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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Gasteazoro F, Catucci G, Barbieri L, De Angelis M, Dalla Costa A, Sadeghi SJ, Gilardi G, Valetti F. Cascade reactions with two non-physiological partners for NAD(P)H regeneration via renewable hydrogen. Biotechnol J 2024; 19:e2300567. [PMID: 38581100 DOI: 10.1002/biot.202300567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 03/14/2024] [Accepted: 03/15/2024] [Indexed: 04/08/2024]
Abstract
An attractive application of hydrogenases, combined with the availability of cheap and renewable hydrogen (i.e., from solar and wind powered electrolysis or from recycled wastes), is the production of high-value electron-rich intermediates such as reduced nicotinamide adenine dinucleotides. Here, the capability of a very robust and oxygen-resilient [FeFe]-hydrogenase (CbA5H) from Clostridium beijerinckii SM10, previously identified in our group, combined with a reductase (BMR) from Bacillus megaterium (now reclassified as Priestia megaterium) was tested. The system shows a good stability and it was demonstrated to reach up to 28 ± 2 nmol NADPH regenerated s-1 mg of hydrogenase-1 (i.e., 1.68 ± 0.12 U mg-1, TOF: 126 ± 9 min-1) and 0.46 ± 0.04 nmol NADH regenerated s-1 mg of hydrogenase-1 (i.e., 0.028 ± 0.002 U mg-1, TOF: 2.1 ± 0.2 min-1), meaning up to 74 mg of NADPH and 1.23 mg of NADH produced per hour by a system involving 1 mg of CbA5H. The TOF is comparable with similar systems based on hydrogen as regenerating molecule for NADPH, but the system is first of its kind as for the [FeFe]-hydrogenase and the non-physiological partners used. As a proof of concept a cascade reaction involving CbA5H, BMR and a mutant BVMO from Acinetobacter radioresistens able to oxidize indole is presented. The data show how the cascade can be exploited for indigo production and multiple reaction cycles can be sustained using the regenerated NADPH.
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Affiliation(s)
- Francisco Gasteazoro
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
- CICATA Unidad Morelos, Instituto Politécnico Nacional, Mexico D. F., Mexico
| | - Gianluca Catucci
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
| | - Lisa Barbieri
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
- University School for Advanced Studies IUSS Pavia, Pavia, Italy
| | - Melissa De Angelis
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
| | | | - Sheila J Sadeghi
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
| | - Gianfranco Gilardi
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
| | - Francesca Valetti
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
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3
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Cao NT, Cha GS, Kim JH, Lee Y, Yun CH, Nguyen NA. Production of an O-desmethylated product, a major human metabolite, of rabeprazole sulfide by bacterial P450 enzymes. Enzyme Microb Technol 2023; 171:110328. [PMID: 37751627 DOI: 10.1016/j.enzmictec.2023.110328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/28/2023] [Accepted: 09/18/2023] [Indexed: 09/28/2023]
Abstract
Rabeprazole is a common type of proton pump inhibitor (PPI) used to treat various peptic disorders. Unlike most PPI drugs, rabeprazole is spontaneously reduced to rabeprazole sulfide (thioether) when it is given to patients. As a result, rabeprazole sulfide is considered one of the active metabolites of rabeprazole. Rabeprazole sulfide is mainly metabolized to desmethyl rabeprazole sulfide by CYP2C19 and CYP2D6 in people. However, the pharmacological efficacy and safety of desmethyl rabeprazole sulfide have not yet been investigated. Its usage is challenging due to the high cost associated with the drug. In this study, we found CYP102A1 mutants that can produce desmethyl rabeprazole sulfide as a major metabolite of rabeprazole sulfide. The chemical characteristics of the major product were confirmed using high-performance liquid chromatography, LC-mass spectrometry, and nuclear magnetic resonance spectroscopy. CYP102A1 mutants R47L/F87V/L188Q, R47L/F87V/L188Q/A335V/Q359R, and R47L/F87V/L188Q/I254V/D351E showed kcat values of 39, 93, and 88 min-1, respectively, for O-desmethylation of rabeprazole sulfide. Furthermore, the highest concentration of desmethyl rabeprazole sulfide product from 2 mM rabeprazole sulfide at optimal conditions was obtained in bacterial whole-cell biotransformation with the R47L/F87V/L188Q mutant, reaching 0.63 mM at 4-h incubation. In conclusion, we present a platform that facilitates the efficient and sustainable production of the desmethylated product from rabeprazole sulfide for use in the biopharmaceutical industry.
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Affiliation(s)
- Ngoc Tan Cao
- School of Biological Sciences and Technology, Chonnam National University, 77 Yongbongro, Gwangju 61186, Republic of Korea
| | - Gun Su Cha
- Namhae Garlic Research Institute, 2465-8 Namhaedaero, Gyeongsangnamdo 52430, Republic of Korea
| | - Jeong-Hoon Kim
- School of Biological Sciences and Biotechnology, Graduate School, Chonnam National University, 77 Yongbongro, Gwangju 61186, Republic of Korea
| | - Yujin Lee
- School of Biological Sciences and Biotechnology, Graduate School, 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.
| | - Ngoc Anh Nguyen
- School of Biological Sciences and Technology, Chonnam National University, 77 Yongbongro, Gwangju 61186, Republic of Korea.
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4
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Koroleva PI, Bulko TV, Agafonova LE, Shumyantseva VV. Catalytic and Electrocatalytic Mechanisms of Cytochromes P450 in the Development of Biosensors and Bioreactors. Biochemistry (Mosc) 2023; 88:1645-1657. [PMID: 38105030 DOI: 10.1134/s0006297923100176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 08/23/2023] [Accepted: 08/25/2023] [Indexed: 12/19/2023]
Abstract
Cytochromes P450 are a unique family of enzymes found in all Kingdoms of living organisms (animals, bacteria, plants, fungi, and archaea), whose main function is biotransformation of exogenous and endogenous compounds. The review discusses approaches to enhancing the efficiency of electrocatalysis by cytochromes P450 for their use in biotechnology and design of biosensors and describes main methods in the development of reconstituted and electrochemical catalytic systems based on the biochemical mechanism of cytochromes P450, as well as and modern trends for their practical application.
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Affiliation(s)
| | | | | | - Victoria V Shumyantseva
- Institute of Biomedical Chemistry, Moscow, 119121, Russia.
- Pirogov Russian National Research Medical University, Moscow, 117997, Russia
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [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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Abstract
Cytochrome P450s (Cyt P450s) and peroxidases are enzymes featuring iron heme cofactors that have wide applicability as biocatalysts in chemical syntheses. Cyt P450s are a family of monooxygenases that oxidize fatty acids, steroids, and xenobiotics, synthesize hormones, and convert drugs and other chemicals to metabolites. Peroxidases are involved in breaking down hydrogen peroxide and can oxidize organic compounds during this process. Both heme-containing enzymes utilize active FeIVO intermediates to oxidize reactants. By incorporating these enzymes in stable thin films on electrodes, Cyt P450s and peroxidases can accept electrons from an electrode, albeit by different mechanisms, and catalyze organic transformations in a feasible and cost-effective way. This is an advantageous approach, often called bioelectrocatalysis, compared to their biological pathways in solution that require expensive biochemical reductants such as NADPH or additional enzymes to recycle NADPH for Cyt P450s. Bioelectrocatalysis also serves as an ex situ platform to investigate metabolism of drugs and bio-relevant chemicals. In this paper we review biocatalytic electrochemical reactions using Cyt P450s including C-H activation, S-oxidation, epoxidation, N-hydroxylation, and oxidative N-, and O-dealkylation; as well as reactions catalyzed by peroxidases including synthetically important oxidations of organic compounds. Design aspects of these bioelectrocatalytic reactions are presented and discussed, including enzyme film formation on electrodes, temperature, pH, solvents, and activation of the enzymes. Finally, we discuss challenges and future perspective of these two important bioelectrocatalytic systems.
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Affiliation(s)
- Neeraj Kumar
- Department of Chemistry, University of Connecticut, Storrs, CT 06269-3136, USA.
| | - Jie He
- Department of Chemistry, University of Connecticut, Storrs, CT 06269-3136, USA.
- Institute of Materials Science, University of Connecticut, Storrs, CT 06269-3136, USA
| | - James F Rusling
- Department of Chemistry, University of Connecticut, Storrs, CT 06269-3136, USA.
- Institute of Materials Science, University of Connecticut, Storrs, CT 06269-3136, USA
- Department of Surgery and Neag Cancer Center, Uconn Health, Farmington, CT 06030, USA
- School of Chemistry, National University of Ireland at Galway, Galway, Ireland
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7
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Hardiyanti Oktavia FAR, Nguyen NA, Park CM, Cha GS, Nguyen THH, Yun CH. CYP102A1 peroxygenase catalyzed reaction via in situ H 2O 2 generation. J Inorg Biochem 2023; 242:112165. [PMID: 36848686 DOI: 10.1016/j.jinorgbio.2023.112165] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 01/17/2023] [Accepted: 02/20/2023] [Indexed: 02/27/2023]
Abstract
CYP102A1 is a promiscuous bacterial cytochrome P450 (CYP or P450) known for its diverse substrates and comparable activity with human P450 enzymes. The development of CYP102A1 peroxygenase activity can contribute significantly to human drug development and drug metabolite production. Peroxygenase has recently emerged as an alternative to a dependency of P450 on NADPH-P450 reductase and NADPH cofactor and gives more opportunity for practical application. However, the H2O2 dependency also leads to challenges regarding its practical application, in which the excessive H2O2 concentration causes the activation of the peroxygenases. Therefore, we need the optimization of H2O2 production to minimize oxidative inactivation. In this study, we report the CYP102A1 peroxygenase-catalyzed atorvastatin hydroxylation reaction with an enzymatic H2O2 generation using glucose oxidase. Random mutagenesis at the CYP102A1 heme domain was used to generate mutant libraries with high throughput screening of highly active mutants, which can pair with the in situ H2O2 generation. The setup of the CYP102A1 peroxygenase reaction was also possible for other statin drugs and could be developed to produce drug metabolites. We also found a relationship between enzyme inactivation and product formation during the catalytic reaction, supported by enzymatic in situ H2O2 supply. It can be suggested that the low product formation is due to enzyme inactivation.
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Affiliation(s)
- Fikri A R Hardiyanti Oktavia
- School of Biological Sciences and Biotechnology, Graduate School, Chonnam National University, Yongbong-ro 77, Gwangju 61186, Republic of Korea
| | - Ngoc Anh Nguyen
- School of Biological Sciences and Technology, Chonnam National University, Yongbong-ro 77, Gwangju 61186, Republic of Korea
| | - Chan Mi Park
- School of Biological Sciences and Technology, Chonnam National University, Yongbong-ro 77, Gwangju 61186, Republic of Korea
| | - Gun Su Cha
- Namhae Garlic Research Institute, 2465-8 Namhaedaero, Gyeongsangnamdo 52430, Republic of Korea
| | - Thi Huong Ha Nguyen
- School of Biological Sciences and Biotechnology, Graduate School, Chonnam National University, Yongbong-ro 77, Gwangju 61186, Republic of Korea
| | - Chul-Ho Yun
- School of Biological Sciences and Biotechnology, Graduate School, Chonnam National University, Yongbong-ro 77, Gwangju 61186, Republic of Korea; School of Biological Sciences and Technology, Chonnam National University, Yongbong-ro 77, Gwangju 61186, Republic of Korea.
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8
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Fabelle NR, Oktavia FARH, Cha GS, Nguyen NA, Choi SK, Yun CH. Production of a major metabolite of niclosamide using bacterial cytochrome P450 enzymes. Enzyme Microb Technol 2023; 165:110210. [PMID: 36764029 DOI: 10.1016/j.enzmictec.2023.110210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/19/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023]
Abstract
Niclosamide has been proposed as a possible candidate for a Covid-19 drug. However, the metabolites of niclosamide are difficult to investigate because they are usually not available commercially or they are quite expensive in the commercial market. In this study, the major metabolite of niclosamide in human liver microsomes (HLMs) was confirmed to be 3-OH niclosamide. Because the production of 3-OH niclosamide using HLMs has a slow turnover rate, a new method of producing niclosamide metabolite with an easier and highly cost-efficient method was thus conducted. Bacterial CYP102A1 (BM3) is one of the bacterial cytochrome P450s (CYPs) from Bacillus megaterium that structurally show similar activities to human CYPs. Here, the BM3 mutants were used to produce niclosamide metabolites and the metabolites were analyzed using high-performance liquid chromatography and LC-mass spectrometry. Among a set of mutants tested here, BM3 M14 mutant was the most active in producing 3-OH niclosamide, the major metabolite of niclosamide. Comparing BM3 M14 and HLMs, BM3 M14 production of 3-OH niclosamide was 34-fold higher than that of HLMs. Hence, the engineering of BM3 can be a cost-efficient method to produce 3-OH niclosamide.
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Affiliation(s)
- Nabilla Rizkia Fabelle
- School of Biological Sciences and Biotechnology, Graduate School, Chonnam National University, 77 Yongbongro, Gwangju 61186, Republic of Korea
| | | | - Gun Su Cha
- Namhae Garlic Research Institute, 2465-8 Namdaero, Gyeongsangnamdo 52430, Republic of Korea
| | - Ngoc Anh Nguyen
- School of Biological Sciences and Technology, Chonnam National University, 77 Yongbongro, Gwangju 61186, Republic of Korea
| | - Soo-Keun Choi
- Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-Ro, Yuseong, Daejon 34141, Republic of Korea.
| | - Chul-Ho Yun
- School of Biological Sciences and Biotechnology, Graduate School, Chonnam National University, 77 Yongbongro, Gwangju 61186, Republic of Korea; School of Biological Sciences and Technology, Chonnam National University, 77 Yongbongro, Gwangju 61186, Republic of Korea.
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9
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Le TK, Park YJ, Cha GS, Oktavia FARH, Kim DH, Yun CH. Roles of Human Liver Cytochrome P450 Enzymes in Tenatoprazole Metabolism. Pharmaceutics 2022; 15:pharmaceutics15010023. [PMID: 36678652 PMCID: PMC9863764 DOI: 10.3390/pharmaceutics15010023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 12/05/2022] [Accepted: 12/17/2022] [Indexed: 12/24/2022] Open
Abstract
Tenatoprazole, a newly developed proton pump inhibitor candidate, was developed as an acid inhibitor for gastric acid hypersecretion disorders such as gastric ulcer and reflux esophagitis. It is known that tenatoprazole is metabolized to three major metabolites of 5'-hydroxy tenatoprazole, tenatoprazole sulfide, and tenatoprazole sulfone in human liver, primarily catalyzed by CYPs 2C19 and 3A4. While CYP2C19 prefers the hydroxylation of tenatoprazole at C-5' position, CYP3A4 is mainly involved in sulfoxidation reaction to make tenatoprazole sulfone. Tenatoprazole sulfide is a major human metabolite of tenatoprazole and is formed spontaneously and non-enzymatically from tenatoprazole. However, its metabolic fate in the human liver is not fully known. Furthermore, no systematic metabolic study has been performed to study tenatoprazole or tenatoprazole sulfide. Here, we studied the functions of human cytochromes P450 in the metabolic pathway of tenatoprazole and tenatoprazole sulfide by using recombinant human P450s and human liver microsomes. Both CYP 2C19 and CYP3A4 showed distinct regioselective and stereospecific monooxygenation activities toward tenatoprazole and tenatoprazole sulfide. Furthermore, a new major metabolite of tenatoprazole sulfide was found, 1'-N-oxy-5'-hydroxytenatoprzole sulfide, which has never been reported. In conclusion, the metabolic fates of tenatoprazole and tenatoprazole sulfide should be considered in the clinical use of tenatoprazole.
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Affiliation(s)
- Thien-Kim Le
- School of Biological Sciences and Technology, Chonnam National University, 77 Yongbongro, Gwangju 61186, Republic of Korea
| | - Young Jin Park
- Department of Pharmacology and Pharmacogenomics Research Center, Inje University, College of Medicine, Bokjiro 75, Busanjin-Gu, Busan 47392, Republic of Korea
| | - Gun Su Cha
- Namhae Garlic Research Institute, 2465-8 Namhaedaero, Namhae-gun, Gyeongsang-namdo 52430, Republic of Korea
| | - Fikri A. R. Hardiyanti Oktavia
- School of Biological Sciences and Biotechnology, Graduate School, Chonnam National University, 77 Yongbongro, Gwangju 61186, Republic of Korea
| | - Dong Hyun Kim
- Department of Pharmacology and Pharmacogenomics Research Center, Inje University, College of Medicine, Bokjiro 75, Busanjin-Gu, Busan 47392, Republic of Korea
- Correspondence: (D.H.K.); (C.-H.Y.)
| | - Chul-Ho Yun
- School of Biological Sciences and Technology, Chonnam National University, 77 Yongbongro, Gwangju 61186, Republic of Korea
- Correspondence: (D.H.K.); (C.-H.Y.)
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10
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Thomson RES, D'Cunha SA, Hayes MA, Gillam EMJ. Use of engineered cytochromes P450 for accelerating drug discovery and development. Adv Pharmacol 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] [What about the content of this article? (0)] [Affiliation(s)] [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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11
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Yanık-Yıldırım KC, Phul OK, Roth OS, Tlatelpa A, Soria-P G, Vardar-Yel N, Vardar-Schara G. 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 DOI: 10.1128/aem.00358-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [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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Nguyen NA, Cao NT, Nguyen THH, Ji JH, Cha GS, Kang HS, Yun CH. Enzymatic Production of 3-OH Phlorizin, a Possible Bioactive Polyphenol from Apples, by Bacillus megaterium CYP102A1 via Regioselective Hydroxylation. Antioxidants (Basel) 2021; 10:1327. [PMID: 34439575 DOI: 10.3390/antiox10081327] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/19/2021] [Accepted: 08/20/2021] [Indexed: 11/17/2022] Open
Abstract
Phlorizin is the most abundant glucoside of phloretin from the apple tree and its products. Phlorizin and its aglycone phloretin are currently considered health-beneficial polyphenols from apples useful in treating hyperglycemia and obesity. Recently, we showed that phloretin could be regioselectively hydroxylated to make 3-OH phloretin by Bacillus megaterium CYP102A1 and human P450 enzymes. The 3-OH phloretin has a potent inhibitory effect on differentiating 3T3-L1 preadipocytes into adipocytes and lipid accumulation. The glucoside of 3-OH phloretin would be a promising agent with increased bioavailability and water solubility compared with its aglycone. However, procedures to make 3-OH phlorizin, a glucoside of 3-OH phloretin, using chemical methods, are not currently available. Here, a biocatalytic strategy for the efficient synthesis of a possibly valuable hydroxylated product, 3-OH phlorizin, was developed via CYP102A1-catalyzed regioselective hydroxylation. The production of 3-OH phlorizin by CYP102A1 was confirmed by HPLC and LC–MS spectroscopy in addition to enzymatic removal of its glucose moiety for comparison to 3-OH phloretin. Taken together, in this study, we found a panel of mutants from B. megaterium CYP102A1 could catalyze regioselective hydroxylation of phlorizin to produce 3-OH phlorizin, a catechol product.
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Schmitz LM, Hageneier F, Rosenthal K, Busche T, Brandt D, Kalinowski J, Lütz S. Recombinant expression and characterization of novel P450s from Actinosynnema mirum. Bioorg Med Chem 2021; 42:116241. [PMID: 34139548 DOI: 10.1016/j.bmc.2021.116241] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 05/21/2021] [Accepted: 05/24/2021] [Indexed: 12/12/2022]
Abstract
Cytochrome P450 monooxygenases (P450s) are the major contributor in the metabolism of xenobiotics, including therapeutic agents. Thus, P450s find broad application in the pharmaceutical industry to synthesize metabolites of new active pharmaceutical ingredients in order to evaluate toxicity and pharmacokinetics. As an alternative to human hepatic P450s, microbial P450s offer several advantages, such as an easier and more efficient heterologous expression as well as higher stability under process conditions. Recently, the wild-type strain Actinosynnema mirum has been reported to catalyze hydroxylation reactions with high activity on a broad range of substrates. In this study, one of these substrates, ritonavir, was used to analyze the transcriptional response of the wild-type strain. Analysis of the differential gene expression pattern allowed the assignment of genes potentially responsible for ritonavir conversion. Heterologous expression of these candidates and activity testing led to the identification of a novel P450 that efficiently converts ritonavir resembling the activity of the human CYP3A4.
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Affiliation(s)
- Lisa Marie Schmitz
- Chair for Bioprocess Engineering, Department of Biochemical and Chemical Engineering, TU Dortmund University, Emil-Figge-Straße 66, 44227 Dortmund, Germany
| | - Felix Hageneier
- Chair for Bioprocess Engineering, Department of Biochemical and Chemical Engineering, TU Dortmund University, Emil-Figge-Straße 66, 44227 Dortmund, Germany
| | - Katrin Rosenthal
- Chair for Bioprocess Engineering, Department of Biochemical and Chemical Engineering, TU Dortmund University, Emil-Figge-Straße 66, 44227 Dortmund, Germany
| | - Tobias Busche
- Microbial Genomic and Biotechnology, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - David Brandt
- Microbial Genomic and Biotechnology, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Jörn Kalinowski
- Microbial Genomic and Biotechnology, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Stephan Lütz
- Chair for Bioprocess Engineering, Department of Biochemical and Chemical Engineering, TU Dortmund University, Emil-Figge-Straße 66, 44227 Dortmund, Germany.
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Nguyen T, Yeom S, Yun C. Production of a Human Metabolite of Atorvastatin by Bacterial CYP102A1 Peroxygenase. Applied Sciences 2021; 11:603. [DOI: 10.3390/app11020603] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Atorvastatin is a widely used statin drug that prevents cardiovascular disease and treats hyperlipidemia. The major metabolites in humans are 2-OH and 4-OH atorvastatin, which are active metabolites known to show highly inhibiting effects on 3-hydroxy-3-methylglutaryl-CoA reductase activity. Producing the hydroxylated metabolites by biocatalysts using enzymes and whole-cell biotransformation is more desirable than chemical synthesis. It is more eco-friendly and can increase the yield of desired products. In this study, we have found an enzymatic strategy of P450 enzymes for highly efficient synthesis of the 4-OH atorvastatin, which is an expensive commercial product, by using bacterial CYP102A1 peroxygenase activity with hydrogen peroxide without NADPH. We obtained a set of CYP102A1 mutants with high catalytic activity toward atorvastatin using enzyme library generation, high-throughput screening of highly active mutants, and enzymatic characterization of the mutants. In the hydrogen peroxide supported reactions, a mutant, with nine changed amino acid residues compared to a wild-type among tested mutants, showed the highest catalytic activity of atorvastatin 4-hydroxylation (1.8 min−1). This result shows that CYP102A1 can catalyze atorvastatin 4-hydroxylation by peroxide-dependent oxidation with high catalytic activity. The advantages of CYP102A1 peroxygenase activity over NADPH-supported monooxygenase activity are discussed. Taken together, we suggest that the P450 peroxygenase activity can be used to produce drugs’ metabolites for further studies of their efficacy and safety.
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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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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. J Agric Food Chem 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Ensari Y, de Almeida Santos G, Ruff AJ, Schwaneberg U. Engineered P450 BM3 and cpADH5 coupled cascade reaction for β-oxo fatty acid methyl ester production in whole cells. Enzyme Microb Technol 2020; 138:109555. [PMID: 32527525 DOI: 10.1016/j.enzmictec.2020.109555] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 03/23/2020] [Accepted: 03/24/2020] [Indexed: 01/01/2023]
Abstract
Hydroxy- or ketone- functionalized fatty acid methyl esters (FAMEs) are important compounds for production of pharmaceuticals, vitamins, cosmetics or dietary supplements. Biocatalysis through enzymatic cascades has drawn attention to the efficient, sustainable, and greener synthetic processes. Furthermore, whole cell catalysts offer important advantages such as cofactor regeneration by cell metabolism, omission of protein purification steps and increased enzyme stability. Here, we report the first whole cell catalysis employing an engineered P450 BM3 variant and cpADH5 coupled cascade reaction for the biosynthesis of hydroxy- and keto-FAMEs. Firstly, P450 BM3 was engineered through the KnowVolution approach yielding P450 BM3 variant YE_M1_2, (R47S/Y51W/T235S/N239R/I401 M) which exhibited boosted performance toward methyl hexanoate. The initial oxidation rate of YE_M1_2 toward methyl hexanoate was determined to be 23-fold higher than the wild type enzyme and a 1.5-fold increase in methyl 3-hydroxyhexanoate production was obtained (YE_M1_2; 2.75 mM and WT; 1.8 mM). Subsequently, the whole cell catalyst for the synthesis of methyl 3-hydroxyhexanoate and methyl 3-oxohexanoate was constructed by combining the engineered P450 BM3 and cpADH5 variants in an artificial operon. A 2.06 mM total product formation was achieved by the whole cell catalyst including co-expressed channel protein, FhuA and co-solvent addition. Moreover, the generated whole cell biocatalyst also accepted methyl valerate, methyl heptanoate as well as methyl octanoate as substrates and yielded ω-1 ketones as the main product.
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González-davis O, Chauhan K, Zapian-merino S, Vazquez-duhalt R. Bi-enzymatic virus-like bionanoreactors for the transformation of endocrine disruptor compounds. Int J Biol Macromol 2020; 146:415-21. [DOI: 10.1016/j.ijbiomac.2019.12.272] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 12/13/2019] [Accepted: 12/31/2019] [Indexed: 12/11/2022]
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Ciaramella A, Catucci G, Di Nardo G, Sadeghi SJ, Gilardi G. Peroxide-driven catalysis of the heme domain of A. radioresistens cytochrome P450 116B5 for sustainable aromatic rings oxidation and drug metabolites production. N Biotechnol 2020; 54:71-79. [DOI: 10.1016/j.nbt.2019.08.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 08/22/2019] [Accepted: 08/23/2019] [Indexed: 02/08/2023]
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Le T, Cha G, Jang H, Nguyen THH, Doan TTM, Lee YJ, Park KD, Shin Y, Kim D, Yun C. Regioselective hydroxylation pathway of tenatoprazole to produce human metabolites by Bacillus megaterium CYP102A1. Process Biochem 2019; 87:95-104. [DOI: 10.1016/j.procbio.2019.09.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Nastri F, D’alonzo D, Leone L, Zambrano G, Pavone V, Lombardi A. Engineering Metalloprotein Functions in Designed and Native Scaffolds. Trends Biochem Sci 2019; 44:1022-40. [DOI: 10.1016/j.tibs.2019.06.006] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 06/05/2019] [Accepted: 06/11/2019] [Indexed: 12/15/2022]
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Schmitz LM, Schäper J, Rosenthal K, Lütz S. Accessing the Biocatalytic Potential for C−H‐Activation by Targeted Genome Mining and Screening. ChemCatChem 2019. [DOI: 10.1002/cctc.201901273] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Lisa Marie Schmitz
- Chair for Bioprocess Engineering Department of Biochemical and Chemical EngineeringTU Dortmund University Emil-Figge-Straße 66 Dortmund 44227 Germany
| | - Jonas Schäper
- Chair for Bioprocess Engineering Department of Biochemical and Chemical EngineeringTU Dortmund University Emil-Figge-Straße 66 Dortmund 44227 Germany
| | - Katrin Rosenthal
- Chair for Bioprocess Engineering Department of Biochemical and Chemical EngineeringTU Dortmund University Emil-Figge-Straße 66 Dortmund 44227 Germany
| | - Stephan Lütz
- Chair for Bioprocess Engineering Department of Biochemical and Chemical EngineeringTU Dortmund University Emil-Figge-Straße 66 Dortmund 44227 Germany
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Sakai K, Matsuzaki F, Wise L, Sakai Y, Jindou S, Ichinose H, Takaya N, Kato M, Wariishi H, Shimizu M. Biochemical Characterization of CYP505D6, a Self-Sufficient Cytochrome P450 from the White-Rot Fungus Phanerochaete chrysosporium. Appl Environ Microbiol 2018; 84:e01091-18. [PMID: 30171007 DOI: 10.1128/AEM.01091-18] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 08/29/2018] [Indexed: 12/29/2022] Open
Abstract
The activity of a self-sufficient cytochrome P450 enzyme, CYP505D6, from the lignin-degrading basidiomycete Phanerochaete chrysosporium was characterized. Recombinant CYP505D6 was produced in Escherichia coli and purified. In the presence of NADPH, CYP505D6 used a series of saturated fatty alcohols with C9-18 carbon chain lengths as the substrates. Hydroxylation occurred at the ω-1 to ω-6 positions of such substrates with C9-15 carbon chain lengths, except for 1-dodecanol, which was hydroxylated at the ω-1 to ω-7 positions. Fatty acids were also substrates of CYP505D6. Based on the sequence alignment, the corresponding amino acid of Tyr51, which is located at the entrance to the active-site pocket in CYP102A1, was Val51 in CYP505D6. To understand the diverse hydroxylation mechanism, wild-type CYP505D6 and its V51Y variant and wild-type CYP102A1 and its Y51V variant were generated, and the products of their reaction with dodecanoic acid were analyzed. Compared with wild-type CYP505D6, its V51Y variant generated few products hydroxylated at the ω-4 to ω-6 positions. The products generated by wild-type CYP102A1 were hydroxylated at the ω-1 to ω-4 positions, whereas its Y51V variant generated ω-1 to ω-7 hydroxydodecanoic acids. These observations indicated that Val51 plays an important role in determining the regiospecificity of fatty acid hydroxylation, at least that at the ω-4 to ω-6 positions. Aromatic compounds, such as naphthalene and 1-naphthol, were also hydroxylated by CYP505D6. These findings highlight a unique broad substrate spectrum of CYP505D6, rendering it an attractive candidate enzyme for the biotechnological industry.IMPORTANCE Phanerochaete chrysosporium is a white-rot fungus whose metabolism of lignin, aromatic pollutants, and lipids has been most extensively studied. This fungus harbors 154 cytochrome P450-encoding genes in the genome. As evidenced in this study, P. chrysosporium CYP505D6, a fused protein of P450 and its reductase, hydroxylates fatty alcohols (C9-15) and fatty acids (C9-15) at the ω-1 to ω-7 or ω-1 to ω-6 positions, respectively. Naphthalene and 1-naphthol were also hydroxylated, indicating that the substrate specificity of CYP505D6 is broader than those of the known fused proteins CYP102A1 and CYP505A1. The substrate versatility of CYP505D6 makes this enzyme an attractive candidate for biotechnological applications.
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Abstract
Human enzymes have been widely studied in various disciplines. The number of reactions taking place in the human body is vast, and so is the number of potential catalysts for synthesis. Herein, we focus on the application of human enzymes that catalyze chemical reactions in course of the metabolism of drugs and xenobiotics. Some of these reactions have been explored on the preparative scale. The major field of application of human enzymes is currently drug development, where they are applied for the synthesis of drug metabolites.
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Affiliation(s)
- Margit Winkler
- Institute for Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria.,acib GmbH, Petersgasse 14, 8010, Graz, Austria
| | | | | | - Bernd Nidetzky
- acib GmbH, Petersgasse 14, 8010, Graz, Austria.,Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 12, 8010, Graz, Austria
| | - Anton Glieder
- Institute for Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria
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27
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Affiliation(s)
- Margit Winkler
- Institut für Molekulare Biotechnologie; Technische Universität Graz; Petersgasse 14 8010 Graz Österreich
- acib GmbH; Petersgasse 14 8010 Graz Österreich
| | | | | | - Bernd Nidetzky
- acib GmbH; Petersgasse 14 8010 Graz Österreich
- Institut für Biotechnologie und Bioprozesstechnik; Technische Universität Graz; Petersgasse 12 8010 Graz Österreich
| | - Anton Glieder
- Institut für Molekulare Biotechnologie; Technische Universität Graz; Petersgasse 14 8010 Graz Österreich
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Dezvarei S, Onoda H, Shoji O, Watanabe Y, Bell SG. Efficient hydroxylation of cycloalkanes by co-addition of decoy molecules to variants of the cytochrome P450 CYP102A1. J Inorg Biochem 2018; 183:137-45. [DOI: 10.1016/j.jinorgbio.2018.03.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Koyani RD, Vazquez-Duhalt R. Enzymatic Activation of the Emerging Drug Resveratrol. Appl Biochem Biotechnol 2018; 185:248-56. [PMID: 29124656 DOI: 10.1007/s12010-017-2645-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 10/19/2017] [Indexed: 10/18/2022]
Abstract
The plant originated stilbene "resveratrol" (3,4',5-trans-trihydroxystilbene) is well known for its diverse health benefits including anti-tumor, anti-inflammatory, anti-microbial, and anti-oxidant properties. Besides a significant amount of reports on different aspects of its application as prodrug in the last 50 years, still, a strategy leading to the production of the active drug is missing. The aim of this work was to evaluate the enzymatic activation of prodrug resveratrol to the effective drug piceatannol, without engaging expensive cofactors. Five different heme proteins were analyzed for the transformation of resveratrol. Kinetic parameters of resveratrol transformation and analysis of the transformed products were conducted through HPLC and GC-MS. Effect of pH and organic solvent on the transformation process had also been evaluated. Among all tested heme proteins, only a variant of cytochrome P450BM3 from Bacillus megaterium (CYPBM3F87A) was found suitable for piceatannol production. The most suitable pH for the reaction conditions was 8.5, while organic solvents did not show any effect on transformation. For resveratrol transformation, the turnover rate (k cat) was 21.7 (± 0.6) min-1, the affinity constant (K M) showed a value of 55.7 (± 16.7) μM for a catalytic efficiency (k cat/K M) of 389 min-1 mM-1. GC-MS analysis showed that the only product from resveratrol transformation by cytochrome P450BM3 is the biologically active piceatannol. The enzymatic transformation of resveratrol, an emerging compound with medical interest, to active product piceatannol by a variant of cytochrome P450BM3 in the absence of expensive NADPH cofactor is demonstrated. This enzymatic process is economically attractive and can be scaled up to cover the increasing medical demand for piceatannol.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Le T, Jang H, Nguyen HTH, Doan TTM, Lee G, Park KD, Ahn T, Joung YH, Kang H, Yun C. 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] [What about the content of this article? (0)] [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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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] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Ebert MCCJC, Dürr SL, A. Houle A, Lamoureux G, Pelletier JN. Evolution of P450 Monooxygenases toward Formation of Transient Channels and Exclusion of Nonproductive Gases. ACS Catal 2016. [DOI: 10.1021/acscatal.6b02154] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Maximilian C. C. J. C. Ebert
- Département
de biochimie, Université de Montréal, Montréal H3T 1J4, Canada
- PROTEO, The Québec Network for Research on Protein Function, Engineering and Applications, Québec G1V 0A6, Canada
- CGCC, the Center for Green Chemistry and Catalysis, Montréal H3T 1J4, Canada
| | - Simon L. Dürr
- PROTEO, The Québec Network for Research on Protein Function, Engineering and Applications, Québec G1V 0A6, Canada
- CGCC, the Center for Green Chemistry and Catalysis, Montréal H3T 1J4, Canada
- Département
de chimie, Université de Montréal, Montréal H3T 1J4, Canada
| | - Armande A. Houle
- Département
de biochimie, Université de Montréal, Montréal H3T 1J4, Canada
- PROTEO, The Québec Network for Research on Protein Function, Engineering and Applications, Québec G1V 0A6, Canada
- CGCC, the Center for Green Chemistry and Catalysis, Montréal H3T 1J4, Canada
| | - Guillaume Lamoureux
- PROTEO, The Québec Network for Research on Protein Function, Engineering and Applications, Québec G1V 0A6, Canada
- Department
of Chemistry and Biochemistry and Centre for Research in Molecular
Modeling (CERMM), Concordia University, Montreal H4B 1R6, Canada
| | - Joelle N. Pelletier
- Département
de biochimie, Université de Montréal, Montréal H3T 1J4, Canada
- PROTEO, The Québec Network for Research on Protein Function, Engineering and Applications, Québec G1V 0A6, Canada
- CGCC, the Center for Green Chemistry and Catalysis, Montréal H3T 1J4, Canada
- Département
de chimie, Université de Montréal, Montréal H3T 1J4, Canada
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Jang HH, Ryu SH, Le TK, Doan TTM, Nguyen THH, Park KD, Yim DE, Kim DH, Kang CK, Ahn T, Kang HS, Yun CH. Regioselective C-H hydroxylation of omeprazole sulfide by Bacillus megaterium CYP102A1 to produce a human metabolite. Biotechnol Lett 2016; 39:105-112. [DOI: 10.1007/s10529-016-2211-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Accepted: 09/08/2016] [Indexed: 12/24/2022]
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Brummund J, Müller M, Schmitges T, Kaluzna I, Mink D, Hilterhaus L, Liese A. Process development for oxidations of hydrophobic compounds applying cytochrome P450 monooxygenases in-vitro. J Biotechnol 2016; 233:143-50. [PMID: 27396939 DOI: 10.1016/j.jbiotec.2016.07.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 06/06/2016] [Accepted: 07/06/2016] [Indexed: 11/18/2022]
Abstract
Cytochrome P450 monooxygenases are a unique family of enzymes that are able to catalyze regio- and stereospecific oxidations for a broad substrate range. However, due to limited enzyme activities and stabilities, hydrophobicity of substrates, as well as the necessity of a continuous electron and oxygen supply the implementation of P450s for industrial processes remains challenging. Aim of this study was to point out key aspects for the development of an efficient synthesis concept for cytochrome P450 catalyzed oxidations. In order to regenerate the natural cofactor NADPH, a glucose dehydrogenase was applied. The low water soluble terpene α-ionone was used as substrate for the model reaction system. The studies reveal that an addition of surfactants in combination with low volumetric amounts of co-solvent can significantly increase substrate availability and reaction rates. Furthermore, these additives facilitated a reliable sampling procedure during the process. Another key factor for the process design was the oxygen supply. Based on various investigations, a bubble-aerated stirred tank reactor in batch mode represents a promising reactor concept for P450 oxidations. Main restriction of the investigated reaction system was the low process stability of the P450 monooxygenase, characterized by maximum total turnover numbers of ∼4100molα-ionone/molP450.
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Affiliation(s)
- Jan Brummund
- Hamburg University of Technology, Institute of Technical Biocatalysis, Denickestr. 15, 21073 Hamburg, Germany
| | - Monika Müller
- DSM Chemical Technology R&D B.V., Urmonderbaan 22, P.O. Box 18, 6160 MD Geleen, The Netherlands
| | - Thomas Schmitges
- DSM Chemical Technology R&D B.V., Urmonderbaan 22, P.O. Box 18, 6160 MD Geleen, The Netherlands
| | - Iwona Kaluzna
- DSM Chemical Technology R&D B.V., Urmonderbaan 22, P.O. Box 18, 6160 MD Geleen, The Netherlands
| | - Daniel Mink
- DSM Chemical Technology R&D B.V., Urmonderbaan 22, P.O. Box 18, 6160 MD Geleen, The Netherlands
| | - Lutz Hilterhaus
- Hamburg University of Technology, Institute of Technical Biocatalysis, Denickestr. 15, 21073 Hamburg, Germany
| | - Andreas Liese
- Hamburg University of Technology, Institute of Technical Biocatalysis, Denickestr. 15, 21073 Hamburg, Germany.
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Sathesh-Prabu C, Lee SK. Production of Long-Chain α,ω-Dicarboxylic Acids by Engineered Escherichia coli from Renewable Fatty Acids and Plant Oils. J Agric Food Chem 2015; 63:8199-8208. [PMID: 26359801 DOI: 10.1021/acs.jafc.5b03833] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Long-chain α,ω-dicarboxylic acids (LDCAs, ≥ C12) are widely used as a raw material for preparing various commodities and polymers. In this study, a CYP450-monooxygenase-mediated ω-oxidation pathway system with high ω-regioselectivity was heterologously expressed in Escherichia coli to produce DCAs from fatty acids. The resulting engineered E. coli produced a maximum of 41 mg/L of C12 DCA and 163 mg/L of C14 DCA from fatty acids (1 g/L), following 20 h of whole cell biotransformation. Addition of a heme precursor and the hydroxyl radical scavenger, thiourea, increased product concentration (159 mg/L of C12 DCA and 410 mg/L of C14 DCA) in a shorter culture duration than that of the corresponding controls. DCAs of various chain lengths were synthesized from coconut oil hydrolysate using the engineered E. coli. This novel synthetic biocatalytic system could be applied to produce high value DCAs in a cost-effective manner from renewable plant oils.
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Affiliation(s)
- Chandran Sathesh-Prabu
- School of Energy and Chemical Engineering, and ‡School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST) , Ulsan 689-798, Republic of Korea
| | - Sung Kuk Lee
- School of Energy and Chemical Engineering, and ‡School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST) , Ulsan 689-798, Republic of Korea
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Pateraki I, Heskes AM, Hamberger B. Cytochromes P450 for Terpene Functionalisation and Metabolic Engineering. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2015; 148:107-39. [DOI: 10.1007/10_2014_301] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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39
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Litzenburger M, Kern F, Khatri Y, Bernhardt R. Conversions of tricyclic antidepressants and antipsychotics with selected P450s from Sorangium cellulosum So ce56. Drug Metab Dispos 2014; 43:392-9. [PMID: 25550480 DOI: 10.1124/dmd.114.061937] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Human cytochromes P450 (P450s) play a major role in the biotransformation of drugs. The generated metabolites are important for pharmaceutical, medical, and biotechnological applications and can be used for derivatization or toxicological studies. The availability of human drug metabolites is restricted and alternative ways of production are requested. For this, microbial P450s turned out to be a useful tool for the conversion of drugs and related derivatives. Here, we used 10 P450s from the myxobacterium Sorangium cellulosum So ce56, which have been cloned, expressed, and purified. The P450s were investigated concerning the conversion of the antidepressant drugs amitriptyline, clomipramine, imipramine, and promethazine; the antipsychotic drugs carbamazepine, chlorpromazine, and thioridazine, as well as their precursors, iminodibenzyl and phenothiazine. Amitriptyline, chlorpromazine, clomipramine, imipramine, and thioridazine are efficiently converted during the in vitro reaction and were chosen to upscale the production by an Escherichia coli-based whole-cell bioconversion system. Two different approaches, a whole-cell system using M9CA medium and a system using resting cells in buffer, were used for the production of sufficient amounts of metabolites for NMR analysis. Amitriptyline, clomipramine, and imipramine are converted to the corresponding 10-hydroxylated products, whereas the conversion of chlorpromazine and thioridazine leads to a sulfoxidation in position 5. It is shown for the first time that myxobacterial P450s are efficient to produce known human drug metabolites in a milligram scale, revealing their ability to synthesize pharmaceutically important compounds.
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Affiliation(s)
- Martin Litzenburger
- Institut für Biochemie, Universität des Saarlandes, Saarbruecken, Germany (M.L., F.K., Y.K., R.B.)
| | - Fredy Kern
- Institut für Biochemie, Universität des Saarlandes, Saarbruecken, Germany (M.L., F.K., Y.K., R.B.)
| | - Yogan Khatri
- Institut für Biochemie, Universität des Saarlandes, Saarbruecken, Germany (M.L., F.K., Y.K., R.B.)
| | - Rita Bernhardt
- Institut für Biochemie, Universität des Saarlandes, Saarbruecken, Germany (M.L., F.K., Y.K., R.B.)
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Park JH, Lee SH, Cha GS, Choi DS, Nam DH, Lee JH, Lee JK, Yun CH, Jeong KJ, Park CB. Cofactor-free light-driven whole-cell cytochrome P450 catalysis. Angew Chem Int Ed Engl 2014; 54:969-73. [PMID: 25430544 DOI: 10.1002/anie.201410059] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Indexed: 11/11/2022]
Abstract
Cytochromes P450 can catalyze various regioselective and stereospecific oxidation reactions of non-functionalized hydrocarbons. Here, we have designed a novel light-driven platform for cofactor-free, whole-cell P450 photo-biocatalysis using eosin Y (EY) as a photosensitizer. EY can easily enter into the cytoplasm of Escherichia coli and bind specifically to the heme domain of P450. The catalytic turnover of P450 was mediated through the direct transfer of photoinduced electrons from the photosensitized EY to the P450 heme domain under visible light illumination. The photoactivation of the P450 catalytic cycle in the absence of cofactors and redox partners is successfully conducted using many bacterial P450s (variants of P450 BM3) and human P450s (CYPs 1A1, 1A2, 1B1, 2A6, 2E1, and 3A4) for the bioconversion of different substrates, including marketed drugs (simvastatin, lovastatin, and omeprazole) and a steroid (17β-estradiol), to demonstrate the general applicability of the light-driven, cofactor-free system.
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Affiliation(s)
- Jong Hyun Park
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology, 335 Science Road, Daejeon 305-701 (Republic of Korea)
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Park JH, Lee SH, Cha GS, Choi DS, Nam DH, Lee JH, Lee JK, Yun CH, Jeong KJ, Park CB. Cofactor-Free Light-Driven Whole-Cell Cytochrome P450 Catalysis. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201410059] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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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] [What about the content of this article? (0)] [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] [What about the content of this article? (0)] [Affiliation(s)] [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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Wang ZJ, Renata H, Peck NE, Farwell CC, Coelho PS, Arnold FH. Improved cyclopropanation activity of histidine-ligated cytochrome P450 enables the enantioselective formal synthesis of levomilnacipran. Angew Chem Int Ed Engl 2014; 53:6810-3. [PMID: 24802161 PMCID: PMC4120663 DOI: 10.1002/anie.201402809] [Citation(s) in RCA: 152] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Indexed: 02/03/2023]
Abstract
Engineering enzymes capable of modes of activation unprecedented in nature will increase the range of industrially important molecules that can be synthesized through biocatalysis. However, low activity for a new function is often a limitation in adopting enzymes for preparative-scale synthesis, reaction with demanding substrates, or when a natural substrate is also present. By mutating the proximal ligand and other key active-site residues of the cytochrome P450 enzyme from Bacillus megaterium (P450-BM3), a highly active His-ligated variant of P450-BM3 that can be employed for the enantioselective synthesis of the levomilnacipran core was engineered. This enzyme, BM3-Hstar, catalyzes the cyclopropanation of N,N-diethyl-2-phenylacrylamide with an estimated initial rate of over 1000 turnovers per minute and can be used under aerobic conditions. Cyclopropanation activity is highly dependent on the electronic properties of the P450 proximal ligand, which can be used to tune this non-natural enzyme activity.
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Affiliation(s)
| | | | - Nicole E. Peck
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd. MC 210-41, Pasadena, CA, 91125 (USA)
| | - Christopher C. Farwell
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd. MC 210-41, Pasadena, CA, 91125 (USA)
| | - Pedro S. Coelho
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd. MC 210-41, Pasadena, CA, 91125 (USA)
| | - Frances H. Arnold
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd. MC 210-41, Pasadena, CA, 91125 (USA)
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Neufeld K, Zu Berstenhorst SM, Pietruszka J. Evaluation of coumarin-based fluorogenic P450 BM3 substrates and prospects for competitive inhibition screenings. Anal Biochem 2014; 456:70-81. [PMID: 24708937 DOI: 10.1016/j.ab.2014.03.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 03/25/2014] [Accepted: 03/28/2014] [Indexed: 12/17/2022]
Abstract
Fluorescence-based assays for the cytochrome P450 BM3 monooxygenase from Bacillus megaterium address an attractive biotechnological challenge by facilitating enzyme engineering and the identification of potential substrates of this highly promising biocatalyst. In the current study, we used the scarcity of corresponding screening systems as an opportunity to evaluate a novel and continuous high-throughput assay for this unique enzyme. A set of nine catalytically diverse P450 BM3 variants was constructed and tested toward the native substrate-inspired fluorogenic substrate 12-(4-trifluoromethylcoumarin-7-yloxy)dodecanoic acid. Particularly high enzyme-mediated O-dealkylation yielding the fluorescent product 7-hydroxy-4-trifluoromethylcoumarin was observed with mutants containing the F87V substitution, with A74G/F87V showing the highest catalytic efficiency (0.458 min(-1)μM(-1)). To simplify the assay procedure and show its versatility, different modes of application were successfully demonstrated, including (i) the direct use of NADPH or its oxidized form NADP(+) along with diverse NADPH recycling systems for electron supply, (ii) the use of cell-free lysates and whole-cell preparations as the biocatalyst source, and (iii) its use for competitive inhibition screens to identify or characterize substrates and inhibitors. A detailed comparison with known, fluorescence-based P450 BM3 assays finally emphasizes the relevance of our contribution to the ongoing research.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Pendyala B, Chaganti SR, Thadikamala S, Reddy Shetty P. Heterologous expression of CYP102A5 variant from Bacillus cereus CYPPB-1: Validation of model for predicting drug metabolism of human P450 probe substrates. Appl Microbiol Biotechnol 2013; 97:8107-19. [DOI: 10.1007/s00253-012-4654-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Revised: 12/10/2012] [Accepted: 12/12/2012] [Indexed: 11/26/2022]
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Rea V, Falck D, Kool J, de Kanter FJJ, Commandeur JNM, Vermeulen NPE, Niessen WMA, Honing M. Combination of biotransformation by P450 BM3 mutants with on-line post-column bioaffinity and mass spectrometric profiling as a novel strategy to diversify and characterize p38α kinase inhibitors. Med Chem Commun 2013. [DOI: 10.1039/c2md20283b] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Prabhulkar S, Tian H, Wang X, Zhu JJ, Li CZ. Engineered proteins: redox properties and their applications. Antioxid Redox Signal 2012; 17:1796-822. [PMID: 22435347 PMCID: PMC3474195 DOI: 10.1089/ars.2011.4001] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2011] [Revised: 03/20/2012] [Accepted: 03/21/2012] [Indexed: 10/28/2022]
Abstract
Oxidoreductases and metalloproteins, representing more than one third of all known proteins, serve as significant catalysts for numerous biological processes that involve electron transfers such as photosynthesis, respiration, metabolism, and molecular signaling. The functional properties of the oxidoreductases/metalloproteins are determined by the nature of their redox centers. Protein engineering is a powerful approach that is used to incorporate biological and abiological redox cofactors as well as novel enzymes and redox proteins with predictable structures and desirable functions for important biological and chemical applications. The methods of protein engineering, mainly rational design, directed evolution, protein surface modifications, and domain shuffling, have allowed the creation and study of a number of redox proteins. This review presents a selection of engineered redox proteins achieved through these methods, resulting in a manipulation in redox potentials, an increase in electron-transfer efficiency, and an expansion of native proteins by de novo design. Such engineered/modified redox proteins with desired properties have led to a broad spectrum of practical applications, ranging from biosensors, biofuel cells, to pharmaceuticals and hybrid catalysis. Glucose biosensors are one of the most successful products in enzyme electrochemistry, with reconstituted glucose oxidase achieving effective electrical communication with the sensor electrode; direct electron-transfer-type biofuel cells are developed to avoid thermodynamic loss and mediator leakage; and fusion proteins of P450s and redox partners make the biocatalytic generation of drug metabolites possible. In summary, this review includes the properties and applications of the engineered redox proteins as well as their significance and great potential in the exploration of bioelectrochemical sensing devices.
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Affiliation(s)
- Shradha Prabhulkar
- Nanobioengineering/Bioelectronics Laboratory, Department of Biomedical Engineering, Florida International University, Miami, Florida
| | - Hui Tian
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida
| | - Xiaotang Wang
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida
| | - Jun-Jie Zhu
- Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - Chen-Zhong Li
- Nanobioengineering/Bioelectronics Laboratory, Department of Biomedical Engineering, Florida International University, Miami, Florida
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Chigorimbo-murefu NT, Njoroge M, Nzila A, Louw S, Masimirembwa C, Chibale K. Biotransformation and biocatalysis: roles and applications in the discovery of antimalarials. Future Med Chem 2012; 4:2325-36. [DOI: 10.4155/fmc.12.173] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Several strategies to discover new antimalarials have been proposed to augment and complement the conventional drug-discovery paradigm. One approach, which has not yet been fully exploited, is the use of drug biotransformation to identify new active molecules. This concept rests on the use of the biotransformation of drugs to their pharmacologically active metabolites. This approach has been used successfully in human chemotherapy, with the discovery and development of several metabolite-based drugs. This review looks at the contribution that biotransformations can play in antimalarial drug discovery.
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