1
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Carrera-Pacheco SE, Mueller A, Puente-Pineda JA, Zúñiga-Miranda J, Guamán LP. Designing cytochrome P450 enzymes for use in cancer gene therapy. Front Bioeng Biotechnol 2024; 12:1405466. [PMID: 38860140 PMCID: PMC11164052 DOI: 10.3389/fbioe.2024.1405466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 04/30/2024] [Indexed: 06/12/2024] Open
Abstract
Cancer is a significant global socioeconomic burden, as millions of new cases and deaths occur annually. In 2020, almost 10 million cancer deaths were recorded worldwide. Advancements in cancer gene therapy have revolutionized the landscape of cancer treatment. An approach with promising potential for cancer gene therapy is introducing genes to cancer cells that encode for chemotherapy prodrug metabolizing enzymes, such as Cytochrome P450 (CYP) enzymes, which can contribute to the effective elimination of cancer cells. This can be achieved through gene-directed enzyme prodrug therapy (GDEPT). CYP enzymes can be genetically engineered to improve anticancer prodrug conversion to its active metabolites and to minimize chemotherapy side effects by reducing the prodrug dosage. Rational design, directed evolution, and phylogenetic methods are some approaches to developing tailored CYP enzymes for cancer therapy. Here, we provide a compilation of genetic modifications performed on CYP enzymes aiming to build highly efficient therapeutic genes capable of bio-activating different chemotherapeutic prodrugs. Additionally, this review summarizes promising preclinical and clinical trials highlighting engineered CYP enzymes' potential in GDEPT. Finally, the challenges, limitations, and future directions of using CYP enzymes for GDEPT in cancer gene therapy are discussed.
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Affiliation(s)
- Saskya E. Carrera-Pacheco
- Centro de Investigación Biomédica (CENBIO), Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
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2
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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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3
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Kim JH, Park CM, Jeong HC, Jeong GH, Cha GS, Lee S, Yun CH. Production of Mono-Hydroxylated Derivatives of Terpinen-4-ol by Bacterial CYP102A1 Enzymes. J Microbiol Biotechnol 2024; 34:725-734. [PMID: 38044690 PMCID: PMC11016761 DOI: 10.4014/jmb.2310.10018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 12/05/2023]
Abstract
CYP102A1 from Bacillus megaterium is an important enzyme in biotechnology, because engineered CYP102A1 enzymes can react with diverse substrates and produce human cytochrome P450-like metabolites. Therefore, CYP102A1 can be applied to drug metabolite production. Terpinen-4-ol is a cyclic monoterpene and the primary component of essential tea tree oil. Terpinen-4-ol was known for therapeutic effects, including antibacterial, antifungal, antiviral, and anti-inflammatory. Because terpenes are natural compounds, examining novel terpenes and investigating the therapeutic effects of terpenes represent responses to social demands for eco-friendly compounds. In this study, we investigated the catalytic activity of engineered CYP102A1 on terpinen-4-ol. Among CYP102A1 mutants tested here, the R47L/F81I/F87V/E143G/L188Q/N213S/E267V mutant showed the highest activity to terpinen-4-ol. Two major metabolites of terpinen-4-ol were generated by engineered CYP102A1. Characterization of major metabolites was confirmed by liquid chromatography-mass spectrometry (LC-MS), gas chromatography-MS, and nuclear magnetic resonance spectroscopy (NMR). Based on the LC-MS results, the difference in mass-to-charge ratio of an ion (m/z) between terpinen-4-ol and its major metabolites was 16. One major metabolite was defined as 1,4-dihydroxy-p-menth-2-ene by NMR. Given these results, we speculate that another major metabolite is also a mono-hydroxylated product. Taken together, we suggest that CYP102A1 can be applied to make novel terpene derivatives.
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Affiliation(s)
- Jeong-Hoon Kim
- School of Biological Sciences and Biotechnology, Graduate School, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Chan Mi Park
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Hae Chan Jeong
- School of Biological Sciences and Biotechnology, Graduate School, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Gyeong Han Jeong
- Research Division for Biotechnology, Advanced Radiation Technology Institute (ARTI), Korea Atomic Energy Research Institute (KAERI), Jeongeup 56212, Republic of Korea
| | - Gun Su Cha
- Namhae Garlic Research Institute, Namhae 52430, Republic of Korea
| | - Sungbeom Lee
- Research Division for Biotechnology, Advanced Radiation Technology Institute (ARTI), Korea Atomic Energy Research Institute (KAERI), Jeongeup 56212, Republic of Korea
- Department of Radiation Science and Technology, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Chul-Ho Yun
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Republic of Korea
- Institute of Synthetic Biology for Carbon Neutralization, Chonnam National University, Gwangju 61186, Republic of Korea
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4
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Yang H, Yu F, Qian Z, Huang T, Peng T, Hu Z. Cytochrome P450 for environmental remediation: catalytic mechanism, engineering strategies and future prospects. World J Microbiol Biotechnol 2023; 40:33. [PMID: 38057619 DOI: 10.1007/s11274-023-03823-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 10/29/2023] [Indexed: 12/08/2023]
Abstract
Environmental pollution is a global concern. Various organic compounds are released into the environment through wastewater, waste gas, and waste residue, ultimately accumulating in the environment and the food chain. This poses a significant threat to both human health and ecology. Currently, a growing body of research has demonstrated that microorganisms employ their Cytochrome P450 (CYP450) system for biodegradation, offering a crucial approach for eliminating these pollutants in environmental remediation. CYP450, a ubiquitous catalyst in nature, includes a vast array of family members distributed widely across various organisms, including bacteria, fungi, and mammals. These enzymes participate in the metabolism of diverse organic compounds. Furthermore, the rapid advancements in enzyme and protein engineering have led to increased utilization of engineered CYP450s in environmental remediation, enhancing their efficiency in pollutant removal. This article presents an overview of the current understanding of various members of the CYP450 superfamily involved in transforming organic pollutants and the engineering of biodegrading CYP450s. Additionally, it explores the catalytic mechanisms, current practical applications of CYP450-based systems, their potential applications, and the prospects in bioremediation.
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Affiliation(s)
- Haichen Yang
- Department of Biology, Shantou University, Shantou, 515063, Guangdong, People's Republic of China
| | - Fei Yu
- Department of Biology, Shantou University, Shantou, 515063, Guangdong, People's Republic of China
| | - Zhihui Qian
- Department of Biology, Shantou University, Shantou, 515063, Guangdong, People's Republic of China
| | - Tongwang Huang
- Department of Biology, Shantou University, Shantou, 515063, Guangdong, People's Republic of China
| | - Tao Peng
- Department of Biology, Shantou University, Shantou, 515063, Guangdong, People's Republic of China.
| | - Zhong Hu
- Department of Biology, Shantou University, Shantou, 515063, Guangdong, People's Republic of China.
- Guangdong Research Center of Offshore Environmental Pollution Control Engineering, Shantou University, Shantou, 515063, Guangdong, People's Republic of China.
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5
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Huang X, Sun Y, Osawa Y, Chen YE, Zhang H. Computational redesign of cytochrome P450 CYP102A1 for highly stereoselective omeprazole hydroxylation by UniDesign. J Biol Chem 2023; 299:105050. [PMID: 37451479 PMCID: PMC10413352 DOI: 10.1016/j.jbc.2023.105050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/03/2023] [Accepted: 07/09/2023] [Indexed: 07/18/2023] Open
Abstract
Cytochrome P450 CYP102A1 is a prototypic biocatalyst that has great potential in chemical synthesis, drug discovery, and biotechnology. CYP102A1 variants engineered by directed evolution and/or rational design are capable of catalyzing the oxidation of a wide range of organic compounds. However, it is difficult to foresee the outcome of engineering CYP102A1 for a compound of interest. Here, we introduce UniDesign as a computational framework for enzyme design and engineering. We tested UniDesign by redesigning CYP102A1 for stereoselective metabolism of omeprazole (OMP), a proton pump inhibitor, starting from an active but nonstereoselective triple mutant (TM: A82F/F87V/L188Q). To shift stereoselectivity toward (R)-OMP, we computationally scanned three active site positions (75, 264, and 328) for mutations that would stabilize the binding of the transition state of (R)-OMP while destabilizing that of (S)-OMP and picked three variants, namely UD1 (TM/L75I), UD2 (TM/A264G), and UD3 (TM/A328V), for experimentation, based on computed energy scores and models. UD1, UD2, and UD3 exhibit high turnover rates of 55 ± 4.7, 84 ± 4.8, and 79 ± 5.7 min-1, respectively, for (R)-OMP hydroxylation, whereas the corresponding rates for (S)-OMP are only 2.2 ± 0.19, 6.0 ± 0.68, and 14 ± 2.8 min-1, yielding an enantiomeric excess value of 92, 87, and 70%, respectively. These results suggest the critical roles of L75I, A264G, and A328V in steering OMP in the optimal orientation for stereoselective oxidation and demonstrate the utility of UniDesign for engineering CYP102A1 to produce drug metabolites of interest. The results are discussed in the context of protein structures.
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Affiliation(s)
- Xiaoqiang Huang
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA.
| | - Yudong Sun
- Department of Pharmacology, University of Michigan, Ann Arbor, Michigan, USA
| | - Yoichi Osawa
- Department of Pharmacology, University of Michigan, Ann Arbor, Michigan, USA
| | - Y Eugene Chen
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Haoming Zhang
- Department of Pharmacology, University of Michigan, Ann Arbor, Michigan, USA.
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6
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Sun Y, Huang X, Osawa Y, Chen YE, Zhang H. The Versatile Biocatalyst of Cytochrome P450 CYP102A1: Structure, Function, and Engineering. Molecules 2023; 28:5353. [PMID: 37513226 PMCID: PMC10383305 DOI: 10.3390/molecules28145353] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/07/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023] Open
Abstract
Wild-type cytochrome P450 CYP102A1 from Bacillus megaterium is a highly efficient monooxygenase for the oxidation of long-chain fatty acids. The unique features of CYP102A1, such as high catalytic activity, expression yield, regio- and stereoselectivity, and self-sufficiency in electron transfer as a fusion protein, afford the requirements for an ideal biocatalyst. In the past three decades, remarkable progress has been made in engineering CYP102A1 for applications in drug discovery, biosynthesis, and biotechnology. The repertoire of engineered CYP102A1 variants has grown tremendously, whereas the substrate repertoire is avalanched to encompass alkanes, alkenes, aromatics, organic solvents, pharmaceuticals, drugs, and many more. In this article, we highlight the major advances in the past five years in our understanding of the structure and function of CYP102A1 and the methodologies used to engineer CYP102A1 for novel applications. The objective is to provide a succinct review of the latest developments with reference to the body of CYP102A1-related literature.
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Affiliation(s)
- Yudong Sun
- Department of Pharmacology, University of Michigan, Ann Arbor, MI 48109, USA; (Y.S.); (Y.O.)
| | - Xiaoqiang Huang
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA;
| | - Yoichi Osawa
- Department of Pharmacology, University of Michigan, Ann Arbor, MI 48109, USA; (Y.S.); (Y.O.)
| | - Yuqing Eugene Chen
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA;
| | - Haoming Zhang
- Department of Pharmacology, University of Michigan, Ann Arbor, MI 48109, USA; (Y.S.); (Y.O.)
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7
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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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8
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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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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: 5] [Impact Index Per Article: 2.5] [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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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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Ren X, Fasan R. Engineered and Artificial Metalloenzymes for Selective C-H Functionalization. CURRENT OPINION IN GREEN AND SUSTAINABLE CHEMISTRY 2021; 31:100494. [PMID: 34395950 PMCID: PMC8357270 DOI: 10.1016/j.cogsc.2021.100494] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The direct functionalization of C-H bonds constitutes a powerful strategy to construct and diversify organic molecules. However, controlling the chemo- and site-selectivity of this transformation in particularly complex molecular settings represents a significant challenge. Metalloenzymes are ideal platforms for achieving catalyst-controlled selective C-H bond functionalization as their reactivities can be tuned by protein engineering and/or redesign of their cofactor environment. In this review, we highlight recent progress in the development of engineered and artificial metalloenzymes for C-H functionalization, with a focus on biocatalytic strategies for selective C-H oxyfunctionalization and halogenation as well as C-H amination and C-H carbene insertion via abiological nitrene and carbene transfer chemistries. Engineered heme- and non-heme iron dependent enzymes have emerged as promising scaffolds for executing these transformations with high chemo-, regio- and stereocontrol as well as tunable selectivity. These emerging systems and methodologies have expanded the toolbox of sustainable strategies for organic synthesis and created new opportunities for the generation of chiral building blocks, the late-stage C-H functionalization of complex molecules, and the total synthesis of natural products.
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Affiliation(s)
- Xinkun Ren
- Department of Chemistry, University of Rochester, Hutchison Hall, 120 Trustee Rd, Rochester NY 14627, USA
| | - Rudi Fasan
- Department of Chemistry, University of Rochester, Hutchison Hall, 120 Trustee Rd, Rochester NY 14627, USA
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12
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Nguyen NA, Jang J, Le TK, Nguyen THH, Woo SM, Yoo SK, Lee YJ, Park KD, Yeom SJ, Kim GJ, Kang HS, Yun CH. Biocatalytic Production of a Potent Inhibitor of Adipocyte Differentiation from Phloretin Using Engineered CYP102A1. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:6683-6691. [PMID: 32468814 DOI: 10.1021/acs.jafc.0c03156] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In this study, we investigated an efficient enzymatic strategy for producing potentially valuable phloretin metabolites from phlorizin, a glucoside of phloretin that is rich in apple pomace. Almond β-glucosidase efficiently removed phlorizin's glucose moiety to produce phloretin. CYP102A1 engineered by site-directed mutagenesis, domain swapping, and random mutagenesis catalyzed the highly regioselective C-hydroxylation of phloretin into 3-OH phloretin with high conversion yields. Under the optimal hydroxylation conditions of 15 g cells L-1 and a 20 mM substrate for whole-cell biocatalysis, phloretin was regioselectively hydroxylated into 3.1 mM 3-OH phloretin each hour. Furthermore, differentiation of 3T3-L1 preadipocytes into adipocytes and lipid accumulation were dramatically inhibited by 3-OH phloretin but promoted by phloretin. Consistent with these inhibitory effects, the expression of adipogenic regulator genes was downregulated by 3-OH phloretin. We propose a platform for the sustainable production and value creation of phloretin metabolites from apple pomace capable of inhibiting adipogenesis.
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Affiliation(s)
- Ngoc Anh Nguyen
- School of Biological Sciences and Technology, Chonnam National University, 77 Yongbongro, Gwangju 61186, Republic of Korea
| | - Jin Jang
- School of Biological Sciences and Technology, Chonnam National University, 77 Yongbongro, Gwangju 61186, Republic of Korea
| | - Thien-Kim Le
- School of Biological Sciences and Technology, Chonnam National University, 77 Yongbongro, Gwangju 61186, Republic of Korea
| | - Thi Huong Ha Nguyen
- School of Biological Sciences and Technology, Chonnam National University, 77 Yongbongro, Gwangju 61186, Republic of Korea
| | - Su-Min Woo
- School of Biological Sciences and Technology, Chonnam National University, 77 Yongbongro, Gwangju 61186, Republic of Korea
| | - Su-Kyoung Yoo
- Department of Biological Sciences and Research Center of Ecomimetics, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Young Ju Lee
- Gwangju Center, Korea Basic Science Institute, Gwangju 61186, Republic of Korea
| | - Ki Deok Park
- Gwangju Center, Korea Basic Science Institute, Gwangju 61186, Republic of Korea
| | - Soo-Jin Yeom
- School of Biological Sciences and Technology, Chonnam National University, 77 Yongbongro, Gwangju 61186, Republic of Korea
| | - Geun-Joong Kim
- Department of Biological Sciences and Research Center of Ecomimetics, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Hyung-Sik Kang
- School of Biological Sciences and Technology, Chonnam National University, 77 Yongbongro, Gwangju 61186, Republic of Korea
| | - Chul-Ho Yun
- School of Biological Sciences and Technology, Chonnam National University, 77 Yongbongro, Gwangju 61186, Republic of Korea
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13
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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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14
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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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15
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Frank R, Prönnecke C, Azendorf R, Jahnke HG, Beck-Sickinger AG, Robitzki AA. Advanced 96-microtiter plate based bioelectrochemical platform reveals molecular short cut of electron flow in cytochrome P450 enzyme. LAB ON A CHIP 2020; 20:1449-1460. [PMID: 32219236 DOI: 10.1039/c9lc01220f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
In bioelectrocatalysis, immobilised redox enzymes are activated in a bioelectronic interface without redox equivalents such as NADPH, thus enabling heterogeneous flow chemistry. The functional contact between enzyme and electrode requires a high degree of optimisation regarding choice of electrode material, electrode pre-treatment, enzyme immobilisation and reaction conditions. So far, however, there are no systems that can easily enable an optimisation procedure at a higher throughput. Here, we present an advanced platform with a vertical divided cell architecture in conjunction with a developed 96-multipotentiostat to be able to drive redox enzymes in 96 well microtiter plate based multielectrode arrays. This platform controls 96 independent three-electrode setups with arbitrary working electrode materials. We demonstrate its applicability in a mutation study of cytochrome P450 BM3 using indium tin oxide as electrode material and the 7-ethoxycoumarin product quantification assay. We show that the bioelectrocatalytic activity of P450 BM3 can be amplified when the cofactor FAD is erased from the enzyme by a single point mutation, so that FMN becomes the first electron entry point. Bioelectrocatalysis thus offers an approach to enzyme simplification as a remedy for the inherent instability of self-sufficient cytochrome P450 enzymes. In addition, we examined native and artificial enzyme activation with respect to ionic strength and buffer composition. The optimal conditions of the activation types differ substantially from each other and exhibit a new molecular facet in enzyme characteristics. In a proof-of-principle we demonstrate that the platform is also compatible with raw cell extracts, thus opening the door for random mutagenesis screenings.
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Affiliation(s)
- Ronny Frank
- Centre for Biotechnology and Biomedicine, Molecular biological-biochemical Processing Technology, Leipzig University, Deutscher Platz 5, D-04103 Leipzig, Germany.
| | - Christoph Prönnecke
- Centre for Biotechnology and Biomedicine, Molecular biological-biochemical Processing Technology, Leipzig University, Deutscher Platz 5, D-04103 Leipzig, Germany.
| | - Ronny Azendorf
- Centre for Biotechnology and Biomedicine, Molecular biological-biochemical Processing Technology, Leipzig University, Deutscher Platz 5, D-04103 Leipzig, Germany.
| | - Heinz-Georg Jahnke
- Centre for Biotechnology and Biomedicine, Molecular biological-biochemical Processing Technology, Leipzig University, Deutscher Platz 5, D-04103 Leipzig, Germany.
| | | | - Andrea A Robitzki
- Centre for Biotechnology and Biomedicine, Molecular biological-biochemical Processing Technology, Leipzig University, Deutscher Platz 5, D-04103 Leipzig, Germany.
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16
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Whole-cell biocatalysis using cytochrome P450 monooxygenases for biotransformation of sustainable bioresources (fatty acids, fatty alkanes, and aromatic amino acids). Biotechnol Adv 2020; 40:107504. [PMID: 31926255 DOI: 10.1016/j.biotechadv.2020.107504] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 12/09/2019] [Accepted: 01/06/2020] [Indexed: 12/25/2022]
Abstract
Cytochrome P450s (CYPs) are heme-thiolated enzymes that catalyze the oxidation of CH bonds in a regio and stereoselective manner. Activation of the non-activated carbon atom can be further enhanced by multistep chemo-enzymatic reactions; moreover, several useful chemicals can be synthesized to provide alternative organic synthesis routes. Given their versatile functionality, CYPs show promise in a number of biotechnological fields. Recently, various CYPs, along with their sequences and functionalities, have been identified owing to rapid developments in sequencing technology and molecular biotechnology. In addition to these discoveries, attempts have been made to utilize CYPs to industrially produce biochemicals from available and sustainable bioresources such as oil, amino acids, carbohydrates, and lignin. Here, these accomplishments, particularly those involving the use of CYP enzymes as whole-cell biocatalysts for bioresource biotransformation, will be reviewed. Further, recently developed biotransformation pathways that result in gram-scale yields of fatty acids and fatty alkanes as well as aromatic amino acids, which depend on the hosts used for CYP expression, and the nature of the multistep reactions will be discussed. These pathways are similar regardless of whether the hosts are CYP-producing or non-CYP-producing; the limitations of these methods and the ways to overcome them are reviewed here.
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17
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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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18
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Production of metabolites of the anti-cancer drug noscapine using a P450 BM3 mutant library. ACTA ACUST UNITED AC 2019; 24:e00372. [PMID: 31516852 PMCID: PMC6728265 DOI: 10.1016/j.btre.2019.e00372] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 08/22/2019] [Accepted: 08/22/2019] [Indexed: 12/27/2022]
Abstract
Mutants of P450BM3 can metabolise noscapine. Noscapine is N-demethylated with high selectivity. The metabolites produced are of interest for drug development. The profile of metabolites generated resembles that of mammalian CYP3A4.
Cytochrome P450 enzymes are a promising tool for the late-stage diversification of lead drug candidates and can provide an alternative route to structural modifications that are difficult to achieve with synthetic chemistry. In this study, a library of P450BM3 mutants was produced using site-directed mutagenesis and the enzymes screened for metabolism of the opium poppy alkaloid noscapine, a drug with anticancer activity. Of the 18 enzyme mutants screened, 12 showed an ability to metabolise noscapine that was not present in the wild-type enzyme. Five noscapine metabolites were detected by LC-MS/MS, with the major metabolite for all mutants being N-demethylated noscapine. The highest observed regioselectivity for N-demethylation was 88%. Two hydroxylated metabolites, a catechol and two C-C cleavage products were also detected. P450-mediated production of hydroxylated and N-demethylated noscapine structures may be useful for the development of noscapine analogues with improved biological activity. The variation in substrate turnover, coupling efficiency and product distribution between the active mutants was considered alongside in silico docking experiments to gain insight into structural and functional effects of the introduced mutations. Selected mutants were identified as targets for further mutagenesis to improve activity and when coupled with an optimised process may provide a route for the preparative-scale production of noscapine metabolites.
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19
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Li Y, Wong LL. Multi‐Functional Oxidase Activity of CYP102A1 (P450BM3) in the Oxidation of Quinolines and Tetrahydroquinolines. Angew Chem Int Ed Engl 2019; 58:9551-9555. [DOI: 10.1002/anie.201904157] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 05/13/2019] [Indexed: 11/06/2022]
Affiliation(s)
- Yushu Li
- Department of ChemistryUniversity of OxfordInorganic Chemistry Laboratory South Parks Road Oxford OX1 3QR UK
| | - Luet L. Wong
- Department of ChemistryUniversity of OxfordInorganic Chemistry Laboratory South Parks Road Oxford OX1 3QR UK
- Oxford Suzhou Centre for Advanced Research Ruo Shui Road, Suzhou Industrial Park Jiangsu 215123 P. R. China
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20
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Li Y, Wong LL. Multi‐Functional Oxidase Activity of CYP102A1 (P450BM3) in the Oxidation of Quinolines and Tetrahydroquinolines. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201904157] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Yushu Li
- Department of ChemistryUniversity of OxfordInorganic Chemistry Laboratory South Parks Road Oxford OX1 3QR UK
| | - Luet L. Wong
- Department of ChemistryUniversity of OxfordInorganic Chemistry Laboratory South Parks Road Oxford OX1 3QR UK
- Oxford Suzhou Centre for Advanced Research Ruo Shui Road, Suzhou Industrial Park Jiangsu 215123 P. R. China
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21
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Frydenvang K, Verkade-Vreeker MCA, Dohmen F, Commandeur JNM, Rafiq M, Mirza O, Jørgensen FS, Geerke DP. Structural analysis of Cytochrome P450 BM3 mutant M11 in complex with dithiothreitol. PLoS One 2019; 14:e0217292. [PMID: 31125381 PMCID: PMC6534296 DOI: 10.1371/journal.pone.0217292] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 05/08/2019] [Indexed: 11/18/2022] Open
Abstract
The bacterial Cytochrome P450 (CYP) BM3 (CYP102A1) is one of the most active CYP isoforms. BM3 mutants can serve as a model for human drug-metabolizing CYPs and/or as biocatalyst for selective formation of drug metabolites. Hence, molecular and computational biologists have in the last two decades shown strong interest in the discovery and design of novel BM3 variants with optimized activity and selectivity for substrate conversion. This led e.g. to the discovery of mutant M11 that is able to metabolize a variety of drugs and drug-like compounds with relatively high activity. In order to further improve our understanding of CYP binding and reactions, we performed a co-crystallization study of mutant M11 and report here the three-dimensional structure M11 in complex with dithiothreitol (DTT) at a resolution of 2.16 Å. The structure shows that DTT can coordinate to the Fe atom in the heme group. UV/Vis spectroscopy and molecular dynamics simulation studies underline this finding and as first structure of the CYP BM3 mutant M11 in complex with a ligand, it offers a basis for structure-based design of novel mutants.
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Affiliation(s)
- Karla Frydenvang
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Marlies C. A. Verkade-Vreeker
- AIMMS Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit, Amsterdam, the Netherlands
| | - Floor Dohmen
- AIMMS Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit, Amsterdam, the Netherlands
| | - Jan N. M. Commandeur
- AIMMS Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit, Amsterdam, the Netherlands
| | - Maria Rafiq
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Osman Mirza
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Flemming Steen Jørgensen
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
- * E-mail: (FSJ); (DPG)
| | - Daan P. Geerke
- AIMMS Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit, Amsterdam, the Netherlands
- * E-mail: (FSJ); (DPG)
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22
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Fürst MJLJ, Kerschbaumer B, Rinnofner C, Migglautsch AK, Winkler M, Fraaije MW. Exploring the Biocatalytic Potential of a Self‐Sufficient Cytochrome P450 from
Thermothelomyces thermophila. Adv Synth Catal 2019. [DOI: 10.1002/adsc.201900076] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
| | - Bianca Kerschbaumer
- Austrian Centre of Industrial Biotechnology (ACIB) Petersgasse 14 8010 Graz Austria
| | - Claudia Rinnofner
- Austrian Centre of Industrial Biotechnology (ACIB) Petersgasse 14 8010 Graz Austria
- Bisy e.U. Wetzawinkel 20 8200 Hofstätten/Raab Austria
| | - Anna K. Migglautsch
- Institute of Organic Chemistry, Graz University of TechnologyNAWI Graz 8010 Graz Austria
| | - Margit Winkler
- Austrian Centre of Industrial Biotechnology (ACIB) Petersgasse 14 8010 Graz Austria
| | - Marco W. Fraaije
- Molecular Enzymology GroupUniversity of Groningen Nijenborgh 4 9747AG Groningen, The Netherlands
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23
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Leth R, Ercig B, Olsen L, Jørgensen FS. Both Reactivity and Accessibility Are Important in Cytochrome P450 Metabolism: A Combined DFT and MD Study of Fenamic Acids in BM3 Mutants. J Chem Inf Model 2019; 59:743-753. [DOI: 10.1021/acs.jcim.8b00750] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Rasmus Leth
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Bogac Ercig
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Lars Olsen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Flemming Steen Jørgensen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
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24
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Vickers C, Backfisch G, Oellien F, Piel I, Lange UEW. Enzymatic Late‐Stage Oxidation of Lead Compounds with Solubilizing Biomimetic Docking/Protecting groups. Chemistry 2018; 24:17936-17947. [DOI: 10.1002/chem.201802331] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 09/12/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Clare Vickers
- Neuroscience Discovery, Medicinal ChemistryAbbVie (Deutschland) GmbH & Co. KG Knollstrasse D-67061 Ludwigshafen Germany
| | - Gisela Backfisch
- Development Sciences, DMPK and Bioanalytical ResearchAbbVie (Deutschland) GmbH & Co. KG Knollstrasse D-67061 Ludwigshafen Germany
| | - Frank Oellien
- Neuroscience Discovery, Medicinal ChemistryAbbVie (Deutschland) GmbH & Co. KG Knollstrasse D-67061 Ludwigshafen Germany
| | - Isabel Piel
- Neuroscience Discovery, Medicinal ChemistryAbbVie (Deutschland) GmbH & Co. KG Knollstrasse D-67061 Ludwigshafen Germany
| | - Udo E. W. Lange
- Neuroscience Discovery, Medicinal ChemistryAbbVie (Deutschland) GmbH & Co. KG Knollstrasse D-67061 Ludwigshafen Germany
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25
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Xu LH, Du YL. Rational and semi-rational engineering of cytochrome P450s for biotechnological applications. Synth Syst Biotechnol 2018; 3:283-290. [PMID: 30533540 PMCID: PMC6263019 DOI: 10.1016/j.synbio.2018.10.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 10/02/2018] [Accepted: 10/04/2018] [Indexed: 01/08/2023] Open
Abstract
The cytochrome P450 enzymes are ubiquitous heme-thiolate proteins performing regioselective and stereoselective oxygenation reactions in cellular metabolism. Due to their broad substrate scope and catalytic versatility, P450 enzymes are also attractive candidates for many industrial and biopharmaceutical applications. For particular uses, enzyme properties of P450s can be further optimized through directed evolution, rational, and semi-rational engineering approaches, all of which introduce mutations within the P450 structures. In this review, we describe the recent applications of these P450 engineering approaches and highlight the key regions and residues that have been identified using such approaches. These “hotspots” lie within critical functional areas of the P450 structure, including the active site, the substrate access channel, and the redox partner interaction interface.
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Affiliation(s)
- Lian-Hua Xu
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, China
- Corresponding author.
| | - Yi-Ling Du
- Institute of Pharmaceutical Biotechnology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
- Corresponding author.
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26
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Geronimo I, Denning CA, Heidary DK, Glazer EC, Payne CM. Molecular Determinants of Substrate Affinity and Enzyme Activity of a Cytochrome P450 BM3 Variant. Biophys J 2018; 115:1251-1263. [PMID: 30224054 DOI: 10.1016/j.bpj.2018.08.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 08/18/2018] [Accepted: 08/20/2018] [Indexed: 12/29/2022] Open
Abstract
Cytochrome P450BM3 catalyzes the hydroxylation and/or epoxidation of fatty acids, fatty amides, and alcohols. Protein engineering has produced P450BM3 variants capable of accepting drug molecules normally metabolized by human P450 enzymes. The enhanced substrate promiscuity has been attributed to the greater flexibility of the lid of the substrate channel. However, it is not well understood how structurally different and highly polar drug molecules can stably bind in the active site nor how the activity and coupling efficiency of the enzyme may be affected by the lack of enzyme-substrate complementarity. To address these important aspects of non-native small molecule binding, this study investigated the binding of drug molecules with different size, charge, polar surface area, and human P450 affinity on the promiscuous R47L/F87V/L188Q/E267V/F81I pentuple mutant of P450BM3. Binding free energy data and energy decomposition analysis showed that pentuple mutant P450BM3 stably binds (i.e., negative ΔGb°) a broad range of substrate and inhibitor types because dispersion interactions with active site residues overcome unfavorable repulsive and electrostatic effects. Molecular dynamics simulations revealed that 1) acidic substrates tend to disrupt the heme propionate A-K69 salt bridge, which may reduce heme oxidizing ability, and 2) the lack of complementarity leads to high substrate mobility and water density in the active site, which may lead to uncoupling. These factors must be considered in future developments of P450BM3 as a biocatalyst in the large-scale production of drug metabolites.
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Affiliation(s)
- Inacrist Geronimo
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky
| | | | - David K Heidary
- Department of Chemistry, University of Kentucky, Lexington, Kentucky
| | - Edith C Glazer
- Department of Chemistry, University of Kentucky, Lexington, Kentucky.
| | - Christina M Payne
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky.
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27
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Zamora A, Denning CA, Heidary DK, Wachter E, Nease LA, Ruiz J, Glazer EC. Ruthenium-containing P450 inhibitors for dual enzyme inhibition and DNA damage. Dalton Trans 2018; 46:2165-2173. [PMID: 28121322 DOI: 10.1039/c6dt04405k] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Cytochrome P450s are key players in drug metabolism, and overexpression in tumors is associated with significant resistance to many medicinal agents. Consequently, inhibition of P450s could serve as a strategy to restore drug efficacy. However, the widespread expression of P450s throughout the human body and the critical roles they play in various biosynthetic pathways motivates the development of P450 inhibitors capable of controlled local administration. Ruthenium complexes containing P450 inhibitors as ligands were synthesized in order to develop pro-drugs that can be triggered to release the inhibitors in a spatially and temporally controlled fashion. Upon light activation the compounds release ligands that directly bind and inhibit P450 enzymes, while the ruthenium center is able to directly damage DNA.
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Affiliation(s)
- Ana Zamora
- Departamento de Química Inorgánica and Regional Campus of International Excellence "Campus Mare Nostrum", Universidad de Murcia, and Institute for Bio-Health Research of Murcia (IMIB-Arrixaca), E-30071 Murcia, Spain
| | - Catherine A Denning
- Department of Chemistry, University of Kentucky, 505 Rose Street, Lexington, KY 40506, USA.
| | - David K Heidary
- Department of Chemistry, University of Kentucky, 505 Rose Street, Lexington, KY 40506, USA.
| | - Erin Wachter
- Department of Chemistry, University of Kentucky, 505 Rose Street, Lexington, KY 40506, USA.
| | - Leona A Nease
- Department of Chemistry, University of Kentucky, 505 Rose Street, Lexington, KY 40506, USA.
| | - José Ruiz
- Departamento de Química Inorgánica and Regional Campus of International Excellence "Campus Mare Nostrum", Universidad de Murcia, and Institute for Bio-Health Research of Murcia (IMIB-Arrixaca), E-30071 Murcia, Spain
| | - Edith C Glazer
- Department of Chemistry, University of Kentucky, 505 Rose Street, Lexington, KY 40506, USA.
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28
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Luirink RA, Dekker SJ, Capoferri L, Janssen LF, Kuiper CL, Ari ME, Vermeulen NP, Vos JC, Commandeur JN, Geerke DP. A combined computational and experimental study on selective flucloxacillin hydroxylation by cytochrome P450 BM3 variants. J Inorg Biochem 2018; 184:115-122. [DOI: 10.1016/j.jinorgbio.2018.04.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Revised: 03/23/2018] [Accepted: 04/18/2018] [Indexed: 12/20/2022]
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29
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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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Beyer N, Kulig JK, Fraaije MW, Hayes MA, Janssen DB. Exploring PTDH-P450BM3 Variants for the Synthesis of Drug Metabolites. Chembiochem 2018; 19:326-337. [DOI: 10.1002/cbic.201700470] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Nina Beyer
- Biotransformation and Biocatalysis; University of Groningen; Nijenborgh 4 9747AG Groningen The Netherlands
| | - Justyna K. Kulig
- Cardiovascular and Metabolic Diseases; DMPK; Innovative Medicines and Early Development; AstraZeneca R&D Gothenburg; Pepparedsleden 1 43150 Mölndal Sweden
- Crop Science Division; Bayer AG; Alfred-Nobel-Strasse 50 40789 Monheim am Rhein Germany
| | - Marco W. Fraaije
- Biotransformation and Biocatalysis; University of Groningen; Nijenborgh 4 9747AG Groningen The Netherlands
| | - Martin A. Hayes
- Cardiovascular and Metabolic Diseases; DMPK; Innovative Medicines and Early Development; AstraZeneca R&D Gothenburg; Pepparedsleden 1 43150 Mölndal Sweden
| | - Dick B. Janssen
- Biotransformation and Biocatalysis; University of Groningen; Nijenborgh 4 9747AG Groningen The Netherlands
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31
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Munday SD, Dezvarei S, Lau IC, Bell SG. Examination of Selectivity in the Oxidation of
ortho
‐ and
meta
‐Disubstituted Benzenes by CYP102A1 (P450 Bm3) Variants. ChemCatChem 2017. [DOI: 10.1002/cctc.201700116] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Samuel D. Munday
- Department of Chemistry University of Adelaide Adelaide. SA 5005 Australia
| | | | - Ian C.‐K. Lau
- Department of Chemistry University of Adelaide Adelaide. SA 5005 Australia
| | - Stephen G. Bell
- Department of Chemistry University of Adelaide Adelaide. SA 5005 Australia
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32
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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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33
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Behrendorff JBYH, Gillam EMJ. Prospects for Applying Synthetic Biology to Toxicology: Future Opportunities and Current Limitations for the Repurposing of Cytochrome P450 Systems. Chem Res Toxicol 2016; 30:453-468. [DOI: 10.1021/acs.chemrestox.6b00396] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
| | - Elizabeth M. J. Gillam
- School
of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane 4072, Australia
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34
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Jang HH, Shin SM, Ma SH, Lee GY, Joung YH, Yun CH. Role of Leu188 in the Fatty Acid Hydroxylase Activity of CYP102A1 from Bacillus megaterium. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2016.07.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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35
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Chu LL, Pandey RP, Jung N, Jung HJ, Kim EH, Sohng JK. Hydroxylation of diverse flavonoids by CYP450 BM3 variants: biosynthesis of eriodictyol from naringenin in whole cells and its biological activities. Microb Cell Fact 2016; 15:135. [PMID: 27495155 PMCID: PMC4974697 DOI: 10.1186/s12934-016-0533-4] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 07/27/2016] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Cytochrome P450 monooxygenase constitutes a significant group of oxidative enzymes that can introduce an oxygen atom in a high regio- and stereo-selectivity mode. We used the Bacillus megaterium cytochrome P450 BM3 (CYP450 BM3) and its variants namely mutant 13 (M13) and mutant 15 (M15) for the hydroxylation of diverse class of flavonoids. RESULTS Among 20 flavonoids, maximum seven flavonoids were hydroxylated by the variants while none of these molecules were accepted by CYP450 BM3 in in vitro reaction. Moreover, M13 exhibited higher conversion of substrates than M15 and CYP450 BM3 enzymes. We found that M13 carried out regiospecific 3'-hydroxylation reaction of naringenin with the highest conversion among all the tested flavonoids. The apparent K m and k cat values of M13 for naringenin were 446 µM and 1.955 s(-1), respectively. In whole-cell biotransformation experiment with 100 µM of naringenin in M9 minimal medium with 2 % glucose in shake flask culture, M13 showed 2.14- and 13.96-folds higher conversion yield in comparison with M15 (16.11 %) and wild type (2.47 %). The yield of eriodictyol was 46.95 µM [~40.7 mg (13.5 mg/L)] in a 3-L volume lab scale fermentor at 48 h in the same medium exhibiting approximately 49.81 % conversion of the substrate. In addition, eriodictyol exhibited higher antibacterial and anticancer potential than naringenin, flavanone and hesperetin. CONCLUSIONS We elucidated that eriodictyol being produced from naringenin using recombinant CYP450 BM3 and its variants from B. megaterium, which shows an approach for the production of important hydroxylated compounds of various polyphenols that may span pharmaceutical industries.
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Affiliation(s)
- Luan Luong Chu
- Department of Life Science and Biochemical Engineering, SunMoon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, Chungnam, 31460, South Korea
| | - Ramesh Prasad Pandey
- Department of Life Science and Biochemical Engineering, SunMoon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, Chungnam, 31460, South Korea.,Department of BT-Convergent Pharmaceutical Engineering, SunMoon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, Chungnam, 31460, South Korea
| | - Narae Jung
- Department of Life Science and Biochemical Engineering, SunMoon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, Chungnam, 31460, South Korea
| | - Hye Jin Jung
- Department of Life Science and Biochemical Engineering, SunMoon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, Chungnam, 31460, South Korea.,Department of BT-Convergent Pharmaceutical Engineering, SunMoon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, Chungnam, 31460, South Korea
| | - Eun-Hee Kim
- Division of Magnetic Resonance, Korea Basic Science Institute, Ochang, Chungbuk, 363-883, South Korea
| | - Jae Kyung Sohng
- Department of Life Science and Biochemical Engineering, SunMoon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, Chungnam, 31460, South Korea. .,Department of BT-Convergent Pharmaceutical Engineering, SunMoon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, Chungnam, 31460, South Korea.
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36
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Geronimo I, Denning CA, Rogers WE, Othman T, Huxford T, Heidary DK, Glazer EC, Payne CM. Effect of Mutation and Substrate Binding on the Stability of Cytochrome P450BM3 Variants. Biochemistry 2016; 55:3594-606. [PMID: 27267136 PMCID: PMC7422958 DOI: 10.1021/acs.biochem.6b00183] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cytochrome P450BM3 is a heme-containing enzyme from Bacillus megaterium that exhibits high monooxygenase activity and has a self-sufficient electron transfer system in the full-length enzyme. Its potential synthetic applications drive protein engineering efforts to produce variants capable of oxidizing nonnative substrates such as pharmaceuticals and aromatic pollutants. However, promiscuous P450BM3 mutants often exhibit lower stability, thereby hindering their industrial application. This study demonstrated that the heme domain R47L/F87V/L188Q/E267V/F81I pentuple mutant (PM) is destabilized because of the disruption of hydrophobic contacts and salt bridge interactions. This was directly observed from crystal structures of PM in the presence and absence of ligands (palmitic acid and metyrapone). The instability of the tertiary structure and heme environment of substrate-free PM was confirmed by pulse proteolysis and circular dichroism, respectively. Binding of the inhibitor, metyrapone, significantly stabilized PM, but the presence of the native substrate, palmitic acid, had no effect. On the basis of high-temperature molecular dynamics simulations, the lid domain, β-sheet 1, and Cys ligand loop (a β-bulge segment connected to the heme) are the most labile regions and, thus, potential sites for stabilizing mutations. Possible approaches to stabilization include improvement of hydrophobic packing interactions in the lid domain and introduction of new salt bridges into β-sheet 1 and the heme region. An understanding of the molecular factors behind the loss of stability of P450BM3 variants therefore expedites site-directed mutagenesis studies aimed at developing thermostability.
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Affiliation(s)
- Inacrist Geronimo
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky 40506-0046, United States
| | - Catherine A. Denning
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506-0055, United States
| | - W. Eric Rogers
- Structural Biochemistry Laboratory, Department of Chemistry & Biochemistry, San Diego State University, San Diego, California 92182-1030, United States
| | - Thaer Othman
- Structural Biochemistry Laboratory, Department of Chemistry & Biochemistry, San Diego State University, San Diego, California 92182-1030, United States
| | - Tom Huxford
- Structural Biochemistry Laboratory, Department of Chemistry & Biochemistry, San Diego State University, San Diego, California 92182-1030, United States
| | - David K. Heidary
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506-0055, United States
| | - Edith C. Glazer
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506-0055, United States
| | - Christina M. Payne
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky 40506-0046, United States
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37
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Gricman Ł, Weissenborn MJ, Hoffmann SM, Borlinghaus N, Hauer B, Pleiss J. Redox Partner Interaction Sites in Cytochrome P450 Monooxygenases:In SilicoAnalysis and Experimental Validation. ChemistrySelect 2016. [DOI: 10.1002/slct.201600369] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Łukasz Gricman
- Institute of Technical Biochemistry; University of Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Martin J. Weissenborn
- Institute of Technical Biochemistry; University of Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Sara M. Hoffmann
- Institute of Technical Biochemistry; University of Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Niels Borlinghaus
- Institute of Technical Biochemistry; University of Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Bernhard Hauer
- Institute of Technical Biochemistry; University of Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Jürgen Pleiss
- Institute of Technical Biochemistry; University of Stuttgart; Allmandring 31 70569 Stuttgart Germany
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38
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Capoferri L, Leth R, ter Haar E, Mohanty AK, Grootenhuis PDJ, Vottero E, Commandeur JNM, Vermeulen NPE, Jørgensen FS, Olsen L, Geerke DP. Insights into regioselective metabolism of mefenamic acid by cytochrome P450 BM3 mutants through crystallography, docking, molecular dynamics, and free energy calculations. Proteins 2016; 84:383-96. [PMID: 26757175 DOI: 10.1002/prot.24985] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 12/21/2015] [Accepted: 01/05/2016] [Indexed: 12/21/2022]
Abstract
Cytochrome P450 BM3 (CYP102A1) mutant M11 is able to metabolize a wide range of drugs and drug-like compounds. Among these, M11 was recently found to be able to catalyze formation of human metabolites of mefenamic acid and other nonsteroidal anti-inflammatory drugs (NSAIDs). Interestingly, single active-site mutations such as V87I were reported to invert regioselectivity in NSAID hydroxylation. In this work, we combine crystallography and molecular simulation to study the effect of single mutations on binding and regioselective metabolism of mefenamic acid by M11 mutants. The heme domain of the protein mutant M11 was expressed, purified, and crystallized, and its X-ray structure was used as template for modeling. A multistep approach was used that combines molecular docking, molecular dynamics (MD) simulation, and binding free-energy calculations to address protein flexibility. In this way, preferred binding modes that are consistent with oxidation at the experimentally observed sites of metabolism (SOMs) were identified. Whereas docking could not be used to retrospectively predict experimental trends in regioselectivity, we were able to rank binding modes in line with the preferred SOMs of mefenamic acid by M11 and its mutants by including protein flexibility and dynamics in free-energy computation. In addition, we could obtain structural insights into the change in regioselectivity of mefenamic acid hydroxylation due to single active-site mutations. Our findings confirm that use of MD and binding free-energy calculation is useful for studying biocatalysis in those cases in which enzyme binding is a critical event in determining the selective metabolism of a substrate.
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Affiliation(s)
- Luigi Capoferri
- AIMMS Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, VU University, De Boelelaan 1083, 1081 HV Amsterdam, the Netherlands
| | - Rasmus Leth
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Ernst ter Haar
- Vertex Pharmaceuticals Incorporated, 50 Northern Avenue, Boston, MA, 02210
| | - Arun K Mohanty
- Vertex Pharmaceuticals Incorporated, 50 Northern Avenue, Boston, MA, 02210
| | | | - Eduardo Vottero
- AIMMS Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, VU University, De Boelelaan 1083, 1081 HV Amsterdam, the Netherlands
| | - Jan N M Commandeur
- AIMMS Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, VU University, De Boelelaan 1083, 1081 HV Amsterdam, the Netherlands
| | - Nico P E Vermeulen
- AIMMS Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, VU University, De Boelelaan 1083, 1081 HV Amsterdam, the Netherlands
| | - Flemming Steen Jørgensen
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Lars Olsen
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Daan P Geerke
- AIMMS Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, VU University, De Boelelaan 1083, 1081 HV Amsterdam, the Netherlands
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39
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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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40
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Di Nardo G, Dell'Angelo V, Catucci G, Sadeghi SJ, Gilardi G. Subtle structural changes in the Asp251Gly/Gln307His P450 BM3 mutant responsible for new activity toward diclofenac, tolbutamide and ibuprofen. Arch Biochem Biophys 2015; 602:106-115. [PMID: 26718083 DOI: 10.1016/j.abb.2015.12.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 12/10/2015] [Accepted: 12/14/2015] [Indexed: 12/25/2022]
Abstract
This paper reports the structure of the double mutant Asp251Gly/Gln307His (named A2) generated by random mutagenesis, able to produce 4'-hydroxydiclofenac, 2-hydroxyibuprofen and 4-hydroxytolbutamide from diclofenac, ibuprofen and tolbutamide, respectively. The 3D structure of the substrate-free mutant shows a conformation similar to the closed one found in the substrate-bound wild type enzyme, but with a higher degree of disorder in the region of the G-helix and F-G loop. This is due to the mutation Asp251Gly that breaks the salt bridge between Aps251 on I-helix and Lys224 on G-helix, allowing the G-helix to move away from I-helix and conferring a higher degree of flexibility to this element. This subtle structural change is accompanied by long-range structural rearrangements of the active site with the rotation of Phe87 and a reorganization of catalytically important water molecules. The impact of these structural features on thermal stability, reduction potential and electron transfer is investigated. The data demonstrate that a single mutation far from the active site triggers an increase in protein flexibility in a key region, shifting the conformational equilibrium toward the closed form that is ready to accept electrons and enter the P450 catalytic cycle as soon as a substrate is accepted.
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Affiliation(s)
- Giovanna Di Nardo
- Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina 13, Torino, Italy; CrisDi, Interdepartmental Center for Crystallography, University of Torino, Via Pietro Giuria 7, Torino, Italy
| | - Valentina Dell'Angelo
- Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina 13, Torino, Italy
| | - Gianluca Catucci
- Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina 13, Torino, Italy
| | - Sheila J Sadeghi
- Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina 13, Torino, Italy
| | - Gianfranco Gilardi
- Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina 13, Torino, Italy; CrisDi, Interdepartmental Center for Crystallography, University of Torino, Via Pietro Giuria 7, Torino, Italy
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41
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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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42
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Ritter C, Nett N, Acevedo‐Rocha CG, Lonsdale R, Kräling K, Dempwolff F, Hoebenreich S, Graumann PL, Reetz MT, Meggers E. Bioorthogonale enzymatische Aktivierung maskierter Verbindungen. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201506739] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Cornelia Ritter
- Fachbereich Chemie, Philipps‐Universität Marburg, Hans‐Meerwein‐Straße 4, 35043 Marburg (Deutschland)
| | - Nathalie Nett
- Fachbereich Chemie, Philipps‐Universität Marburg, Hans‐Meerwein‐Straße 4, 35043 Marburg (Deutschland)
| | - Carlos G. Acevedo‐Rocha
- Fachbereich Chemie, Philipps‐Universität Marburg, Hans‐Meerwein‐Straße 4, 35043 Marburg (Deutschland)
- Max‐Planck‐Institut für Kohlenforschung, Kaiser‐Wilhelm‐Platz 1, 45470 Mülheim an der Ruhr (Deutschland)
- LOEWE‐Zentrum für Synthetische Mikrobiologie (SYNMIKRO), Hans‐Meerwein‐Straße, 35043 Marburg (Deutschland)
- Max‐Planck‐Institut für terrestrische Mikrobiologie, Karl‐von‐Frisch‐Straße 10, 35043 Marburg (Deutschland)
| | - Richard Lonsdale
- Fachbereich Chemie, Philipps‐Universität Marburg, Hans‐Meerwein‐Straße 4, 35043 Marburg (Deutschland)
- Max‐Planck‐Institut für Kohlenforschung, Kaiser‐Wilhelm‐Platz 1, 45470 Mülheim an der Ruhr (Deutschland)
| | - Katja Kräling
- Fachbereich Chemie, Philipps‐Universität Marburg, Hans‐Meerwein‐Straße 4, 35043 Marburg (Deutschland)
| | - Felix Dempwolff
- LOEWE‐Zentrum für Synthetische Mikrobiologie (SYNMIKRO), Hans‐Meerwein‐Straße, 35043 Marburg (Deutschland)
| | - Sabrina Hoebenreich
- Fachbereich Chemie, Philipps‐Universität Marburg, Hans‐Meerwein‐Straße 4, 35043 Marburg (Deutschland)
| | - Peter L. Graumann
- Fachbereich Chemie, Philipps‐Universität Marburg, Hans‐Meerwein‐Straße 4, 35043 Marburg (Deutschland)
- LOEWE‐Zentrum für Synthetische Mikrobiologie (SYNMIKRO), Hans‐Meerwein‐Straße, 35043 Marburg (Deutschland)
| | - Manfred T. Reetz
- Fachbereich Chemie, Philipps‐Universität Marburg, Hans‐Meerwein‐Straße 4, 35043 Marburg (Deutschland)
- Max‐Planck‐Institut für Kohlenforschung, Kaiser‐Wilhelm‐Platz 1, 45470 Mülheim an der Ruhr (Deutschland)
| | - Eric Meggers
- Fachbereich Chemie, Philipps‐Universität Marburg, Hans‐Meerwein‐Straße 4, 35043 Marburg (Deutschland)
- College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005 (China)
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43
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Ritter C, Nett N, Acevedo-Rocha CG, Lonsdale R, Kräling K, Dempwolff F, Hoebenreich S, Graumann PL, Reetz MT, Meggers E. Bioorthogonal Enzymatic Activation of Caged Compounds. Angew Chem Int Ed Engl 2015; 54:13440-3. [PMID: 26356324 DOI: 10.1002/anie.201506739] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 08/14/2015] [Indexed: 11/06/2022]
Abstract
Engineered cytochrome P450 monooxygenase variants are reported as highly active and selective catalysts for the bioorthogonal uncaging of propargylic and benzylic ether protected substrates, including uncaging in living E. coli. observed selectivity is supported by induced-fit docking and molecular dynamics simulations. This proof-of-principle study points towards the utility of bioorthogonal enzyme/protecting group pairs for applications in the life sciences.
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Affiliation(s)
- Cornelia Ritter
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35043 Marburg (Germany)
| | - Nathalie Nett
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35043 Marburg (Germany)
| | - Carlos G Acevedo-Rocha
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35043 Marburg (Germany).,Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr (Germany).,LOEWE Zentrum für Synthetische Mikrobiologie (SYNMIKRO), Hans-Meerwein-Straße, 35043 Marburg (Germany).,Max-Planck-Institut für terrestrische Mikrobiologie, Karl-von-Frisch-Straße 10, 35043 Marburg (Germany)
| | - Richard Lonsdale
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35043 Marburg (Germany).,Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr (Germany)
| | - Katja Kräling
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35043 Marburg (Germany)
| | - Felix Dempwolff
- LOEWE Zentrum für Synthetische Mikrobiologie (SYNMIKRO), Hans-Meerwein-Straße, 35043 Marburg (Germany)
| | - Sabrina Hoebenreich
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35043 Marburg (Germany)
| | - Peter L Graumann
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35043 Marburg (Germany).,LOEWE Zentrum für Synthetische Mikrobiologie (SYNMIKRO), Hans-Meerwein-Straße, 35043 Marburg (Germany)
| | - Manfred T Reetz
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35043 Marburg (Germany). .,Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr (Germany).
| | - Eric Meggers
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35043 Marburg (Germany). .,College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005 (P. R. China).
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Ren X, Yorke JA, Taylor E, Zhang T, Zhou W, Wong LL. Drug Oxidation by Cytochrome P450BM3 : Metabolite Synthesis and Discovering New P450 Reaction Types. Chemistry 2015; 21:15039-47. [PMID: 26311271 DOI: 10.1002/chem.201502020] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Indexed: 11/06/2022]
Abstract
There is intense interest in late-stage catalytic C-H bond functionalization as an integral part of synthesis. Effective catalysts must have a broad substrate range and tolerate diverse functional groups. Drug molecules provide a good test of these attributes of a catalyst. A library of P450BM3 mutants developed from four base mutants with high activity for hydrocarbon oxidation produced human metabolites of a panel of drugs that included neutral (chlorzoxazone, testosterone), cationic (amitriptyline, lidocaine) and anionic (diclofenac, naproxen) compounds. No single mutant was active for all the tested drugs but multiple variants in the library showed high activity with each compound. The high conversions enabled full product characterization that led to the discovery of the new P450 reaction type of oxidative decarboxylation of an α-hydroxy carboxylic acid and the formation a protected imine from an amine, offering a novel route to α-functionalization of amines. The substrate range and varied product profiles suggest that this library of enzymes is a good basis for developing late-stage C-H activation catalysts.
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Affiliation(s)
- Xinkun Ren
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Rd., Oxford OX1 3QR (UK)
| | - Jake A Yorke
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Rd., Oxford OX1 3QR (UK)
| | - Emily Taylor
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Rd., Oxford OX1 3QR (UK)
| | - Ting Zhang
- College of Life Sciences and The State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071 (P. R. China)
| | - Weihong Zhou
- College of Life Sciences and The State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071 (P. R. China).
| | - Luet Lok Wong
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Rd., Oxford OX1 3QR (UK).
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Le-Huu P, Heidt T, Claasen B, Laschat S, Urlacher VB. Chemo-, Regio-, and Stereoselective Oxidation of the Monocyclic Diterpenoid β-Cembrenediol by P450 BM3. ACS Catal 2015. [DOI: 10.1021/cs5020404] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Priska Le-Huu
- Institute of Biochemistry, Heinrich-Heine University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Tanja Heidt
- Institute of Organic Chemistry, University Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Birgit Claasen
- Institute of Organic Chemistry, University Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Sabine Laschat
- Institute of Organic Chemistry, University Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Vlada B. Urlacher
- Institute of Biochemistry, Heinrich-Heine University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
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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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Monooxygenase, peroxidase and peroxygenase properties and reaction mechanisms of cytochrome P450 enzymes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 851:1-61. [PMID: 26002730 DOI: 10.1007/978-3-319-16009-2_1] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
This review examines the monooxygenase, peroxidase and peroxygenase properties and reaction mechanisms of cytochrome P450 (CYP) enzymes in bacterial, archaeal and mammalian systems. CYP enzymes catalyze monooxygenation reactions by inserting one oxygen atom from O2 into an enormous number and variety of substrates. The catalytic versatility of CYP stems from its ability to functionalize unactivated carbon-hydrogen (C-H) bonds of substrates through monooxygenation. The oxidative prowess of CYP in catalyzing monooxygenation reactions is attributed primarily to a porphyrin π radical ferryl intermediate known as Compound I (CpdI) (Por•+FeIV=O), or its ferryl radical resonance form (FeIV-O•). CYP-mediated hydroxylations occur via a consensus H atom abstraction/oxygen rebound mechanism involving an initial abstraction by CpdI of a H atom from the substrate, generating a highly-reactive protonated Compound II (CpdII) intermediate (FeIV-OH) and a carbon-centered alkyl radical that rebounds onto the ferryl hydroxyl moiety to yield the hydroxylated substrate. CYP enzymes utilize hydroperoxides, peracids, perborate, percarbonate, periodate, chlorite, iodosobenzene and N-oxides as surrogate oxygen atom donors to oxygenate substrates via the shunt pathway in the absence of NAD(P)H/O2 and reduction-oxidation (redox) auxiliary proteins. It has been difficult to isolate the historically elusive CpdI intermediate in the native NAD(P)H/O2-supported monooxygenase pathway and to determine its precise electronic structure and kinetic and physicochemical properties because of its high reactivity, unstable nature (t½~2 ms) and short life cycle, prompting suggestions for participation in monooxygenation reactions of alternative CYP iron-oxygen intermediates such as the ferric-peroxo anion species (FeIII-OO-), ferric-hydroperoxo species (FeIII-OOH) and FeIII-(H2O2) complex.
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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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Vredenburg G, den Braver-Sewradj S, van Vugt-Lussenburg BMA, Vermeulen NPE, Commandeur JNM, Vos JC. Activation of the anticancer drugs cyclophosphamide and ifosfamide by cytochrome P450 BM3 mutants. Toxicol Lett 2014; 232:182-92. [PMID: 25448283 DOI: 10.1016/j.toxlet.2014.11.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 10/27/2014] [Accepted: 11/03/2014] [Indexed: 11/17/2022]
Abstract
Cyclophosphamide (CPA) and ifosfamide (IFA) are widely used anticancer agents that require metabolic activation by cytochrome P450 (CYP) enzymes. While 4-hydroxylation yields DNA-alkylating and cytotoxic metabolites, N-dechloroethylation results in the generation of neuro- and nephrotoxic byproducts. Gene-directed enzyme prodrug therapies (GDEPT) have been suggested to facilitate local CPA and IFA bioactivation by expressing CYP enzymes within the tumor cells, thereby increasing efficacy. We screened bacterial CYP BM3 mutants, previously engineered to metabolize drug-like compounds, for their ability to catalyze 4-hydroxylation of CPA and IFA. Two CYP BM3 mutants showed very rapid initial bioactivation of CPA and IFA, followed by a slower phase of product formation. N-dechloroethylation by these mutants was very low (IFA) to undetectable (CPA). Using purified CYP BM3 as an extracellular bioactivation tool, cytotoxicity of CPA and IFA metabolism was confirmed in U2OS cells. This novel application of CYP BM3 possibly provides a clean and catalytically efficient alternative to liver microsomes or S9 for the study of CYP-mediated drug toxicity. To our knowledge, the observed rate of CPA and IFA 4-hydroxylation by these CYP BM3 mutants is the fastest reported to date, and might be of potential interest for CPA and IFA GDEPT.
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Affiliation(s)
- Galvin Vredenburg
- AIMMS-Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences (CPS), VU University Amsterdam, De Boelelaan 1083, Amsterdam 1081 HV, The Netherlands
| | - Shalenie den Braver-Sewradj
- AIMMS-Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences (CPS), VU University Amsterdam, De Boelelaan 1083, Amsterdam 1081 HV, The Netherlands
| | | | - Nico P E Vermeulen
- AIMMS-Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences (CPS), VU University Amsterdam, De Boelelaan 1083, Amsterdam 1081 HV, The Netherlands
| | - Jan N M Commandeur
- AIMMS-Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences (CPS), VU University Amsterdam, De Boelelaan 1083, Amsterdam 1081 HV, The Netherlands
| | - J Chris Vos
- AIMMS-Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences (CPS), VU University Amsterdam, De Boelelaan 1083, Amsterdam 1081 HV, The Netherlands.
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50
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Oostenbrink C. Structure‐Based Methods for Predicting the Sites and Products of Metabolism. ACTA ACUST UNITED AC 2014. [DOI: 10.1002/9783527673261.ch10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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