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Fansher D, Besna JN, Fendri A, Pelletier JN. Choose Your Own Adventure: A Comprehensive Database of Reactions Catalyzed by Cytochrome P450 BM3 Variants. ACS Catal 2024; 14:5560-5592. [PMID: 38660610 PMCID: PMC11036407 DOI: 10.1021/acscatal.4c00086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 03/11/2024] [Accepted: 03/12/2024] [Indexed: 04/26/2024]
Abstract
Cytochrome P450 BM3 monooxygenase is the topic of extensive research as many researchers have evolved this enzyme to generate a variety of products. However, the abundance of information on increasingly diversified variants of P450 BM3 that catalyze a broad array of chemistry is not in a format that enables easy extraction and interpretation. We present a database that categorizes variants by their catalyzed reactions and includes details about substrates to provide reaction context. This database of >1500 P450 BM3 variants is downloadable and machine-readable and includes instructions to maximize ease of gathering information. The database allows rapid identification of commonly reported substitutions, aiding researchers who are unfamiliar with the enzyme in identifying starting points for enzyme engineering. For those actively engaged in engineering P450 BM3, the database, along with this review, provides a powerful and user-friendly platform to understand, predict, and identify the attributes of P450 BM3 variants, encouraging the further engineering of this enzyme.
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Affiliation(s)
- Douglas
J. Fansher
- Chemistry
Department, Université de Montréal, Montreal, QC, Canada H2V 0B3
- PROTEO,
The Québec Network for Research on Protein Function, Engineering,
and Applications, 201
Av. du Président-Kennedy, Montréal, QC, Canada H2X 3Y7
- CGCC,
Center in Green Chemistry and Catalysis, Montreal, QC, Canada H2V 0B3
| | - Jonathan N. Besna
- PROTEO,
The Québec Network for Research on Protein Function, Engineering,
and Applications, 201
Av. du Président-Kennedy, Montréal, QC, Canada H2X 3Y7
- CGCC,
Center in Green Chemistry and Catalysis, Montreal, QC, Canada H2V 0B3
- Department
of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC, Canada H3T 1J4
| | - Ali Fendri
- Chemistry
Department, Université de Montréal, Montreal, QC, Canada H2V 0B3
- PROTEO,
The Québec Network for Research on Protein Function, Engineering,
and Applications, 201
Av. du Président-Kennedy, Montréal, QC, Canada H2X 3Y7
- CGCC,
Center in Green Chemistry and Catalysis, Montreal, QC, Canada H2V 0B3
| | - Joelle N. Pelletier
- Chemistry
Department, Université de Montréal, Montreal, QC, Canada H2V 0B3
- PROTEO,
The Québec Network for Research on Protein Function, Engineering,
and Applications, 201
Av. du Président-Kennedy, Montréal, QC, Canada H2X 3Y7
- CGCC,
Center in Green Chemistry and Catalysis, Montreal, QC, Canada H2V 0B3
- Department
of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC, Canada H3T 1J4
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2
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Schottlender G, Prieto JM, Clemente C, Schuster CD, Dumas V, Fernández Do Porto D, Martí MA. Bacterial cytochrome P450s: a bioinformatics odyssey of substrate discovery. Front Microbiol 2024; 15:1343029. [PMID: 38384262 PMCID: PMC10879549 DOI: 10.3389/fmicb.2024.1343029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 01/23/2024] [Indexed: 02/23/2024] Open
Abstract
Bacterial P450 cytochromes (BacCYPs) are versatile heme-containing proteins responsible for oxidation reactions on a wide range of substrates, contributing to the production of valuable natural products with limitless biotechnological potential. While the sequencing of microbial genomes has provided a wealth of BacCYP sequences, functional characterization lags behind, hindering our understanding of their roles. This study employs a comprehensive approach to predict BacCYP substrate specificity, bridging the gap between sequence and function. We employed an integrated approach combining sequence and functional data analysis, genomic context exploration, 3D structural modeling with molecular docking, and phylogenetic clustering. The research begins with an in-depth analysis of BacCYP sequence diversity and structural characteristics, revealing conserved motifs and recurrent residues in the active site. Phylogenetic analysis identifies distinct groups within the BacCYP family based on sequence similarity. However, our study reveals that sequence alone does not consistently predict substrate specificity, necessitating additional perspectives. The study delves into the genetic context of BacCYPs, utilizing neighboring gene information to infer potential substrates, a method proven very effective in many cases. Molecular docking is employed to assess BacCYP-substrate interactions, confirming potential substrates and providing insights into selectivity. Finally, a comprehensive strategy is proposed for predicting BacCYP substrates, involving all the evaluated approaches. The effectiveness of this strategy is demonstrated with two case studies, highlighting its potential for substrate discovery.
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Affiliation(s)
- Gustavo Schottlender
- Facultad de Ciencias Exactas y Naturales, Instituto de Cálculo, Universidad de Buenos Aires, CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Juan Manuel Prieto
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Buenos Aires, Argentina
| | - Camila Clemente
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Buenos Aires, Argentina
| | - Claudio David Schuster
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Buenos Aires, Argentina
| | - Victoria Dumas
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA), Buenos Aires, Argentina
| | - Darío Fernández Do Porto
- Facultad de Ciencias Exactas y Naturales, Instituto de Cálculo, Universidad de Buenos Aires, CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA), Buenos Aires, Argentina
| | - Marcelo Adrian Martí
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Buenos Aires, Argentina
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA), Buenos Aires, Argentina
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Regiospecific Oxidation of Chlorobenzene to 4-Chlororesorcinol, Chlorohydroquinone, 3-Chlorocatechol and 4-Chlorocatechol by Engineered Toluene o-Xylene Monooxygenases. Appl Environ Microbiol 2022; 88:e0035822. [PMID: 35736230 PMCID: PMC9275245 DOI: 10.1128/aem.00358-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Toluene o-xylene monooxygenase (ToMO) was found to oxidize chlorobenzene to form 2-chlorophenol (2-CP, 4%), 3-CP (12%), and 4-CP (84%) with a total product formation rate of 1.2 ± 0.17 nmol/min/mg protein. It was also discovered that ToMO forms 4-chlorocatechol (4-CC) from 3-CP and 4-CP with initial rates of 0.54 ± 0.10 and 0.40 ± 0.04 nmol/min/mg protein, respectively, and chlorohydroquinone (CHQ, 13%), 4-chlororesorcinol (4-CR, 3%), and 3-CC (84%) from 2-CP with an initial product formation rate of 1.1 ± 0.32 nmol/min/mg protein. To increase the oxidation rate and alter the oxidation regiospecificity of chloroaromatics, as well as to study the roles of active site residues L192 and A107 of the alpha hydroxylase fragment of ToMO (TouA), we used the saturation mutagenesis approach of protein engineering. Thirteen TouA variants were isolated, among which some of the best substitutions uncovered here have never been studied before. Specifically, TouA variant L192V was identified which had 1.8-, 1.4-, 2.4-, and 4.8-fold faster hydroxylation activity toward chlorobenzene, 2-CP, 3-CP, and 4-CP, respectively, compared to the native ToMO. The L192V variant also had the regiospecificity of chlorobenzene changed from 4% to 13% 2-CP and produced the novel product 3-CC (4%) from 3-CP. Most of the isolated variants were identified to change the regiospecificity of oxidation. For example, compared to the native ToMO, variants A107T, A107N, and A107M produced 6.3-, 7.0-, and 7.3-fold more 4-CR from 2-CP, respectively, and variants A107G and A107G/L192V produced 3-CC (33 and 39%, respectively) from 3-CP whereas native ToMO did not. IMPORTANCE Chlorobenzene is a commonly used toxic solvent and listed as a priority environmental pollutant by the US Environmental Protection Agency. Here, we report that Escherichia coli TG1 cells expressing toluene o-xylene monooxygenase (ToMO) can successfully oxidize chlorobenzene to form dihydroxy chloroaromatics, which are valuable industrial compounds. ToMO performs this at room temperature in water using only molecular oxygen and a cofactor supplied by the cells. Using protein engineering techniques, we also isolated ToMO variants with enhanced oxidation activity as well as fine-tuned regiospecificities which make direct microbial oxygenations even more attractive. The significance of this work lies in the ability to degrade environmental pollutants while at the same time producing valuable chemicals using environmentally benign biological methods rather than expensive, complex chemical processes.
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Maxel S, King E, Zhang Y, Luo R, Li H. Leveraging Oxidative Stress to Regulate Redox Balance-Based, In Vivo Growth Selections for Oxygenase Engineering. ACS Synth Biol 2020; 9:3124-3133. [PMID: 32966747 PMCID: PMC10441625 DOI: 10.1021/acssynbio.0c00380] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Directed evolution methods based on high-throughput growth selection enable efficient discovery of enzymes with improved function in vivo. High-throughput selection is particularly useful when engineering oxygenases, which are sensitive to structural perturbations and prone to uncoupled activity. In this work, we combine the principle that reactive oxygen species (ROS) produced by uncoupled oxygenase activity are detrimental to cell fitness with a redox balance-based growth selection method for oxygenase engineering that enables concurrent advancement in catalytic activity and coupling efficiency. As a proof-of-concept, we engineered P450-BM3 for degradation of acenaphthene (ACN), a recalcitrant environmental pollutant. Selection of site-saturation mutagenesis libraries in E. coli strain MX203 identified P450-BM3 variants GVQ-AL and GVQ-D222N, which have both improved coupling efficiency and catalytic activity compared to the starting variant. Computational modeling indicates that the discovered mutations cooperatively optimize binding pocket shape complementarity to ACN, and shift the protein's conformational dynamics to favor the lid-closed, catalytically competent state. We further demonstrated that the selective pressure on coupling efficiency can be tuned by modulating cellular ROS defense mechanisms.
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5
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Mechanism of deep eutectic solvents enhancing catalytic function of cytochrome P450 enzymes in biosynthesis and organic synthesis. J Biotechnol 2020; 323:264-273. [PMID: 32653640 DOI: 10.1016/j.jbiotec.2020.07.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 07/03/2020] [Accepted: 07/08/2020] [Indexed: 11/23/2022]
Abstract
Indigo is an insoluble blue dye, which generates serious pollution in its production process. Increasing focus has come to the biosynthesis of indigo that are more environment-preserved and high-efficient. Hence, this study was designed to explore the specific role of various deep eutectic solvents (DESs) on cytochromeP45-BM-3 catalyzing indole to produce indigo. DESs were synthesized by heating and stirring. The structure of the solvent was analyzed by nuclear magnetic resonance (NMR) and fourier transform infrared spectrum (FT-IR), and the relationship between the viscosity, density and refractive index of the solvent, and the water content of the solvent was examined. Circular dichroism spectrometer was used to detect the tertiary structure of the enzyme protein. The effect of solvent type, concentration, pH, temperature, and water content on the catalytic activity and stability of P450 BM-3 was measured using an ultraviolet spectrophotometer. A new solvent biphasic system was established using DESs and buffers, and indigo was prepared using recombinant E. coli-biocatalyzed indole. DESs were low-melting eutectics formed by molecules interaction of components through hydrogen bonding. The physical properties of DESs such as density, viscosity, and refractive index varied with water content and temperature of the solvent. The pH, water content, and temperature of DESs were positively correlated with the catalytic activity of P450 BM-3. To sum up, DESs can improve the catalytic activity and thermal stability of P450 BM-3. Indigo can be efficiently prepared using the DESs-buffer biphasic system.
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Abstract
Rhododendrol (RD) is a naturally occurring phenolic compound found in many plants. Tyrosinase (Ty) converts RD to RD-catechol and subsequently RD-quinone via two-step oxidation reactions, after which RD-melanin forms spontaneously from RD-quinone. RD is cytotoxic in melanocytes and lung cancer cells, but not in keratinocytes and fibroblasts. However, the function of RD metabolites has not been possible to investigate due to the lack of available high purity metabolites. In this study, an enzymatic strategy for RD-catechol production was devised using engineered cytochrome P450 102A1 (CYP102A1) and Ty, and the product was analyzed using high-performance liquid chromatography (HPLC), LC-MS, and NMR spectroscopy. Engineered CYP102A1 regioselectively produced RD-catechol via hydroxylation at the ortho position of RD. Although RD-quinone was subsequently formed by two step oxidation in Ty catalyzed reactions, L-ascorbic acid (LAA) inhibited RD-quinone formation and contributed to regioselective production of RD-catechol. When LAA was present, the productivity of RD-catechol by Ty was 5.3-fold higher than that by engineered CYP102A1. These results indicate that engineered CYP102A1 and Ty can be used as effective biocatalysts to produce hydroxylated products, and Ty is a more cost-effective biocatalyst for industrial applications than engineered CYP102A1.
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7
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Regioselective Hydroxylation of Naringin Dihydrochalcone to Produce Neoeriocitrin Dihydrochalcone by CYP102A1 (BM3) Mutants. Catalysts 2020. [DOI: 10.3390/catal10080823] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Naringin dihydrochalcone (DC) is originally derived from the flavonoid naringin, which occurs naturally in citrus fruits, especially in grapefruit. It is used as an artificial sweetener with a strong antioxidant activity with potential applications in food and pharmaceutical fields. At present, enzymatic and chemical methods to make products of naringin DC by hydroxylation reactions have not been developed. Here, an enzymatic strategy for the efficient synthesis of potentially valuable products from naringin DC, a glycoside of phloretin, was developed using Bacillus megaterium CYP102A1 monooxygenase. The major product was identified to be neoeriocitrin DC by NMR and LC-MS analyses. Sixty-seven mutants of CYP102A1 were tested for hydroxylation of naringin DC to produce neoeriocitrin DC. Six mutants with high activity were selected to determine the kinetic parameters and total turnover numbers (TTNs). The kcat value of the most active mutant was 11 min−1 and its TTN was 315. The productivity of neoeriocitrin DC production increased up to 1.1 mM h−1, which corresponds to 0.65 g L−1 h−1. In this study, we achieved a regioselective hydroxylation of naringin DC to produce neoeriocitrin DC.
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8
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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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Rousseau O, Ebert MCCJC, Quaglia D, Fendri A, Parisien AH, Besna JN, Iyathurai S, Pelletier JN. Indigo Formation and Rapid NADPH Consumption Provide Robust Prediction of Raspberry Ketone Synthesis by Engineered Cytochrome P450 BM3. ChemCatChem 2019. [DOI: 10.1002/cctc.201901974] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Olivier Rousseau
- Department of ChemistryUniversité de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
- Center for Green Chemistry and Catalysis (CGCC)Université de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
- PROTEOThe Québec Network for Research on Protein Function Engineering and Applications Québec QC−G1V 0A6 Canada
| | - Maximilian C. C. J. C. Ebert
- Center for Green Chemistry and Catalysis (CGCC)Université de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
- PROTEOThe Québec Network for Research on Protein Function Engineering and Applications Québec QC−G1V 0A6 Canada
- Department of BiochemistryUniversité de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
| | - Daniela Quaglia
- Department of ChemistryUniversité de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
- Center for Green Chemistry and Catalysis (CGCC)Université de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
- PROTEOThe Québec Network for Research on Protein Function Engineering and Applications Québec QC−G1V 0A6 Canada
| | - Ali Fendri
- Department of ChemistryUniversité de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
- Center for Green Chemistry and Catalysis (CGCC)Université de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
- PROTEOThe Québec Network for Research on Protein Function Engineering and Applications Québec QC−G1V 0A6 Canada
| | - Adem H. Parisien
- Center for Green Chemistry and Catalysis (CGCC)Université de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
- PROTEOThe Québec Network for Research on Protein Function Engineering and Applications Québec QC−G1V 0A6 Canada
- Department of BiochemistryUniversité de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
| | - Jonathan N. Besna
- Center for Green Chemistry and Catalysis (CGCC)Université de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
- PROTEOThe Québec Network for Research on Protein Function Engineering and Applications Québec QC−G1V 0A6 Canada
- Department of BiochemistryUniversité de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
| | - Saathanan Iyathurai
- Center for Green Chemistry and Catalysis (CGCC)Université de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
- PROTEOThe Québec Network for Research on Protein Function Engineering and Applications Québec QC−G1V 0A6 Canada
- Department of BiochemistryUniversité de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
| | - Joelle N. Pelletier
- Department of ChemistryUniversité de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
- Center for Green Chemistry and Catalysis (CGCC)Université de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
- PROTEOThe Québec Network for Research on Protein Function Engineering and Applications Québec QC−G1V 0A6 Canada
- Department of BiochemistryUniversité de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
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Regioselective hydroxylation pathway of tenatoprazole to produce human metabolites by Bacillus megaterium CYP102A1. Process Biochem 2019. [DOI: 10.1016/j.procbio.2019.09.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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11
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Feng WY, Wen J, Stauber K. In vitro Drug Metabolism Investigation of 7-Ethoxycoumarin in Human, Monkey, Dog and Rat Hepatocytes by High Resolution LC-MS/MS. Drug Metab Lett 2018; 12:33-53. [PMID: 29669508 PMCID: PMC6416465 DOI: 10.2174/1872312812666180418142056] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Revised: 03/18/2018] [Accepted: 04/12/2018] [Indexed: 11/22/2022]
Abstract
Background: Recently, it has been an increasing concern on the bioactivation and adverse re-actions associated with consumption of herbal and nature products. 7-Ethoxycoumarin is one of coumarin family compounds, but little information is available regarding its potential reactive metabolites. Method: 7-ethoxylcoumarin was incubated individually with human, monkey, dog and rat hepatocytes for 2 hr, metabolites were detected, identified and characterized using high resolution liquid chromagraphy – tandem mass spectrometry. Results: Twenty-eight metabolites (M1 - M28) were detected and identified. O-deethylation, glucuronida-tion, sulfation, oxygenation, oxidative ring-opening, hydrogenation, glutathionation, dehydrogenation, cysteination, glucosidation, methylation, and hydrolysis were observed. At least sixteen metabolites not reported previously, were newly identified. M1 (O-deethylation, mono-oxygenation and glucuronidation), M3 (O-deethylation and glucuronidation), M5 (hydrolysis and mono-oxygenation), M14 (O-deethylation), M16 (hydrolysis), M22 (oxidative ring-opening and oxygenation) and M27 (mono-oxygenation) exhibited high mass spectrometric responses in human hepatocytes. M3, M5, M8, M13 (mono-oxygenation), M14, M16, M18 (O-deethylation and sulfation), M22 and M27 exhibited high mass spectrometric responses in monkey hepatocytes. M14, M16, M18, M20 (glutathionation and dehy-drogenation) and M27 exhibited high mass spectrometric responses in dog hepatocytes. M1 (O-deethylation, mono-oxygenation and glucuronidation), M3, M5, M13, M14, M16, M17 (cysteination), M18, M20, and M22 exhibited high mass spectrometric responses in rat hepatocytes. Conclusion: Most of new metabolites via oxidative ring-opening and glutathionation were identified. Species differences in metabolism of 7-ethoxylcoumarin in hepatocytes were observed. The analysis of metabolites suggests that 7-ethoxylcoumarin may undergo 3,4-epoxidation responsible for formation of glutathione and its derived cysteine conjugates, carboxylic acid and its glucuronides, glucosides and sul-fate.
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Affiliation(s)
- Wan-Yong Feng
- Drug Metabolism and Pharmacokinetics, Dart NeuroScience, San Diego, CA 92131, United States
| | - Jenny Wen
- Drug Metabolism and Pharmacokinetics, Dart NeuroScience, San Diego, CA 92131, United States
| | - Kathe Stauber
- Drug Metabolism and Pharmacokinetics, Dart NeuroScience, San Diego, CA 92131, United States
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12
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Jin M, Zhang X, Zhen Q, He Y, Chen X, Lyu W, Han R, Ding M. An electrochemical sensor for indole in plasma based on MWCNTs-chitosan modified screen-printed carbon electrode. Biosens Bioelectron 2017; 98:392-397. [DOI: 10.1016/j.bios.2017.07.018] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 06/27/2017] [Accepted: 07/07/2017] [Indexed: 11/29/2022]
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13
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Ebert MCCJC, Guzman Espinola J, Lamoureux G, Pelletier JN. Substrate-Specific Screening for Mutational Hotspots Using Biased Molecular Dynamics Simulations. ACS Catal 2017. [DOI: 10.1021/acscatal.7b02634] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Maximilian C. C. J. C. Ebert
- Département
de Biochimie and Center for Green Chemistry and Catalysis (CGCC), Université de Montréal, Montréal, QC H3T 1J4, Canada
- PROTEO, The Québec
Network for Research on Protein Function, Engineering and Applications, Québec, QC G1V 0A6, Canada
| | - Joaquin Guzman Espinola
- Département
de Biochimie and Center for Green Chemistry and Catalysis (CGCC), Université de Montréal, Montréal, QC H3T 1J4, Canada
- PROTEO, The Québec
Network for Research on Protein Function, Engineering and Applications, Québec, QC G1V 0A6, Canada
| | - Guillaume Lamoureux
- PROTEO, The Québec
Network for Research on Protein Function, Engineering and Applications, Québec, QC G1V 0A6, Canada
- Department
of Chemistry and Biochemistry and Centre for Research in Molecular
Modeling (CERMM), Concordia University, Montréal, QC H4B 1R6, Canada
| | - Joelle N. Pelletier
- Département
de Biochimie and Center for Green Chemistry and Catalysis (CGCC), Université de Montréal, Montréal, QC H3T 1J4, Canada
- PROTEO, The Québec
Network for Research on Protein Function, Engineering and Applications, Québec, QC G1V 0A6, Canada
- Département
de Chimie, Université de Montréal, Montréal, QC H3T 1J4, Canada
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14
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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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15
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Highly regioselective hydroxylation of polydatin, a resveratrol glucoside, for one-step synthesis of astringin, a piceatannol glucoside, by P450 BM3. Enzyme Microb Technol 2017; 97:34-42. [DOI: 10.1016/j.enzmictec.2016.11.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 11/01/2016] [Accepted: 11/07/2016] [Indexed: 11/18/2022]
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16
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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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17
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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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18
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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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19
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Zeng L, Zhou Y, Gui J, Fu X, Mei X, Zhen Y, Ye T, Du B, Dong F, Watanabe N, Yang Z. Formation of Volatile Tea Constituent Indole During the Oolong Tea Manufacturing Process. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2016; 64:5011-9. [PMID: 27263428 DOI: 10.1021/acs.jafc.6b01742] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Indole is a characteristic volatile constituent in oolong tea. Our previous study indicated that indole was mostly accumulated at the turn over stage of oolong tea manufacturing process. However, formation of indole in tea leaves remains unknown. In this study, one tryptophan synthase α-subunit (TSA) and three tryptophan synthase β-subunits (TSBs) from tea leaves were isolated, cloned, sequenced, and functionally characterized. Combination of CsTSA and CsTSB2 recombinant protein produced in Escherichia coli exhibited the ability of transformation from indole-3-glycerol phosphate to indole. CsTSB2 was highly expressed during the turn over process of oolong tea. Continuous mechanical damage, simulating the turn over process, significantly enhanced the expression level of CsTSB2 and amount of indole. These suggested that accumulation of indole in oolong tea was due to the activation of CsTSB2 by continuous wounding stress from the turn over process. Black teas contain much less indole, although wounding stress is also involved in the manufacturing process. Stable isotope labeling indicated that tea leaf cell disruption from the rolling process of black tea did not lead to the conversion of indole, but terminated the synthesis of indole. Our study provided evidence concerning formation of indole in tea leaves for the first time.
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Affiliation(s)
- Lanting Zeng
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences , Xingke Road 723, Tianhe District, Guangzhou 510650, China
- University of Chinese Academy of Sciences , No.19A Yuquan Road, Beijing 100049, China
| | - Ying Zhou
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences , Xingke Road 723, Tianhe District, Guangzhou 510650, China
| | - Jiadong Gui
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences , Xingke Road 723, Tianhe District, Guangzhou 510650, China
- University of Chinese Academy of Sciences , No.19A Yuquan Road, Beijing 100049, China
| | - Xiumin Fu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences , Xingke Road 723, Tianhe District, Guangzhou 510650, China
| | - Xin Mei
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences , Xingke Road 723, Tianhe District, Guangzhou 510650, China
| | - Yunpeng Zhen
- Waters Technologies (Shanghai) Ltd. , No. 1000 Jinhai Road, Shanghai 201203, China
| | - Tingxiang Ye
- Waters Technologies (Shanghai) Ltd. , No. 1000 Jinhai Road, Shanghai 201203, China
| | - Bing Du
- College of Food, South China Agricultural University , Wushan Road, Tianhe District, Guangzhou 510642, China
- Juxiangyuan Health Food (Zhongshan) Co.,Ltd. , No. 13, Yandong Second Road, Torch Development Zone, Zhongshan 528400, China
| | - Fang Dong
- Guangdong Food and Drug Vocational College , Longdongbei Road 321, Tianhe District, Guangzhou 510520, China
| | - Naoharu Watanabe
- Graduate School of Science and Technology, Shizuoka University , 3-5-1 Johoku, Naka-ku, Hamamatsu 432-8561, Japan
| | - Ziyin Yang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences , Xingke Road 723, Tianhe District, Guangzhou 510650, China
- University of Chinese Academy of Sciences , No.19A Yuquan Road, Beijing 100049, China
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20
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Roberts AG, Katayama J, Kaspera R, Ledwitch KV, Le Trong I, Stenkamp RE, Thompson JA, Totah RA. The role of cytochrome P450 BM3 phenylalanine-87 and threonine-268 in binding organic hydroperoxides. Biochim Biophys Acta Gen Subj 2016; 1860:669-77. [DOI: 10.1016/j.bbagen.2015.12.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 12/09/2015] [Accepted: 12/18/2015] [Indexed: 11/28/2022]
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21
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Cook D, Finnigan J, Cook K, Black G, Charnock S. Cytochromes P450. INSIGHTS INTO ENZYME MECHANISMS AND FUNCTIONS FROM EXPERIMENTAL AND COMPUTATIONAL METHODS 2016; 105:105-26. [DOI: 10.1016/bs.apcsb.2016.07.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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22
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Kelly PP, Eichler A, Herter S, Kranz DC, Turner NJ, Flitsch SL. Active site diversification of P450cam with indole generates catalysts for benzylic oxidation reactions. Beilstein J Org Chem 2015; 11:1713-1720. [PMID: 26664590 PMCID: PMC4660908 DOI: 10.3762/bjoc.11.186] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 09/03/2015] [Indexed: 12/27/2022] Open
Abstract
Cytochrome P450 monooxygenases are useful biocatalysts for C-H activation, and there is a need to expand the range of these enzymes beyond what is naturally available. A panel of 93 variants of active self-sufficient P450cam[Tyr96Phe]-RhFRed fusion enzymes with a broad diversity in active site amino acids was developed by screening a large mutant library of 16,500 clones using a simple, highly sensitive colony-based colorimetric screen against indole. These mutants showed distinct fingerprints of activity not only when screened in oxidations of substituted indoles but also for unrelated oxidations such as benzylic hydroxylations.
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Affiliation(s)
- Paul P Kelly
- School of Chemistry & Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, M1 7DN, Manchester, United Kingdom
| | - Anja Eichler
- School of Chemistry & Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, M1 7DN, Manchester, United Kingdom
| | - Susanne Herter
- School of Chemistry & Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, M1 7DN, Manchester, United Kingdom
| | - David C Kranz
- School of Chemistry & Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, M1 7DN, Manchester, United Kingdom
| | - Nicholas J Turner
- School of Chemistry & Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, M1 7DN, Manchester, United Kingdom
| | - Sabine L Flitsch
- School of Chemistry & Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, M1 7DN, Manchester, United Kingdom
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23
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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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24
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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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25
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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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26
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Regioselectivity-driven evolution of CYP102D1 for improved synthesis of 3′-ortho-dihydroxyisoflavone. Enzyme Microb Technol 2015; 71:20-7. [DOI: 10.1016/j.enzmictec.2015.01.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 01/14/2015] [Accepted: 01/16/2015] [Indexed: 01/07/2023]
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27
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Directed evolution of cytochrome P450 enzymes for biocatalysis: exploiting the catalytic versatility of enzymes with relaxed substrate specificity. Biochem J 2015; 467:1-15. [DOI: 10.1042/bj20141493] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Cytochrome P450 enzymes are renowned for their ability to insert oxygen into an enormous variety of compounds with a high degree of chemo- and regio-selectivity under mild conditions. This property has been exploited in Nature for an enormous variety of physiological functions, and representatives of this ancient enzyme family have been identified in all kingdoms of life. The catalytic versatility of P450s makes them well suited for repurposing for the synthesis of fine chemicals such as drugs. Although these enzymes have not evolved in Nature to perform the reactions required for modern chemical industries, many P450s show relaxed substrate specificity and exhibit some degree of activity towards non-natural substrates of relevance to applications such as drug development. Directed evolution and other protein engineering methods can be used to improve upon this low level of activity and convert these promiscuous generalist enzymes into specialists capable of mediating reactions of interest with exquisite regio- and stereo-selectivity. Although there are some notable successes in exploiting P450s from natural sources in metabolic engineering, and P450s have been proven repeatedly to be excellent material for engineering, there are few examples to date of practical application of engineered P450s. The purpose of the present review is to illustrate the progress that has been made in altering properties of P450s such as substrate range, cofactor preference and stability, and outline some of the remaining challenges that must be overcome for industrial application of these powerful biocatalysts.
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28
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Salamanca D, Engesser KH. Isolation and characterization of two novel strains capable of using cyclohexane as carbon source. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2014; 21:12757-12766. [PMID: 24969427 DOI: 10.1007/s11356-014-3206-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Accepted: 06/12/2014] [Indexed: 06/03/2023]
Abstract
Two strains capable of degrading cyclohexane were isolated from the soil and sludge of the wastewater treatment plant of the University of Stuttgart and a biotrickling filter system. The strains were classified as gram negative and identified as Acidovorax sp. CHX100 and Chelatococcus sp. CHX1100. Both strains have demonstrated the capability to degrade cycloalkanes (C5-C8), while only strain CHX1100 used as well short linear n-alkanes (C5-C8) as the sole source of carbon and energy. The growth of Acidovorax sp. CHX100 using cyclohexane was much faster compared to Chelatococcus sp. CHX1100. Degenerated primers were optimized from a set sequences of cyclohexanol dehydrogenase genes (chnA) as well as cyclohexanone monooxygenases (chnB) and used to amplify the gene cluster, which encodes the conversion of cyclohexanol to caprolactone. Phylogenetic analysis has indicated that the two gene clusters belong to different groups. The cyclohexane monooxygenase-induced activity which oxidizes also indole to 5-hydroxyindole has indicated the presence of a CYP-type system monooxygenase involved in the transformation of cyclohexane to cyclohexanol.
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Affiliation(s)
- Diego Salamanca
- Institute for Sanitary Engineering, Water Quality and Solid Waste Management, University of Stuttgart, Bandtäle 2, 70569, Stuttgart, Germany,
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Lee GY, Kim HM, Ma SH, Park SH, Joung YH, Yun CH. Heterologous expression and functional characterization of the NADPH-cytochrome P450 reductase from Capsicum annuum. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2014; 82:116-22. [PMID: 24935229 DOI: 10.1016/j.plaphy.2014.05.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 05/20/2014] [Indexed: 05/27/2023]
Abstract
Two NADPH-cytochrome P450 reductase (CPR) genes (CaCPR1 and CaCPR2) were isolated from hot pepper (Capsicum annuum L. cv. Bukang). At the red ripe stage, the expression level of CaCPR1 was more than 6-fold greater than that in leaves or flowers. It gradually increased during fruit ripening. The CaCPR2 gene seemed to be expressed constitutively in all of the tested tissues. To investigate the enzymatic properties of CaCPR1, the cDNA of CaCPR1 was heterologously expressed in Escherichia coli without any modification of amino acid sequences, and CaCPR1 was purified. The enzymatic properties of CaCPR1 were confirmed using cytochrome c and cytochrome b5 as protein substrates. The CaCPR1 could support human CYP1A2-catalyzed reaction. It also reduced tetrazolium salts and ferricyanide. These results show that CaCPR1 is the major CPR in most hot pepper tissues. It is suggested that the CaCPR1 can be used a prototype for studying biological functions and biotechnological applications of plant CPRs.
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Affiliation(s)
- Ga-Young Lee
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 500-757, Republic of Korea
| | - Hyun Min Kim
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 500-757, Republic of Korea
| | - Sang Hoon Ma
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 500-757, Republic of Korea
| | - Se Hee Park
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 500-757, Republic of Korea
| | - Young Hee Joung
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 500-757, Republic of Korea.
| | - Chul-Ho Yun
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 500-757, Republic of Korea.
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Cha GS, Ryu SH, Ahn T, Yun CH. Regioselective hydroxylation of 17β-estradiol by mutants of CYP102A1 from Bacillus megaterium. Biotechnol Lett 2014; 36:2501-6. [DOI: 10.1007/s10529-014-1628-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 08/06/2014] [Indexed: 10/24/2022]
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Ryu SH, Park BY, Kim SY, Park SH, Jung HJ, Park M, Park KD, Ahn T, Kang HS, Yun CH. Regioselective hydroxylation of omeprazole enantiomers by bacterial CYP102A1 mutants. Drug Metab Dispos 2014; 42:1493-7. [PMID: 25008345 DOI: 10.1124/dmd.114.058636] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
A large set of Bacillus megaterium CYP102A1 mutants are known to metabolize various drugs to form human metabolites. Omeprazole (OMP), a proton pump inhibitor, has been widely used as an acid inhibitory agent for the treatment of gastric acid hypersecretion disorders. It is primarily metabolized by human CYP2C19 and CYP3A4 to 5'-OH OMP and a sulfone product, respectively. It was recently reported that several CYP102A1 mutants can oxidize racemic and S-OMP to 5'-OH OMP and that these mutants can further oxidize 5'-OH racemic OMP to 5'-COOH OMP. Here, we report that the S- and R-enantiomers of OMP are hydroxylated by 26 mutants of CYP102A1 to produce 1 major metabolite (5'-OH OMP) regardless of the chirality of the parent substrates. Although the binding of R-OMP to the CYP102A1 active site caused a more apparent change of heme environment compared with binding of S-OMP, there was no correlation between the spectral change upon substrate binding and catalytic activity of either enantiomer. The 5'-OH OMP produced from racemic, S-, and R-OMP could be obtained with a high conversion rate and high selectivity when the triple R47L/F87V/L188Q mutant was used. These results suggest that bacterial CYP102A1 mutants can be used to produce the human metabolite 5'-OH OMP from both the S- and R-enantiomers of OMP.
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Affiliation(s)
- Sang Hoon Ryu
- School of Biological Sciences and Technology (S.H.R., B.-Y.P., S.-Y.K, S.-H.P., H.-J.J., M.P., H.-S.K., C.-H.Y.), and Department of Biochemistry, College of Veterinary Medicine (T.A.), Chonnam National University, Gwangju, Republic of Korea; and Gwangju Center, Korea Basic Science Institute, Gwangju, Republic of Korea (K.D.P.)
| | - Bo-Yeon Park
- School of Biological Sciences and Technology (S.H.R., B.-Y.P., S.-Y.K, S.-H.P., H.-J.J., M.P., H.-S.K., C.-H.Y.), and Department of Biochemistry, College of Veterinary Medicine (T.A.), Chonnam National University, Gwangju, Republic of Korea; and Gwangju Center, Korea Basic Science Institute, Gwangju, Republic of Korea (K.D.P.)
| | - So-Young Kim
- School of Biological Sciences and Technology (S.H.R., B.-Y.P., S.-Y.K, S.-H.P., H.-J.J., M.P., H.-S.K., C.-H.Y.), and Department of Biochemistry, College of Veterinary Medicine (T.A.), Chonnam National University, Gwangju, Republic of Korea; and Gwangju Center, Korea Basic Science Institute, Gwangju, Republic of Korea (K.D.P.)
| | - Sun-Ha Park
- School of Biological Sciences and Technology (S.H.R., B.-Y.P., S.-Y.K, S.-H.P., H.-J.J., M.P., H.-S.K., C.-H.Y.), and Department of Biochemistry, College of Veterinary Medicine (T.A.), Chonnam National University, Gwangju, Republic of Korea; and Gwangju Center, Korea Basic Science Institute, Gwangju, Republic of Korea (K.D.P.)
| | - Hyun-Jin Jung
- School of Biological Sciences and Technology (S.H.R., B.-Y.P., S.-Y.K, S.-H.P., H.-J.J., M.P., H.-S.K., C.-H.Y.), and Department of Biochemistry, College of Veterinary Medicine (T.A.), Chonnam National University, Gwangju, Republic of Korea; and Gwangju Center, Korea Basic Science Institute, Gwangju, Republic of Korea (K.D.P.)
| | - Min Park
- School of Biological Sciences and Technology (S.H.R., B.-Y.P., S.-Y.K, S.-H.P., H.-J.J., M.P., H.-S.K., C.-H.Y.), and Department of Biochemistry, College of Veterinary Medicine (T.A.), Chonnam National University, Gwangju, Republic of Korea; and Gwangju Center, Korea Basic Science Institute, Gwangju, Republic of Korea (K.D.P.)
| | - Ki Deok Park
- School of Biological Sciences and Technology (S.H.R., B.-Y.P., S.-Y.K, S.-H.P., H.-J.J., M.P., H.-S.K., C.-H.Y.), and Department of Biochemistry, College of Veterinary Medicine (T.A.), Chonnam National University, Gwangju, Republic of Korea; and Gwangju Center, Korea Basic Science Institute, Gwangju, Republic of Korea (K.D.P.)
| | - Taeho Ahn
- School of Biological Sciences and Technology (S.H.R., B.-Y.P., S.-Y.K, S.-H.P., H.-J.J., M.P., H.-S.K., C.-H.Y.), and Department of Biochemistry, College of Veterinary Medicine (T.A.), Chonnam National University, Gwangju, Republic of Korea; and Gwangju Center, Korea Basic Science Institute, Gwangju, Republic of Korea (K.D.P.)
| | - Hyung-Sik Kang
- School of Biological Sciences and Technology (S.H.R., B.-Y.P., S.-Y.K, S.-H.P., H.-J.J., M.P., H.-S.K., C.-H.Y.), and Department of Biochemistry, College of Veterinary Medicine (T.A.), Chonnam National University, Gwangju, Republic of Korea; and Gwangju Center, Korea Basic Science Institute, Gwangju, Republic of Korea (K.D.P.)
| | - Chul-Ho Yun
- School of Biological Sciences and Technology (S.H.R., B.-Y.P., S.-Y.K, S.-H.P., H.-J.J., M.P., H.-S.K., C.-H.Y.), and Department of Biochemistry, College of Veterinary Medicine (T.A.), Chonnam National University, Gwangju, Republic of Korea; and Gwangju Center, Korea Basic Science Institute, Gwangju, Republic of Korea (K.D.P.)
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Kang JY, Ryu SH, Park SH, Cha GS, Kim DH, Kim KH, Hong AW, Ahn T, Pan JG, Joung YH, Kang HS, Yun CH. Chimeric cytochromes P450 engineered by domain swapping and random mutagenesis for producing human metabolites of drugs. Biotechnol Bioeng 2014; 111:1313-22. [DOI: 10.1002/bit.25202] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2013] [Revised: 01/15/2014] [Accepted: 01/21/2014] [Indexed: 11/11/2022]
Affiliation(s)
- Ji-Yeon Kang
- School of Biological Sciences and Technology; Chonnam National University; Gwangju 500-757 Republic of Korea
| | - Sang Hoon Ryu
- School of Biological Sciences and Technology; Chonnam National University; Gwangju 500-757 Republic of Korea
| | - Sun-Ha Park
- School of Biological Sciences and Technology; Chonnam National University; Gwangju 500-757 Republic of Korea
| | - Gun Su Cha
- School of Biological Sciences and Technology; Chonnam National University; Gwangju 500-757 Republic of Korea
| | - Dong-Hyun Kim
- School of Biological Sciences and Technology; Chonnam National University; Gwangju 500-757 Republic of Korea
| | - Keon-Hee Kim
- School of Biological Sciences and Technology; Chonnam National University; Gwangju 500-757 Republic of Korea
| | | | - Taeho Ahn
- Department of Biochemistry, College of Veterinary Medicine; Chonnam National University; Gwangju Republic of Korea
| | - Jae-Gu Pan
- Superbacteria Research Center; Korea Research Institute of Bioscience and Biotechnology (KRIBB); Daejon Republic of Korea
| | - Young Hee Joung
- School of Biological Sciences and Technology; Chonnam National University; Gwangju 500-757 Republic of Korea
| | - Hyung-Sik Kang
- School of Biological Sciences and Technology; Chonnam National University; Gwangju 500-757 Republic of Korea
| | - Chul-Ho Yun
- School of Biological Sciences and Technology; Chonnam National University; Gwangju 500-757 Republic of Korea
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Choi KY, Jung EO, Yun H, Yang YH, Kazlauskas RJ, Kim BG. Development of colorimetric HTS assay of cytochrome p450 for ortho-specific hydroxylation, and engineering of CYP102D1 with enhanced catalytic activity and regioselectivity. Chembiochem 2013; 14:1231-8. [PMID: 23780920 DOI: 10.1002/cbic.201300212] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Indexed: 11/10/2022]
Abstract
A current challenge in high-throughput screening (HTS) of hydroxylation reactions by P450 is a fast and sensitive assay for regioselective hydroxylation against millions of mutants. We have developed a solid-agar plate-based HTS assay for screening ortho-specific hydroxylation of daidzein by sensing formaldehyde generated from the O-dealkylation reaction. This method adopts a colorimetric dye, pararosaniline, which has previously been used as an aldehyde-specific probe within cells. The rationale for this method lies in the fact that the hydroxylation activity at ortho-carbon position to COH correlates with a linear relationship to O-dealkylation activity on chemically introduced methoxy group at the corresponding COH. As a model system, a 4',7-dihydroxyisoflavone (daidzein) hydroxylase (CYP102D1 F96V/M246I), which catalyzes hydroxylation at ortho positions of the daidzein A/B-ring, was examined for O-dealklyation activity, by using permethylated daidzein as a surrogate substrate. By using the developed indirect bishydroxylation screening assay, the correlation coefficient between O-dealkylation and bishydroxylation activity for the template enzyme was 0.72. For further application of this assay, saturation mutants at A273/G274/T277 were examined by mutant screening with a permethylated daidzein analogue substrate (A-ring inactivated in order to find enhanced 3'-regioselectiviy). The whole-cell biotransformation of daidzein by final screened mutant G1 (A273H/G274E/T277G) showed fourfold increased conversion yield, with 14.3 mg L(-1) production titer and greatly increased 3'-regioselectiviy (3'/6=11.8). These results show that there is a remarkably high correlation (both in vitro and in vivo), thus suggesting that this assay would be ideal for a primary HTS assay for P450 reactions.
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Affiliation(s)
- Kwon-Young Choi
- School of Chemical and Biological Engineering, Seoul National University, 1 Kwanak-ro, 151-742 Seoul, South Korea
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McClay K, Wan B, Wang Y, Cho S, Yu J, Santarsiero B, Mehboob S, Johnson M, Franzblau S, Steffan R. A novel combinatorial biocatalytic approach for producing antibacterial compounds effective against Mycobacterium tuberculosis (TB). Appl Microbiol Biotechnol 2013; 97:7151-63. [DOI: 10.1007/s00253-013-5012-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 05/18/2013] [Accepted: 05/20/2013] [Indexed: 11/30/2022]
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Di Nardo G, Gilardi G. Optimization of the bacterial cytochrome P450 BM3 system for the production of human drug metabolites. Int J Mol Sci 2012; 13:15901-24. [PMID: 23443101 PMCID: PMC3546669 DOI: 10.3390/ijms131215901] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Revised: 11/01/2012] [Accepted: 11/13/2012] [Indexed: 12/28/2022] Open
Abstract
Drug metabolism in human liver is a process involving many different enzymes. Among them, a number of cytochromes P450 isoforms catalyze the oxidation of most of the drugs commercially available. Each P450 isoform acts on more than one drug, and one drug may be oxidized by more than one enzyme. As a result, multiple products may be obtained from the same drug, and as the metabolites can be biologically active and may cause adverse drug reactions (ADRs), the metabolic profile of a new drug has to be known before this can be commercialized. Therefore, the metabolites of a certain drug must be identified, synthesized and tested for toxicity. Their synthesis must be in sufficient quantities to be used for metabolic tests. This review focuses on the progresses done in the field of the optimization of a bacterial self-sufficient and efficient cytochrome P450, P450 BM3 from Bacillus megaterium, used for the production of metabolites of human enzymes. The progress made in the improvement of its catalytic performance towards drugs, the substitution of the costly NADPH cofactor and its immobilization and scale-up of the process for industrial application are reported.
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Affiliation(s)
- Giovanna Di Nardo
- Department of Life Sciences and Systems Biology, University of Torino, via Accademia Albertina 13, 10123 Torino, Italy; E-Mail:
| | - Gianfranco Gilardi
- Department of Life Sciences and Systems Biology, University of Torino, via Accademia Albertina 13, 10123 Torino, Italy; E-Mail:
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Ruff AJ, Dennig A, Wirtz G, Blanusa M, Schwaneberg U. Flow Cytometer-Based High-Throughput Screening System for Accelerated Directed Evolution of P450 Monooxygenases. ACS Catal 2012. [DOI: 10.1021/cs300115d] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Anna Joëlle Ruff
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 1, 52074 Aachen,
Germany
| | - Alexander Dennig
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 1, 52074 Aachen,
Germany
| | - Georgette Wirtz
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 1, 52074 Aachen,
Germany
| | - Milan Blanusa
- School of Engineering
and Science, Jacobs University Bremen,
Campus Ring 1, 28759 Bremen,
Germany
| | - Ulrich Schwaneberg
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 1, 52074 Aachen,
Germany
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Affiliation(s)
- Rudi Fasan
- Department of Chemistry,
Hutchison Hall, University of Rochester, Rochester, New York 14627,
United States
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Choi KY, Jung E, Jung DH, Pandey BP, Yun H, Park HY, Kazlauskas RJ, Kim BG. Cloning, expression and characterization of CYP102D1, a self-sufficient P450 monooxygenase from Streptomyces avermitilis. FEBS J 2012; 279:1650-62. [PMID: 22188665 DOI: 10.1111/j.1742-4658.2011.08462.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Among 33 cytochrome P450s (CYPs) of Streptomyces avermitilis, CYP102D1 encoded by the sav575 gene is naturally a unique and self-sufficient CYP. Since the native cyp102D1 gene could not be expressed well in Escherichia coli, its expression was attempted using codon-optimized synthetic DNA. The gene was successfully overexpressed and the recombinant CYP102D1 was functionally active, showing a Soret peak at 450 nm in the reduced CO difference spectrum. FMN/FAD isolated from the reductase domain showed the same fluorescence in thin layer chromatography separation as the authentic standards. Characterization of the substrate specificity of CYP102D1 based on NADPH oxidation rate revealed that it catalysed the oxidation of saturated and unsaturated fatty acids with very good regioselectivity, similar to other CYP102A families depending on NADPH supply. In particular, CYP102D1 catalysed the rapid oxidation of myristoleic acid with a k(cat)/K(m) value of 453.4 ± 181.5 μM(-1)·min(-1). Homology models of CYP102D1 based on other members of the CYP102A family allowed us to alter substrate specificity to aromatic compounds such as daidzein. Interestingly, replacement of F96V/M246I in the active site increased catalytic activity for daidzein with a k(cat)/K(m) value of 100.9 ± 10.4 μM(-1)·min(-1) (15-fold).
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Affiliation(s)
- Kwon-Young Choi
- School of Chemical and Biological Engineering, Institute of Bioengineering, Seoul National University, Seoul, South Korea
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Urlacher VB, Girhard M. Cytochrome P450 monooxygenases: an update on perspectives for synthetic application. Trends Biotechnol 2012; 30:26-36. [DOI: 10.1016/j.tibtech.2011.06.012] [Citation(s) in RCA: 342] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2011] [Revised: 06/10/2011] [Accepted: 06/16/2011] [Indexed: 01/14/2023]
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Abstract
P450(BM3) (CYP102A1), a fatty acid hydroxylase from Bacillus megaterium, has been extensively studied over a period of almost forty years. The enzyme has been redesigned to catalyse the oxidation of non-natural substrates as diverse as pharmaceuticals, terpenes and gaseous alkanes using a variety of engineering strategies. Crystal structures have provided a basis for several of the catalytic effects brought about by mutagenesis, while changes to reduction potentials, inter-domain electron transfer rates and catalytic parameters have yielded functional insights. Areas of active research interest include drug metabolite production, the development of process-scale techniques, unravelling general mechanistic aspects of P450 chemistry, methane oxidation, and improving selectivity control to allow the synthesis of fine chemicals. This review draws together the disparate research themes and places them in a historical context with the aim of creating a resource that can be used as a gateway to the field.
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Affiliation(s)
- Christopher J C Whitehouse
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford OX1 3QR, UK
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Insight into functional diversity of cytochrome P450 in the white-rot basidiomycete Phanerochaete chrysosporium: Involvement of versatile monooxygenase. Biochem Biophys Res Commun 2011; 407:118-23. [DOI: 10.1016/j.bbrc.2011.02.121] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2011] [Accepted: 02/24/2011] [Indexed: 01/25/2023]
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Kang JY, Kim SY, Kim D, Kim DH, Shin SM, Park SH, Kim KH, Jung HC, Pan JG, Joung YH, Chi YT, Chae HZ, Ahn T, Yun CH. Characterization of diverse natural variants of CYP102A1 found within a species of Bacillus megaterium. AMB Express 2011; 1:1. [PMID: 21906327 PMCID: PMC3159907 DOI: 10.1186/2191-0855-1-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Accepted: 03/28/2011] [Indexed: 12/03/2022] Open
Abstract
An extreme diversity of substrates and catalytic reactions of cytochrome P450 (P450) enzymes is considered to be the consequence of evolutionary adaptation driven by different metabolic or environmental demands. Here we report the presence of numerous natural variants of P450 BM3 (CYP102A1) within a species of Bacillus megaterium. Extensive amino acid substitutions (up to 5% of the total 1049 amino acid residues) were identified from the variants. Phylogenetic analyses suggest that this P450 gene evolve more rapidly than the rRNA gene locus. It was found that key catalytic residues in the substrate channel and active site are retained. Although there were no apparent variations in hydroxylation activity towards myristic acid (C14) and palmitic acid (C16), the hydroxylation rates of lauric acid (C12) by the variants varied in the range of >25-fold. Interestingly, catalytic activities of the variants are promiscuous towards non-natural substrates including human P450 substrates. It can be suggested that CYP102A1 variants can acquire new catalytic activities through site-specific mutations distal to the active site.
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Whitehouse CJC, Yang W, Yorke JA, Rowlatt BC, Strong AJF, Blanford CF, Bell SG, Bartlam M, Wong LL, Rao Z. Structural Basis for the Properties of Two Single-Site Proline Mutants of CYP102A1 (P450BM3). Chembiochem 2010; 11:2549-56. [DOI: 10.1002/cbic.201000421] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Kim KH, Kang JY, Kim DH, Park SH, Park SH, Kim D, Park KD, Lee YJ, Jung HC, Pan JG, Ahn T, Yun CH. Generation of Human Chiral Metabolites of Simvastatin and Lovastatin by Bacterial CYP102A1 Mutants. Drug Metab Dispos 2010; 39:140-50. [DOI: 10.1124/dmd.110.036392] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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