Holtmann D, Roccatano D. Unraveling Binding Effects of Cobalt(II) Sepulchrate with the Monooxygenase P450 BM-3 Heme Domain Using Molecular Dynamics Simulations. J Chem Theory Comput 2015; 12:353-63. [DOI: 10.1021/acs.jctc.5b00290] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rajni Verma
- Department
of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Ulrich Schwaneberg
- Department
of Biotechnology, RWTH Aachen University, Worringer Weg 1, 52074 Aachen, Germany
| | - Dirk Holtmann
- Biochemical
Engineering Group, DECHEMA-Forschungsinstitut, Theodor-Heuss-Allee 25, 60486 Frankfurt am Main, Germany
| | - Danilo Roccatano
- School
of Mathematics and Physics, University of Lincoln, Brayford Pool, Lincoln LN6 7TS, United Kingdom
- School
of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
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29
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Denard CA, Bartlett MJ, Wang Y, Lu L, Hartwig JF, Zhao H. Development of a One-Pot Tandem Reaction Combining Ruthenium-Catalyzed Alkene Metathesis and Enantioselective Enzymatic Oxidation To Produce Aryl Epoxides. ACS Catal 2015. [DOI: 10.1021/acscatal.5b00533] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Carl A. Denard
- Department
of Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Mark J. Bartlett
- Department
of Chemistry, University of California−Berkeley, Berkeley, California 94720, United States
| | - Yajie Wang
- Department
of Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Lu Lu
- Department
of Molecular and Cellular Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - John F. Hartwig
- Department
of Chemistry, University of California−Berkeley, Berkeley, California 94720, United States
| | - Huimin Zhao
- Department
of Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Departments
of Chemistry, Biochemistry, and Bioengineering, Carl R. Woese Institute
for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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30
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Directed evolution of cytochrome P450 enzymes for biocatalysis: exploiting the catalytic versatility of enzymes with relaxed substrate specificity. Biochem J 2015; 467:1-15. [DOI: 10.1042/bj20141493] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Cytochrome P450 enzymes are renowned for their ability to insert oxygen into an enormous variety of compounds with a high degree of chemo- and regio-selectivity under mild conditions. This property has been exploited in Nature for an enormous variety of physiological functions, and representatives of this ancient enzyme family have been identified in all kingdoms of life. The catalytic versatility of P450s makes them well suited for repurposing for the synthesis of fine chemicals such as drugs. Although these enzymes have not evolved in Nature to perform the reactions required for modern chemical industries, many P450s show relaxed substrate specificity and exhibit some degree of activity towards non-natural substrates of relevance to applications such as drug development. Directed evolution and other protein engineering methods can be used to improve upon this low level of activity and convert these promiscuous generalist enzymes into specialists capable of mediating reactions of interest with exquisite regio- and stereo-selectivity. Although there are some notable successes in exploiting P450s from natural sources in metabolic engineering, and P450s have been proven repeatedly to be excellent material for engineering, there are few examples to date of practical application of engineered P450s. The purpose of the present review is to illustrate the progress that has been made in altering properties of P450s such as substrate range, cofactor preference and stability, and outline some of the remaining challenges that must be overcome for industrial application of these powerful biocatalysts.
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31
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Use of chemical auxiliaries to control p450 enzymes for predictable oxidations at unactivated C-h bonds of substrates. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 851:209-28. [PMID: 26002737 DOI: 10.1007/978-3-319-16009-2_8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Cytochrome P450 enzymes (P450s) have the ability to oxidize unactivated C-H bonds of substrates with remarkable regio- and stereoselectivity. Comparable selectivity for chemical oxidizing agents is typically difficult to achieve. Hence, there is an interest in exploiting P450s as potential biocatalysts. Despite their impressive attributes, the current use of P450s as biocatalysts is limited. While bacterial P450 enzymes typically show higher activity, they tend to be highly selective for one or a few substrates. On the other hand, mammalian P450s, especially the drug-metabolizing enzymes, display astonishing substrate promiscuity. However, product prediction continues to be challenging. This review discusses the use of small molecules for controlling P450 substrate specificity and product selectivity. The focus will be on two approaches in the area: (1) the use of decoy molecules, and (2) the application of substrate engineering to control oxidation by the enzyme.
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32
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Polic V, Auclair K. Controlling substrate specificity and product regio- and stereo-selectivities of P450 enzymes without mutagenesis. Bioorg Med Chem 2014; 22:5547-54. [PMID: 25035263 PMCID: PMC5177023 DOI: 10.1016/j.bmc.2014.06.034] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2014] [Revised: 06/12/2014] [Accepted: 06/17/2014] [Indexed: 01/25/2023]
Abstract
P450 enzymes (P450s) are well known for their ability to oxidize unactivated CH bonds with high regio- and stereoselectivity. Hence, there is emerging interest in exploiting P450s as potential biocatalysts. Although bacterial P450s typically show higher activity than their mammalian counterparts, they tend to be more substrate selective. Most drug-metabolizing P450s on the other hand, display remarkable substrate promiscuity, yet product prediction remains challenging. Protein engineering is one established strategy to overcome these issues. A less explored, yet promising alternative involves substrate engineering. This review discusses the use of small molecules for controlling the substrate specificity and product selectivity of P450s. The focus is on two approaches, one taking advantage of non-covalent decoy molecules, and the other involving covalent substrate modifications.
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Affiliation(s)
- Vanja Polic
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Karine Auclair
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada.
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33
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Yin YC, Yu HL, Luan ZJ, Li RJ, Ouyang PF, Liu J, Xu JH. Unusually Broad Substrate Profile of Self-Sufficient Cytochrome P450 Monooxygenase CYP116B4 fromLabrenzia aggregata. Chembiochem 2014; 15:2443-9. [DOI: 10.1002/cbic.201402309] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Indexed: 11/11/2022]
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34
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Allouche D, André I, Barbe S, Davies J, de Givry S, Katsirelos G, O'Sullivan B, Prestwich S, Schiex T, Traoré S. Computational protein design as an optimization problem. ARTIF INTELL 2014. [DOI: 10.1016/j.artint.2014.03.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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35
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Controlled oxidation of aliphatic CH bonds in metallo-monooxygenases: Mechanistic insights derived from studies on deuterated and fluorinated hydrocarbons. J Inorg Biochem 2014; 134:118-33. [DOI: 10.1016/j.jinorgbio.2014.02.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2013] [Revised: 01/06/2014] [Accepted: 02/11/2014] [Indexed: 01/01/2023]
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36
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Kellermann SJ, Rentmeister A. Current Developments in Cellulase Engineering. CHEMBIOENG REVIEWS 2014. [DOI: 10.1002/cben.201300006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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37
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Metalloenzyme design and engineering through strategic modifications of native protein scaffolds. Curr Opin Chem Biol 2014; 19:67-75. [PMID: 24513641 DOI: 10.1016/j.cbpa.2014.01.006] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Revised: 01/03/2014] [Accepted: 01/03/2014] [Indexed: 10/25/2022]
Abstract
Metalloenzymes are among the major targets of protein design and engineering efforts aimed at attaining novel and efficient catalysis for biochemical transformation and biomedical applications, due to the diversity of functions imparted by the metallo-cofactors along with the versatility of the protein environment. Naturally evolved protein scaffolds can often serve as robust foundations for sustaining artificial active sites constructed by rational design, directed evolution, or a combination of the two strategies. Accumulated knowledge of structure-function relationship and advancement of tools such as computational algorithms and unnatural amino acids incorporation all contribute to the design of better metalloenzymes with catalytic properties approaching the needs of practical applications.
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38
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Lee H, Kim JH, Han S, Lim YR, Park HG, Chun YJ, Park SW, Kim D. Directed-evolution analysis of human cytochrome P450 2A6 for enhanced enzymatic catalysis. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART A 2014; 77:1409-1418. [PMID: 25343290 DOI: 10.1080/15287394.2014.951757] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Cytochrome P450 2A6 (P450 2A6) is the major enzyme responsible for the oxidation of coumarin, nicotine, and tobacco-specific nitrosamines in human liver. In this study, the catalytic turnover of coumarin oxidation was improved by directed-evolution analysis of P450 2A6 enzyme. A random mutant library was constructed using error-prone polymerase chain reaction (PCR) of the open reading frame of the P450 2A6 gene and individual mutant clones were screened for improved catalytic activity in analysis of fluorescent coumarin 7-hydroxylation. Four consecutive rounds of random mutagenesis and screening were performed and catalytically enhanced mutants were selected in each round of screening. The selected mutants showed the sequentially accumulated mutations of amino acid residues of P450 2A6: B1 (F209S), C1 (F209S, S369G), D1 (F209S, S369G, E277K), and E1 (F209S, S369G, E277K, A10V). E1 mutants displayed approximately 13-fold increased activity based on fluorescent coumarin hydroxylation assays at bacterial whole cell level. Steady-state kinetic parameters for coumarin 7-hydroxylation and nicotine oxidation were measured in purified mutant enzymes and indicated catalytic turnover numbers (kcat) of selected mutants were enhanced up to sevenfold greater than wild-type P450 2A6. However, all mutants displayed elevated Km values and therefore catalytic efficiencies (kcat/Km) were not improved. The increase in Km values was partially attributed to reduction in substrate binding affinities measured in the analysis of substrate binding titration. The structural analysis of P450 2A6 indicates that F209S mutation is sufficient to affect direct interaction of substrate at the active site.
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Affiliation(s)
- Hwayoun Lee
- a Department of Biological Sciences , Konkuk University , Seoul , Korea
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Giordano M, Iadonisi A. Tin-Mediated Regioselective Benzylation and Allylation of Polyols: Applicability of a Catalytic Approach Under Solvent-Free Conditions. J Org Chem 2013; 79:213-22. [DOI: 10.1021/jo402399n] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Maddalena Giordano
- Department
of Chemical Sciences, University of Naples “Federico II”, Via Cintia 4, Naples 80126, Italy
| | - Alfonso Iadonisi
- Department
of Chemical Sciences, University of Naples “Federico II”, Via Cintia 4, Naples 80126, Italy
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Catalano J, Sadre-Bazzaz K, Amodeo GA, Tong L, McDermott A. Structural evidence: a single charged residue affects substrate binding in cytochrome P450 BM-3. Biochemistry 2013; 52:6807-15. [PMID: 23829560 PMCID: PMC5945292 DOI: 10.1021/bi4000645] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cytochrome P450 BM-3 is a bacterial enzyme with sequence similarity to mammalian P450s that catalyzes the hydroxylation of fatty acids with high efficiency. Enzyme-substrate binding and dynamics has been an important topic of study for cytochromes P450 because most of the crystal structures of substrate-bound structures show the complex in an inactive state. We have determined a new crystal structure for cytochrome P450 BM-3 in complex with N-palmitoylglycine (NPG), which unexpectedly showed a direct bidentate ion pair between NPG and arginine 47 (R47). We further explored the role of R47, the only charged residue in the binding pocket in cytochrome P450 BM-3, through mutagenesis and crystallographic studies. The mutations of R47 to glutamine (R47Q), glutamic acid (R47E), and lysine (R47K) were designed to investigate the role of its charge in binding and catalysis. The oppositely charged R47E mutation had the greatest effect on activity and binding. The crystal structure of R47E BMP shows that the glutamic acid side chain is blocking the entrance to the binding pocket, accounting for NPG's low binding affinity and charge repulsion. For R47Q and R47K BM-3, the mutations caused only a slight change in kcat and a large change in Km and Kd, which suggests that R47 mostly is involved in binding and that our crystal structure, 4KPA , represents an initial binding step in the P450 cycle.
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Affiliation(s)
- Jaclyn Catalano
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York 10027, United States
| | - Kianoush Sadre-Bazzaz
- Department of Biological Sciences, Columbia University, 1212 Amsterdam Avenue, New York, New York 10027, United States
| | - Gabriele A. Amodeo
- Department of Biological Sciences, Columbia University, 1212 Amsterdam Avenue, New York, New York 10027, United States
| | - Liang Tong
- Department of Biological Sciences, Columbia University, 1212 Amsterdam Avenue, New York, New York 10027, United States
| | - Ann McDermott
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York 10027, United States
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Chiang CH, Ramu R, Tu YJ, Yang CL, Ng KY, Luo WI, Chen CH, Lu YY, Liu CL, Yu SSF. Regioselective Hydroxylation of C12-C15Fatty Acids with Fluorinated Substituents by Cytochrome P450 BM3. Chemistry 2013; 19:13680-91. [DOI: 10.1002/chem.201302402] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2013] [Indexed: 11/09/2022]
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42
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43
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O'Reilly E, Corbett M, Hussain S, Kelly PP, Richardson D, Flitsch SL, Turner NJ. Substrate promiscuity of cytochrome P450 RhF. Catal Sci Technol 2013. [DOI: 10.1039/c3cy00091e] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Coelho PS, Brustad EM, Kannan A, Arnold FH. Olefin Cyclopropanation via Carbene Transfer Catalyzed by Engineered Cytochrome P450 Enzymes. Science 2012; 339:307-10. [DOI: 10.1126/science.1231434] [Citation(s) in RCA: 574] [Impact Index Per Article: 47.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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45
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Lee D, Williamson CL, Chan L, Taylor MS. Regioselective, Borinic Acid-Catalyzed Monoacylation, Sulfonylation and Alkylation of Diols and Carbohydrates: Expansion of Substrate Scope and Mechanistic Studies. J Am Chem Soc 2012; 134:8260-7. [DOI: 10.1021/ja302549c] [Citation(s) in RCA: 163] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Doris Lee
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto ON M5S 3H6, Canada
| | - Caitlin L. Williamson
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto ON M5S 3H6, Canada
| | - Lina Chan
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto ON M5S 3H6, Canada
| | - Mark S. Taylor
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto ON M5S 3H6, Canada
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Affiliation(s)
- Rudi Fasan
- Department of Chemistry,
Hutchison Hall, University of Rochester, Rochester, New York 14627,
United States
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47
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Chen MMY, Snow CD, Vizcarra CL, Mayo SL, Arnold FH. Comparison of random mutagenesis and semi-rational designed libraries for improved cytochrome P450 BM3-catalyzed hydroxylation of small alkanes. Protein Eng Des Sel 2012; 25:171-8. [DOI: 10.1093/protein/gzs004] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
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Rea V, Kolkman AJ, Vottero E, Stronks EJ, Ampt KAM, Honing M, Vermeulen NPE, Wijmenga SS, Commandeur JNM. Active site substitution A82W improves the regioselectivity of steroid hydroxylation by cytochrome P450 BM3 mutants as rationalized by spin relaxation nuclear magnetic resonance studies. Biochemistry 2012; 51:750-60. [PMID: 22208729 DOI: 10.1021/bi201433h] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Cytochrome P450 BM3 from Bacillus megaterium is a monooxygenase with great potential for biotechnological applications. In this paper, we present engineered drug-metabolizing P450 BM3 mutants as a novel tool for regioselective hydroxylation of steroids at position 16β. In particular, we show that by replacing alanine at position 82 with a tryptophan in P450 BM3 mutants M01 and M11, the selectivity toward 16β-hydroxylation for both testosterone and norethisterone was strongly increased. The A82W mutation led to a ≤42-fold increase in V(max) for 16β-hydroxylation of these steroids. Moreover, this mutation improves the coupling efficiency of the enzyme, which might be explained by a more efficient exclusion of water from the active site. The substrate affinity for testosterone increased at least 9-fold in M11 with tryptophan at position 82. A change in the orientation of testosterone in the M11 A82W mutant as compared to the orientation in M11 was observed by T(1) paramagnetic relaxation nuclear magnetic resonance. Testosterone is oriented in M11 with both the A- and D-ring protons closest to the heme iron. Substituting alanine at position 82 with tryptophan results in increased A-ring proton-iron distances, consistent with the relative decrease in the level of A-ring hydroxylation at position 2β.
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Affiliation(s)
- V Rea
- LACDR/Division of Molecular Toxicology, Department of Pharmacochemistry, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
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Filice M, Palomo JM. Monosaccharide derivatives as central scaffolds in the synthesis of glycosylated drugs. RSC Adv 2012. [DOI: 10.1039/c2ra00515h] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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50
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de Souza GG, Oliveira TS, Takahashi JA, Collado IG, Macías-Sánchez AJ, Hernández-Galán R. Biotransformation of clovane derivatives. Whole cell fungi mediated domino synthesis of rumphellclovane A. Org Biomol Chem 2012; 10:3315-20. [DOI: 10.1039/c2ob07114b] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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