1
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Zhou J, Qin X, Zhou S, MacKenzie KR, Li F. CYP3A-Mediated Carbon-Carbon Bond Cleavages in Drug Metabolism. Biomolecules 2024; 14:1125. [PMID: 39334891 PMCID: PMC11430781 DOI: 10.3390/biom14091125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 08/28/2024] [Accepted: 09/03/2024] [Indexed: 09/30/2024] Open
Abstract
Cytochrome P450 enzymes (P450s) play a critical role in drug metabolism, with the CYP3A subfamily being responsible for the biotransformation of over 50% of marked drugs. While CYP3A enzymes are known for their extensive catalytic versatility, one intriguing and less understood function is the ability to mediate carbon-carbon (C-C) bond cleavage. These uncommon reactions can lead to unusual metabolites and potentially influence drug safety and efficacy. This review focuses on examining examples of C-C bond cleavage catalyzed by CYP3A, exploring the mechanisms, physiological significance, and implications for drug metabolism. Additionally, examples of CYP3A-mediated ring expansion via C-C bond cleavages are included in this review. This work will enhance our understanding of CYP3A-catalyzed C-C bond cleavages and their mechanisms by carefully examining and analyzing these case studies. It may also guide future research in drug metabolism and drug design, improving drug safety and efficacy in clinical practice.
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Affiliation(s)
- Junhui Zhou
- Center for Drug Discovery, Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030, USA; (J.Z.); (X.Q.); (S.Z.); (K.R.M.)
| | - Xuan Qin
- Center for Drug Discovery, Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030, USA; (J.Z.); (X.Q.); (S.Z.); (K.R.M.)
- NMR and Drug Metabolism Core, Advanced Technology Cores, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shenzhi Zhou
- Center for Drug Discovery, Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030, USA; (J.Z.); (X.Q.); (S.Z.); (K.R.M.)
| | - Kevin R. MacKenzie
- Center for Drug Discovery, Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030, USA; (J.Z.); (X.Q.); (S.Z.); (K.R.M.)
- NMR and Drug Metabolism Core, Advanced Technology Cores, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Feng Li
- Center for Drug Discovery, Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030, USA; (J.Z.); (X.Q.); (S.Z.); (K.R.M.)
- NMR and Drug Metabolism Core, Advanced Technology Cores, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA
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2
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Qin X, Wang Y, Ye Q, Hakenjos JM, Wang J, Teng M, Guo L, Tan Z, Young DW, MacKenzie KR, Li F. CYP3A Mediates an Unusual C(sp 2)-C(sp 3) Bond Cleavage via Ipso-Addition of Oxygen in Drug Metabolism. Angew Chem Int Ed Engl 2024; 63:e202405197. [PMID: 38574245 PMCID: PMC11126355 DOI: 10.1002/anie.202405197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/03/2024] [Accepted: 04/04/2024] [Indexed: 04/06/2024]
Abstract
Mammalian cytochrome P450 drug-metabolizing enzymes rarely cleave carbon-carbon (C-C) bonds and the mechanisms of such cleavages are largely unknown. We identified two unusual cleavages of non-polar, unstrained C(sp2)-C(sp3) bonds in the FDA-approved tyrosine kinase inhibitor pexidartinib that are mediated by CYP3A4/5, the major human phase I drug metabolizing enzymes. Using a synthetic ketone, we rule out the Baeyer-Villiger oxidation mechanism that is commonly invoked to address P450-mediated C-C bond cleavages. Our studies in 18O2 and H2 18O enriched systems reveal two unusual distinct mechanisms of C-C bond cleavage: one bond is cleaved by CYP3A-mediated ipso-addition of oxygen to a C(sp2) site of N-protected pyridin-2-amines, and the other occurs by a pseudo-retro-aldol reaction after hydroxylation of a C(sp3) site. This is the first report of CYP3A-mediated C-C bond cleavage in drug metabolism via ipso-addition of oxygen mediated mechanism. CYP3A-mediated ipso-addition is also implicated in the regioselective C-C cleavages of several pexidartinib analogs. The regiospecificity of CYP3A-catalyzed oxygen ipso-addition under environmentally friendly conditions may be attractive and inspire biomimetic or P450-engineering methods to address the challenging task of C-C bond cleavages.
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Affiliation(s)
- Xuan Qin
- Center for Drug Discovery, Department of Pathology and Immunology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas, 77030, USA
| | - Yong Wang
- Center for Drug Discovery, Department of Pathology and Immunology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas, 77030, USA
| | - Qiuji Ye
- Center for Drug Discovery, Department of Pathology and Immunology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas, 77030, USA
| | - John M Hakenjos
- Center for Drug Discovery, Department of Pathology and Immunology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas, 77030, USA
| | - Jin Wang
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas, 77030, USA
| | - Mingxing Teng
- Center for Drug Discovery, Department of Pathology and Immunology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas, 77030, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas, 77030, USA
| | - Lei Guo
- National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Rd, Jefferson, Arkansas, USA
| | - Zhi Tan
- Center for Drug Discovery, Department of Pathology and Immunology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas, 77030, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas, 77030, USA
| | - Damian W Young
- Center for Drug Discovery, Department of Pathology and Immunology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas, 77030, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas, 77030, USA
| | - Kevin R MacKenzie
- Center for Drug Discovery, Department of Pathology and Immunology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas, 77030, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas, 77030, USA
- NMR and Drug Metabolism Core, Advanced Technology Cores, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas, 77030, USA
| | - Feng Li
- Center for Drug Discovery, Department of Pathology and Immunology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas, 77030, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas, 77030, USA
- NMR and Drug Metabolism Core, Advanced Technology Cores, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas, 77030, USA
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3
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Jiang B, Gao L, Wang H, Sun Y, Zhang X, Ke H, Liu S, Ma P, Liao Q, Wang Y, Wang H, Liu Y, Du R, Rogge T, Li W, Shang Y, Houk KN, Xiong X, Xie D, Huang S, Lei X, Yan J. Characterization and heterologous reconstitution of Taxus biosynthetic enzymes leading to baccatin III. Science 2024; 383:622-629. [PMID: 38271490 DOI: 10.1126/science.adj3484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 01/10/2024] [Indexed: 01/27/2024]
Abstract
Paclitaxel is a well known anticancer compound. Its biosynthesis involves the formation of a highly functionalized diterpenoid core skeleton (baccatin III) and the subsequent assembly of a phenylisoserinoyl side chain. Despite intensive investigation for half a century, the complete biosynthetic pathway of baccatin III remains unknown. In this work, we identified a bifunctional cytochrome P450 enzyme [taxane oxetanase 1 (TOT1)] in Taxus mairei that catalyzes an oxidative rearrangement in paclitaxel oxetane formation, which represents a previously unknown enzyme mechanism for oxetane ring formation. We created a screening strategy based on the taxusin biosynthesis pathway and uncovered the enzyme responsible for the taxane oxidation of the C9 position (T9αH1). Finally, we artificially reconstituted a biosynthetic pathway for the production of baccatin III in tobacco.
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Affiliation(s)
- Bin Jiang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Lei Gao
- Beijing National Laboratory for Molecular Sciences, Peking-Tsinghua Center for Life Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Haijun Wang
- Beijing National Laboratory for Molecular Sciences, Peking-Tsinghua Center for Life Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Yaping Sun
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Xiaolin Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Han Ke
- Beijing National Laboratory for Molecular Sciences, Peking-Tsinghua Center for Life Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Shengchao Liu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Pengchen Ma
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Qinggang Liao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yue Wang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Huan Wang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yugeng Liu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Ran Du
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Torben Rogge
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Wei Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yi Shang
- Yunnan Key Laboratory of Potato Biology, The CAAS-YNNU-YINMORE Joint Academy of Potato Sciences, Yunnan Normal University, Kunming, China
| | - K N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Xingyao Xiong
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Daoxin Xie
- Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Sanwen Huang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xiaoguang Lei
- Beijing National Laboratory for Molecular Sciences, Peking-Tsinghua Center for Life Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- Institute for Cancer Research, Shenzhen Bay Laboratory, Shenzhen, China
| | - Jianbin Yan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
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4
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Guengerich FP. Ninety-eight semesters of cytochrome P450 enzymes and related topics-What have I taught and learned? J Biol Chem 2024; 300:105625. [PMID: 38185246 PMCID: PMC10847173 DOI: 10.1016/j.jbc.2024.105625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/03/2024] [Indexed: 01/09/2024] Open
Abstract
This Reflection article begins with my family background and traces my career through elementary and high school, followed by time at the University of Illinois, Vanderbilt University, the University of Michigan, and then for 98 semesters as a Vanderbilt University faculty member. My research career has dealt with aspects of cytochrome P450 enzymes, and the basic biochemistry has had applications in fields as diverse as drug metabolism, toxicology, medicinal chemistry, pharmacogenetics, biological engineering, and bioremediation. I am grateful for the opportunity to work with the Journal of Biological Chemistry not only as an author but also for 34 years as an Editorial Board Member, Associate Editor, Deputy Editor, and interim Editor-in-Chief. Thanks are extended to my family and my mentors, particularly Profs. Harry Broquist and Minor J. Coon, and the more than 170 people who have trained with me. I have never lost the enthusiasm for research that I learned in the summer of 1968 with Harry Broquist, and I have tried to instill this in the many trainees I have worked with. A sentence I use on closing slides is "It's not just a laboratory-it's a fraternity."
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Affiliation(s)
- F Peter Guengerich
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.
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5
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Lappe A, Luelf UJ, Keilhammer M, Bokel A, Urlacher VB. Bacterial cytochrome P450 enzymes: Semi-rational design and screening of mutant libraries in recombinant Escherichia coli cells. Methods Enzymol 2023; 693:133-170. [PMID: 37977729 DOI: 10.1016/bs.mie.2023.09.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Bacterial cytochromes P450 (P450s) have been recognized as attractive targets for biocatalysis and protein engineering. They are soluble cytosolic enzymes that demonstrate higher stability and activity than their membrane-associated eukaryotic counterparts. Many bacterial P450s possess broad substrate spectra and can be produced in well-known expression hosts like Escherichia coli at high levels, which enables quick and convenient mutant libraries construction. However, the majority of bacterial P450s interacts with two auxiliary redox partner proteins, which significantly increase screening efforts. We have established recombinant E. coli cells for screening of P450 variants that rely on two separate redox partners. In this chapter, a case study on construction of a selective P450 to synthesize a precursor of several chemotherapeutics, (-)-podophyllotoxin, is described. The procedure includes co-expression of P450 and redox partner genes in E. coli with subsequent whole-cell conversion of the substrate (-)-deoxypodophyllotoxin in 96-deep-well plates. By omitting the chromatographic separation while measuring mass-to-charge ratios specific for the substrate and product via MS in so-called multiple injections in a single experimental run (MISER) LC/MS, the analysis time could be drastically reduced to roughly 1 min per sample. Screening results were verified by using isolated P450 variants and purified redox partners.
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Affiliation(s)
- Alessa Lappe
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - U Joost Luelf
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Mirco Keilhammer
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Ansgar Bokel
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Vlada B Urlacher
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
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6
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Rhee KY, Jansen RS, Grundner C. Activity-based annotation: the emergence of systems biochemistry. Trends Biochem Sci 2022; 47:785-794. [PMID: 35430135 PMCID: PMC9378515 DOI: 10.1016/j.tibs.2022.03.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 03/10/2022] [Accepted: 03/22/2022] [Indexed: 01/21/2023]
Abstract
Current tools to annotate protein function have failed to keep pace with the speed of DNA sequencing and exponentially growing number of proteins of unknown function (PUFs). A major contributing factor to this mismatch is the historical lack of high-throughput methods to experimentally determine biochemical activity. Activity-based methods, such as activity-based metabolite and protein profiling, are emerging as new approaches for unbiased, global, biochemical annotation of protein function. In this review, we highlight recent experimental, activity-based approaches that offer new opportunities to determine protein function in a biologically agnostic and systems-level manner.
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Affiliation(s)
- Kyu Y Rhee
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA.
| | - Robert S Jansen
- Department of Microbiology, Radboud University, Nijmegen, The Netherlands.
| | - Christoph Grundner
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA; Department of Global Health, University of Washington, Seattle, WA, USA; Department of Pediatrics, University of Washington, Seattle, WA, USA.
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7
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Finnigan JD, Young C, Cook DJ, Charnock SJ, Black GW. Cytochromes P450 (P450s): A review of the class system with a focus on prokaryotic P450s. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020; 122:289-320. [PMID: 32951814 DOI: 10.1016/bs.apcsb.2020.06.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Cytochromes P450 (P450s) are a large superfamily of heme-containing monooxygenases. P450s are found in all Kingdoms of life and exhibit incredible diversity, both at sequence level and also on a biochemical basis. In the majority of cases, P450s can be assigned into one of ten classes based on their associated redox partners, domain architecture and cellular localization. Prokaryotic P450s now represent a large diverse collection of annotated/known enzymes, of which many have great potential biocatalytic potential. The self-sufficient P450 classes (Class VII/VIII) have been explored significantly over the past decade, with many annotated and biochemically characterized members. It is clear that the prokaryotic P450 world is expanding rapidly, as the number of published genomes and metagenome studies increases, and more P450 families are identified and annotated (CYP families).
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Affiliation(s)
| | - Carl Young
- Prozomix Limited, Haltwhistle, Northumberland, United Kingdom
| | - Darren J Cook
- Prozomix Limited, Haltwhistle, Northumberland, United Kingdom
| | | | - Gary W Black
- Hub for Biotechnology in the Built Environment, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
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8
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Jaladanki CK, Gahlawat A, Rathod G, Sandhu H, Jahan K, Bharatam PV. Mechanistic studies on the drug metabolism and toxicity originating from cytochromes P450. Drug Metab Rev 2020; 52:366-394. [DOI: 10.1080/03602532.2020.1765792] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Chaitanya K. Jaladanki
- Department of Medicinal Chemistry and Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), SAS Nagar, Punjab, India
| | - Anuj Gahlawat
- Department of Medicinal Chemistry and Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), SAS Nagar, Punjab, India
| | - Gajanan Rathod
- Department of Medicinal Chemistry and Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), SAS Nagar, Punjab, India
| | - Hardeep Sandhu
- Department of Medicinal Chemistry and Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), SAS Nagar, Punjab, India
| | - Kousar Jahan
- Department of Medicinal Chemistry and Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), SAS Nagar, Punjab, India
| | - Prasad V. Bharatam
- Department of Medicinal Chemistry and Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), SAS Nagar, Punjab, India
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9
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Mnguni FC, Padayachee T, Chen W, Gront D, Yu JH, Nelson DR, Syed K. More P450s Are Involved in Secondary Metabolite Biosynthesis in Streptomyces Compared to Bacillus, Cyanobacteria, and Mycobacterium. Int J Mol Sci 2020; 21:ijms21134814. [PMID: 32646068 PMCID: PMC7369989 DOI: 10.3390/ijms21134814] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 02/11/2020] [Accepted: 02/13/2020] [Indexed: 12/18/2022] Open
Abstract
Unraveling the role of cytochrome P450 monooxygenases (CYPs/P450s), heme-thiolate proteins present in living and non-living entities, in secondary metabolite synthesis is gaining momentum. In this direction, in this study, we analyzed the genomes of 203 Streptomyces species for P450s and unraveled their association with secondary metabolism. Our analyses revealed the presence of 5460 P450s, grouped into 253 families and 698 subfamilies. The CYP107 family was found to be conserved and highly populated in Streptomyces and Bacillus species, indicating its key role in the synthesis of secondary metabolites. Streptomyces species had a higher number of P450s than Bacillus and cyanobacterial species. The average number of secondary metabolite biosynthetic gene clusters (BGCs) and the number of P450s located in BGCs were higher in Streptomyces species than in Bacillus, mycobacterial, and cyanobacterial species, corroborating the superior capacity of Streptomyces species for generating diverse secondary metabolites. Functional analysis via data mining confirmed that many Streptomyces P450s are involved in the biosynthesis of secondary metabolites. This study was the first of its kind to conduct a comparative analysis of P450s in such a large number (203) of Streptomyces species, revealing the P450s’ association with secondary metabolite synthesis in Streptomyces species. Future studies should include the selection of Streptomyces species with a higher number of P450s and BGCs and explore the biotechnological value of secondary metabolites they produce.
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Affiliation(s)
- Fanele Cabangile Mnguni
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa; (F.C.M.); (T.P.)
| | - Tiara Padayachee
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa; (F.C.M.); (T.P.)
| | - Wanping Chen
- Department of Molecular Microbiology and Genetics, University of Göttingen, 37077 Göttingen, Germany;
| | - Dominik Gront
- Faculty of Chemistry, Biological and Chemical Research Center, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland;
| | - Jae-Hyuk Yu
- Department of Bacteriology, University of Wisconsin-Madison, 3155 MSB, 1550 Linden Drive, Madison, WI 53706, USA;
- Department of Systems Biotechnology, Konkuk University, Seoul 05029, Korea
| | - David R. Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA
- Correspondence: (D.R.N.); (K.S.)
| | - Khajamohiddin Syed
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa; (F.C.M.); (T.P.)
- Correspondence: (D.R.N.); (K.S.)
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10
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Dangi B, Park H, Oh TJ. Effects of Alternative Redox Partners and Oxidizing Agents on CYP154C8 Catalytic Activity and Product Distribution. Chembiochem 2018; 19:2273-2282. [PMID: 30136363 DOI: 10.1002/cbic.201800284] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Revised: 08/23/2018] [Indexed: 12/11/2022]
Abstract
CYP154C8 catalyzes the hydroxylation of diverse steroids, as has previously been demonstrated, by using an NADH-dependent system including putidaredoxin and putidaredoxin reductase as redox partner proteins carrying electrons from NADH. In other reactions, CYP154C8 reconstituted with spinach ferredoxin and NADPH-dependent ferredoxin reductase displayed catalytic activity different from that of the NADH-dependent system. The NADPH-dependent system showed multistep oxidation of progesterone and other substrates including androstenedione, testosterone, and nandrolone. (Diacetoxyiodo)benzene was employed to generate compound I (FeO3+ ), actively supporting the redox reactions catalyzed by CYP154C8. In addition to 16α-hydroxylation, progesterone and 11-oxoprogesterone also underwent hydroxylation at the 6β-position in reactions supported by (diacetoxyiodo)benzene. CYP154C8 was active in the presence of high concentrations (>10 mm) of H2 O2 , with optimum conversion surprisingly being achieved at ≈75 mm H2 O2 . More importantly, H2 O2 tolerance by CYP154C8 was evident in the very low heme oxidation rate constant (K) even at high concentrations of H2 O2 . Our results demonstrate that alternative redox partners and oxidizing agents influence the catalytic efficiency and product distribution of a cytochrome P450 enzyme. More importantly, these choices affected the type and selectivity of reaction catalyzed by the P450 enzyme.
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Affiliation(s)
- Bikash Dangi
- Department of Life Science and Biochemical Engineering, SunMoon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, Chungnam, 31460, Republic of Korea
| | - Hyun Park
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, 21990, Republic of Korea.,Department of Polar Sciences, University of Science and Technology, Incheon, 21990, Republic of Korea
| | - Tae-Jin Oh
- Department of Life Science and Biochemical Engineering, SunMoon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, Chungnam, 31460, Republic of Korea.,Department of Pharmaceutical Engineering and Biotechnology, SunMoon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, Chungnam, 31460, Republic of Korea.,Genome-based BioIT Convergence Institute, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, Chungnam, 31460, Republic of Korea
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11
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Guengerich FP, Yoshimoto FK. Formation and Cleavage of C-C Bonds by Enzymatic Oxidation-Reduction Reactions. Chem Rev 2018; 118:6573-6655. [PMID: 29932643 DOI: 10.1021/acs.chemrev.8b00031] [Citation(s) in RCA: 159] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Many oxidation-reduction (redox) enzymes, particularly oxygenases, have roles in reactions that make and break C-C bonds. The list includes cytochrome P450 and other heme-based monooxygenases, heme-based dioxygenases, nonheme iron mono- and dioxygenases, flavoproteins, radical S-adenosylmethionine enzymes, copper enzymes, and peroxidases. Reactions involve steroids, intermediary metabolism, secondary natural products, drugs, and industrial and agricultural chemicals. Many C-C bonds are formed via either (i) coupling of diradicals or (ii) generation of unstable products that rearrange. C-C cleavage reactions involve several themes: (i) rearrangement of unstable oxidized products produced by the enzymes, (ii) oxidation and collapse of radicals or cations via rearrangement, (iii) oxygenation to yield products that are readily hydrolyzed by other enzymes, and (iv) activation of O2 in systems in which the binding of a substrate facilitates O2 activation. Many of the enzymes involve metals, but of these, iron is clearly predominant.
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Affiliation(s)
- F Peter Guengerich
- Department of Biochemistry , Vanderbilt University School of Medicine , Nashville , Tennessee 37232-0146 , United States.,Department of Chemistry , University of Texas-San Antonio , San Antonio , Texas 78249-0698 , United States
| | - Francis K Yoshimoto
- Department of Biochemistry , Vanderbilt University School of Medicine , Nashville , Tennessee 37232-0146 , United States.,Department of Chemistry , University of Texas-San Antonio , San Antonio , Texas 78249-0698 , United States
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12
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Dangi B, Kim KH, Kang SH, Oh TJ. Tracking Down a New Steroid-Hydroxylating Promiscuous Cytochrome P450: CYP154C8 fromStreptomycessp. W2233-SM. Chembiochem 2018. [DOI: 10.1002/cbic.201800018] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Bikash Dangi
- Department of Life Science and Biochemical Engineering; SunMoon University; 70 Sunmoon-ro 221 Tangjeong-myeon Asan-si Chungnam 31460 Republic of Korea
| | - Ki-Hwa Kim
- Department of Life Science and Biochemical Engineering; SunMoon University; 70 Sunmoon-ro 221 Tangjeong-myeon Asan-si Chungnam 31460 Republic of Korea
| | - Sang-Ho Kang
- Genomics Division; National Institute of Agricultural Sciences, RDA; Jeonju 54874 Republic of Korea
| | - Tae-Jin Oh
- Department of Life Science and Biochemical Engineering; SunMoon University; 70 Sunmoon-ro 221 Tangjeong-myeon Asan-si Chungnam 31460 Republic of Korea
- Department of Pharmaceutical Engineering and Biotechnology; SunMoon University; 70 Sunmoon-ro 221 Tangjeong-myeon Asan-si Chungnam 31460 Republic of Korea
- Genome-based BioIT Convergence Institute; 70 Sunmoon-ro 221 Tangjeong-myeon Asan-si Chungnam 31460 Republic of Korea
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13
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Rudolf JD, Chang CY, Ma M, Shen B. Cytochromes P450 for natural product biosynthesis in Streptomyces: sequence, structure, and function. Nat Prod Rep 2017; 34:1141-1172. [PMID: 28758170 PMCID: PMC5585785 DOI: 10.1039/c7np00034k] [Citation(s) in RCA: 145] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Covering: up to January 2017Cytochrome P450 enzymes (P450s) are some of the most exquisite and versatile biocatalysts found in nature. In addition to their well-known roles in steroid biosynthesis and drug metabolism in humans, P450s are key players in natural product biosynthetic pathways. Natural products, the most chemically and structurally diverse small molecules known, require an extensive collection of P450s to accept and functionalize their unique scaffolds. In this review, we survey the current catalytic landscape of P450s within the Streptomyces genus, one of the most prolific producers of natural products, and comprehensively summarize the functionally characterized P450s from Streptomyces. A sequence similarity network of >8500 P450s revealed insights into the sequence-function relationships of these oxygen-dependent metalloenzymes. Although only ∼2.4% and <0.4% of streptomycete P450s have been functionally and structurally characterized, respectively, the study of streptomycete P450s involved in the biosynthesis of natural products has revealed their diverse roles in nature, expanded their catalytic repertoire, created structural and mechanistic paradigms, and exposed their potential for biomedical and biotechnological applications. Continued study of these remarkable enzymes will undoubtedly expose their true complement of chemical and biological capabilities.
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Affiliation(s)
- Jeffrey D Rudolf
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
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14
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Zhang X, Li S. Expansion of chemical space for natural products by uncommon P450 reactions. Nat Prod Rep 2017; 34:1061-1089. [DOI: 10.1039/c7np00028f] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
This review focuses on unusual P450 reactions related to new chemistry, skeleton construction, structure re-shaping, and protein–protein interactions in natural product biosynthesis, which play significant roles in chemical space expansion for natural products.
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Affiliation(s)
- Xingwang Zhang
- Shandong Provincial Key Laboratory of Synthetic Biology
- CAS Key Laboratory of Biofuels at Qingdao Institute of Bioenergy and Bioprocess Technology
- Chinese Academy of Sciences
- Qingdao
- China
| | - Shengying Li
- Shandong Provincial Key Laboratory of Synthetic Biology
- CAS Key Laboratory of Biofuels at Qingdao Institute of Bioenergy and Bioprocess Technology
- Chinese Academy of Sciences
- Qingdao
- China
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15
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Yoshimoto FK, Peng HM, Zhang H, Anderson SM, Auchus RJ. Epoxidation activities of human cytochromes P450c17 and P450c21. Biochemistry 2014; 53:7531-40. [PMID: 25386927 PMCID: PMC4263428 DOI: 10.1021/bi5011865] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
![]()
Some cytochrome P450 enzymes epoxidize
unsaturated substrates,
but this activity has not been described for the steroid hydroxylases.
Physiologic steroid substrates, however, lack carbon–carbon
double bonds in the parts of the pregnane molecules where steroidogenic
hydroxylations occur. Limited data on the reactivity of steroidogenic
P450s toward olefinic substrates exist, and the study of occult activities
toward alternative substrates is a fundamental aspect of the growing
field of combinatorial biosynthesis. We reasoned that human P450c17
(steroid 17-hydroxylase/17,20-lyase, CYP17A1), which 17- and 16α-hydroxylates
progesterone, might catalyze the formation of the 16α,17-epoxide
from 16,17-dehydroprogesterone (pregna-4,16-diene-3,20-dione). CYP17A1
catalyzed the novel 16α,17-epoxidation and the ordinarily minor
21-hydroxylation of 16,17-dehydroprogesterone in a 1:1 ratio. CYP17A1
mutation A105L, which has reduced progesterone 16α-hydroxylase
activity, gave a 1:5 ratio of epoxide:21-hydroxylated products. In
contrast, human P450c21 (steroid 21-hydroxylase, CYP21A2) converted
16,17-dehydroprogesterone to the 21-hydroxylated product and only
a trace of epoxide. CYP21A2 mutation V359A, which has significant
16α-hydroxylase activity, likewise afforded the 21-hydroxylated
product and slightly more epoxide. CYP17A1 wild-type and mutation
A105L do not 21- or 16α-hydroxylate pregnenolone, but the enzymes
21-hydroxylated and 16α,17-epoxidized 16,17-dehydropregnenolone
(pregna-5,16-diene-3β-ol-20-one) in 4:1 or 12:1 ratios, respectively.
Catalase and superoxide dismutase did not prevent epoxide formation.
The progesterone epoxide was not a time-dependent, irreversible CYP17A1
inhibitor. Our substrate modification studies have revealed occult
epoxidase and 21-hydroxylase activities of CYP17A1, and the fraction
of epoxide formed correlated with the 16α-hydroxylase activity
of the enzymes.
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Affiliation(s)
- Francis K Yoshimoto
- Division of Metabolism, Endocrinology, & Diabetes, Department of Internal Medicine and ‡Department of Pharmacology, University of Michigan , Ann Arbor, Michigan 48109, United States
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16
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Herzog K, Bracco P, Onoda A, Hayashi T, Hoffmann K, Schallmey A. Enzyme-substrate complex structures of CYP154C5 shed light on its mode of highly selective steroid hydroxylation. ACTA ACUST UNITED AC 2014; 70:2875-89. [PMID: 25372679 DOI: 10.1107/s1399004714019129] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 08/25/2014] [Indexed: 01/06/2023]
Abstract
CYP154C5 from Nocardia farcinica is a bacterial cytochrome P450 monooxygenase active on steroid molecules. The enzyme has recently been shown to exhibit exclusive regioselectivity and stereoselectivity in the conversion of various pregnans and androstans, yielding 16α-hydroxylated steroid products. This makes the enzyme an attractive candidate for industrial application in steroid hormone synthesis. Here, crystal structures of CYP154C5 in complex with four different steroid molecules were solved at resolutions of up to 1.9 Å. These are the first reported P450 structures from the CYP154 family in complex with a substrate. The active site of CYP154C5 forms a flattened hydrophobic channel with two opposing polar regions, perfectly resembling the size and polarity distribution of the steroids and thus resulting in highly specific steroid binding with Kd values in the range 10-100 nM. Key enzyme-substrate interactions were identified that accounted for the exclusive regioselectivity and stereoselectivity of the enzyme. Additionally, comparison of the four CYP154C5-steroid structures revealed distinct structural differences, explaining the observed variations in kinetic data obtained for this P450 with the steroids pregnenolone, dehydroepiandrosterone, progesterone, androstenedione, testosterone and nandrolone. This will facilitate the generation of variants with improved activity or altered selectivity in the future by means of protein engineering.
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Affiliation(s)
- Konrad Herzog
- Junior Professorship for Biocatalysis, Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Paula Bracco
- Junior Professorship for Biocatalysis, Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Akira Onoda
- Department of Applied Chemistry, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Takashi Hayashi
- Department of Applied Chemistry, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kurt Hoffmann
- Institute of Molecular Biotechnology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Anett Schallmey
- Junior Professorship for Biocatalysis, Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
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17
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Arfeen M, Patel DS, Abbat S, Taxak N, Bharatam PV. Importance of cytochromes in cyclization reactions: Quantum chemical study on a model reaction of proguanil to cycloguanil. J Comput Chem 2014; 35:2047-55. [DOI: 10.1002/jcc.23719] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2014] [Revised: 08/04/2014] [Accepted: 08/06/2014] [Indexed: 12/23/2022]
Affiliation(s)
- Minhajul Arfeen
- Department of Medicinal Chemistry; National Institute of Pharmaceutical Education and Research (NIPER); S. A. S. Nagar (Mohali) 160 062 Punjab India
| | - Dhilon S. Patel
- Department of Medicinal Chemistry; National Institute of Pharmaceutical Education and Research (NIPER); S. A. S. Nagar (Mohali) 160 062 Punjab India
| | - Sheenu Abbat
- Department of Pharmacoinformatics; National Institute of Pharmaceutical Education and Research (NIPER); S. A. S. Nagar (Mohali) 160 062 Punjab India
| | - Nikhil Taxak
- Department of Medicinal Chemistry; National Institute of Pharmaceutical Education and Research (NIPER); S. A. S. Nagar (Mohali) 160 062 Punjab India
| | - Prasad V. Bharatam
- Department of Medicinal Chemistry; National Institute of Pharmaceutical Education and Research (NIPER); S. A. S. Nagar (Mohali) 160 062 Punjab India
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18
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Prosser GA, Larrouy-Maumus G, de Carvalho LPS. Metabolomic strategies for the identification of new enzyme functions and metabolic pathways. EMBO Rep 2014; 15:657-69. [PMID: 24829223 PMCID: PMC4197876 DOI: 10.15252/embr.201338283] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Recent technological advances in accurate mass spectrometry and data analysis have revolutionized
metabolomics experimentation. Activity-based and global metabolomic profiling methods allow
simultaneous and rapid screening of hundreds of metabolites from a variety of chemical classes,
making them useful tools for the discovery of novel enzymatic activities and metabolic pathways. By
using the metabolome of the relevant organism or close species, these methods capitalize on
biological relevance, avoiding the assignment of artificial and non-physiological functions. This
review discusses state-of-the-art metabolomic approaches and highlights recent examples of their use
for enzyme annotation, discovery of new metabolic pathways, and gene assignment of orphan metabolic
activities across diverse biological sources.
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Affiliation(s)
- Gareth A Prosser
- Mycobacterial Research Division, MRC National Institute for Medical Research, London, UK
| | - Gerald Larrouy-Maumus
- Mycobacterial Research Division, MRC National Institute for Medical Research, London, UK
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19
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Regio- and stereospecific hydroxylation of various steroids at the 16α position of the D ring by the Streptomyces griseus cytochrome P450 CYP154C3. Appl Environ Microbiol 2013; 80:1371-9. [PMID: 24334658 DOI: 10.1128/aem.03504-13] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cytochrome P450 monooxygenases (P450s), which constitute a superfamily of heme-containing proteins, catalyze the direct oxidation of a variety of compounds in a regio- and stereospecific manner; therefore, they are promising catalysts for use in the oxyfunctionalization of chemicals. In the course of our comprehensive substrate screening for all 27 putative P450s encoded by the Streptomyces griseus genome, we found that Escherichia coli cells producing an S. griseus P450 (CYP154C3), which was fused C terminally with the P450 reductase domain (RED) of a self-sufficient P450 from Rhodococcus sp., could transform various steroids (testosterone, progesterone, Δ(4)-androstene-3,17-dione, adrenosterone, 1,4-androstadiene-3,17-dione, dehydroepiandrosterone, 4-pregnane-3,11,20-trione, and deoxycorticosterone) into their 16α-hydroxy derivatives as determined by nuclear magnetic resonance and high-resolution mass spectrometry analyses. The purified CYP154C3, which was not fused with RED, also catalyzed the regio- and stereospecific hydroxylation of these steroids at the same position with the aid of ferredoxin and ferredoxin reductase from spinach. The apparent equilibrium dissociation constant (Kd) values of the binding between CYP154C3 and these steroids were less than 8 μM as determined by the heme spectral change, indicating that CYP154C3 strongly binds to these steroids. Furthermore, kinetic parameters of the CYP154C3-catalyzed hydroxylation of Δ(4)-androstene-3,17-dione were determined (Km, 31.9 ± 9.1 μM; kcat, 181 ± 4.5 s(-1)). We concluded that CYP154C3 is a steroid D-ring 16α-specific hydroxylase which has considerable potential for industrial applications. This is the first detailed enzymatic characterization of a P450 enzyme that has a steroid D-ring 16α-specific hydroxylation activity.
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von Bühler C, Le-Huu P, Urlacher VB. Cluster Screening: An Effective Approach for Probing the Substrate Space of Uncharacterized Cytochrome P450s. Chembiochem 2013; 14:2189-98. [DOI: 10.1002/cbic.201300271] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Indexed: 11/12/2022]
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21
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Abstract
Cytochrome P450 enzymes primarily catalyze mixed-function oxidation reactions, plus some reductions and rearrangements of oxygenated species, e.g. prostaglandins. Most of these reactions can be rationalized in a paradigm involving Compound I, a high-valent iron-oxygen complex (FeO(3+)), to explain seemingly unusual reactions, including ring couplings, ring expansion and contraction, and fusion of substrates. Most P450s interact with flavoenzymes or iron-sulfur proteins to receive electrons from NAD(P)H. In some cases, P450s are fused to protein partners. Other P450s catalyze non-redox isomerization reactions. A number of permutations on the P450 theme reveal the diversity of cytochrome P450 form and function.
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Affiliation(s)
- F Peter Guengerich
- Department of Biochemistry and Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA.
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22
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Lamb DC, Waterman MR. Unusual properties of the cytochrome P450 superfamily. Philos Trans R Soc Lond B Biol Sci 2013; 368:20120434. [PMID: 23297356 PMCID: PMC3538423 DOI: 10.1098/rstb.2012.0434] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
During the early years of cytochrome P450 research, a picture of conserved properties arose from studies of mammalian forms of these monooxygenases. They included the protohaem prosthetic group, the cysteine residue that coordinates to the haem iron and the reduced CO difference spectrum. Alternatively, the most variable feature of P450s was the enzymatic activities, which led to the conclusion that there are a large number of these enzymes, most of which have yet to be discovered. More recently, studies of these enzymes in other eukaryotes and in prokaryotes have led to the discovery of unexpected P450 properties. Many are variations of the original properties, whereas others are difficult to explain because of their unique nature relative to the rest of the known members of the superfamily. These novel properties expand our appreciation of the broad view of P450 structure and function, and generate curiosity concerning the evolution of P450s. In some cases, structural properties, previously not found in P450s, can lead to enzymatic activities impacting the biological function of organisms containing these enzymes; whereas, in other cases, the biological reason for the variations are not easily understood. Herein, we present particularly interesting examples in detail rather than cataloguing them all.
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Affiliation(s)
- David C Lamb
- Institute of Life Science, Medical School, Swansea University, Singleton Park, Swansea SA2 8PP, UK.
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23
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Tian Z, Cheng Q, Yoshimoto FK, Lei L, Lamb DC, Guengerich FP. Cytochrome P450 107U1 is required for sporulation and antibiotic production in Streptomyces coelicolor. Arch Biochem Biophys 2013; 530:101-7. [PMID: 23357279 PMCID: PMC3600146 DOI: 10.1016/j.abb.2013.01.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Revised: 01/02/2013] [Accepted: 01/04/2013] [Indexed: 11/15/2022]
Abstract
The filamentous bacterium Streptomyces coelicolor has a complex life cycle involving the formation of hair-like aerial mycelia on the colony surface, which differentiate into chains of spores. Genes required for the initiation of aerial mycelium formation have been termed 'bld' (bald), describing the smooth, undifferentiated colonies of mutant strains. We report the identification of a new bld gene designated as sco3099 and biochemical analysis of its encoded enzyme, cytochrome P450 (P450, or CYP) 107U1. Deletion of sco3099 resulted in a mutant defective in aerial hyphae sporulation and sensitive to heat shock, indicating that P450 107U1 plays a key role in growth and development of S. coelicolor. This is the first P450 reported to participate in a sporulation process in Streptomycetes. The substrate and catalytic properties of P450 107U1 were further investigated in mass spectrometry-based metabolomic studies. Glycocholic acid (from the medium) was identified as a substrate of P450 107U1 and was oxidized to glyco-7-oxo-deoxycholic acid. Although this reaction is apparently not relevant to the observed sporulation deficiency, it suggests that P450 107U1 might exert its physiological function by oxidizing other steroid-like molecules.
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Affiliation(s)
- Zhenghua Tian
- Department of Biochemistry and Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Qian Cheng
- Department of Biochemistry and Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Francis K. Yoshimoto
- Department of Biochemistry and Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Li Lei
- Department of Biochemistry and Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - David C. Lamb
- Institute of Life Science and Swansea Medical School, University of Wales, Swansea, SA2 8PP, UK
| | - F. Peter Guengerich
- Department of Biochemistry and Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
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24
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Kelly SL, Kelly DE. Microbial cytochromes P450: biodiversity and biotechnology. Where do cytochromes P450 come from, what do they do and what can they do for us? Philos Trans R Soc Lond B Biol Sci 2013; 368:20120476. [PMID: 23297358 DOI: 10.1098/rstb.2012.0476] [Citation(s) in RCA: 136] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The first eukaryote genome revealed three yeast cytochromes P450 (CYPs), hence the subsequent realization that some microbial fungal genomes encode these proteins in 1 per cent or more of all genes (greater than 100) has been surprising. They are unique biocatalysts undertaking a wide array of stereo- and regio-specific reactions and so hold promise in many applications. Based on ancestral activities that included 14α-demethylation during sterol biosynthesis, it is now seen that CYPs are part of the genes and metabolism of most eukaryotes. In contrast, Archaea and Eubacteria often do not contain CYPs, while those that do are frequently interesting as producers of natural products undertaking their oxidative tailoring. Apart from roles in primary and secondary metabolism, microbial CYPs are actual/potential targets of drugs/agrochemicals and CYP51 in sterol biosynthesis is exhibiting evolution to resistance in the clinic and the field. Other CYP applications include the first industrial biotransformation for corticosteroid production in the 1950s, the diversion into penicillin synthesis in early mutations in fungal strain improvement and bioremediation using bacteria and fungi. The vast untapped resource of orphan CYPs in numerous genomes is being probed and new methods for discovering function and for discovering desired activities are being investigated.
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Affiliation(s)
- Steven L Kelly
- Centre for Cytochrome P450 Biodiversity, Institute of Life Science and College of Medicine, Swansea University, Singleton Park, Swansea SA2 8PP, UK.
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25
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Cheng Q, Guengerich FP. Identification of endogenous substrates of orphan cytochrome P450 enzymes through the use of untargeted metabolomics approaches. Methods Mol Biol 2013; 987:71-7. [PMID: 23475668 DOI: 10.1007/978-1-62703-321-3_6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Metabolomics provides an invaluable means to interrogate the function of "orphan" enzymes, i.e., those whose endogenous substrates are not known. Here we describe a high-performance liquid chromatography-coupled mass spectrometry (HPLC-MS)-based metabolomics approach to identify an endogenous substrate of an orphan cytochrome P450.
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Affiliation(s)
- Qian Cheng
- Department of Biochemistry and Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, TN, USA
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26
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Abstract
Diverse oxygenation patterns of natural products generated by secondary metabolic pathways in microorganisms and plants are largely achieved through the tailoring reactions catalysed by cytochrome P450 enzymes (P450s). P450s are a large family of oxidative hemoproteins found in all life forms from prokaryotes to humans. Understanding the reactivity and selectivity of these fascinating C-H bond-activating catalysts will advance their use in generating valuable pharmaceuticals and products for medicine, agriculture and industry. A major strength of this P450 group is its set of established enzyme-substrate relationships, the source of the most detailed knowledge on how P450 enzymes work. Engineering microbial-derived P450 enzymes to accommodate alternative substrates and add new functions continues to be an important near- and long-term practical goal driving the structural characterization of these molecules. Understanding the natural evolution of P450 structure-function should accelerate metabolic engineering and directed evolutionary approaches to enhance diversification of natural product structures and other biosynthetic applications.
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Affiliation(s)
- Larissa M. Podust
- Department of Pathology, Molecular Structure Group and Center for Discovery and Innovation in Parasitic Diseases (CDIPD), University of California San Francisco, San Francisco, California, 94158, USA. Fax: 415 502 8193; Tel: 415 514 1381;
| | - David H. Sherman
- Life Sciences Institute, Departments of Medicinal Chemistry, Chemistry, and Microbiology & Immunology, University of Michigan, Ann Arbor, Michigan, 48109, USA. Fax: 734-615-3641; Tel: 734 615 9907;
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27
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Xiao Y, Guengerich FP. Metabolomic analysis and identification of a role for the orphan human cytochrome P450 2W1 in selective oxidation of lysophospholipids. J Lipid Res 2012; 53:1610-7. [PMID: 22591743 DOI: 10.1194/jlr.m027185] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Human cytochrome P450 (P450) 2W1 is still considered an "orphan" because its physiological function is not characterized. To identify its substrate specificity, the purified recombinant enzyme was incubated with colorectal cancer extracts for untargeted substrate searches using an LC/MS-based metabolomic and isotopic labeling approach. In addition to previously reported fatty acids, oleyl (18:1) lysophosphatidylcholine (LPC, lysolecithin) was identified as a substrate for P450 2W1. Other human P450 enzymes tested showed little activity with 18:1 LPC. In addition to the LPCs, P450 2W1 acted on a series of other lysophospholipids, including lysophosphatidylinositol, lysophosphatidylserine, lysophosphatidylglycerol, lysophosphatidylethanolamine, and lysophosphatidic acid but not diacylphospholipids. P450 2W1 utilized sn-1 18:1 LPC as a substrate much more efficiently than the sn-2 isomer; we conclude that the sn-1 isomers of lysophospholipids are preferred substrates. Chiral analysis was performed on the 18:1 epoxidation products and showed enantio-selectivity for formation of (9R,10S) over (9S,10R). [corrected]. The kinetics and position specificities of P450 2W1-catalyzed oxygenation of lysophospholipids (16:0 LPC and 18:1 LPC) and fatty acids (C16:0 and C18:1) were also determined. Epoxidation and hydroxylation of 18:1 LPC are considerably more efficient than for the C18:1 free fatty acid.
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Affiliation(s)
- Yi Xiao
- Department of Biochemistry and Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA
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28
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Guengerich FP, Cheng Q. Orphans in the human cytochrome P450 superfamily: approaches to discovering functions and relevance in pharmacology. Pharmacol Rev 2011; 63:684-99. [PMID: 21737533 DOI: 10.1124/pr.110.003525] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
As a result of technical advances in recombinant DNA technology and nucleotide sequencing, entire genome sequences have become available in the past decade and offer potential in understanding diseases. However, a central problem in the biochemical sciences is that the functions of only a fraction of the genes/proteins are known, and this is also an issue in pharmacology. This review is focused on issues related to the functions of cytochrome P450 (P450) enzymes. P450 functions can be categorized in several groups: 1) Some P450s have critical roles in the metabolism of endogenous substrates (e.g., sterols and fat-soluble vitamins). 2) Some P450s are not generally critical to normal physiology but function in relatively nonselective protection from the many xenobiotic chemicals to which mammals (including humans) are exposed in their diets [as well as more anthropomorphic chemicals (e.g., drugs, pesticides)]. 3) Some P450s have not been extensively studied and are termed "orphans" here. With regard to elucidation of any physiological functions of the orphan P450s, the major subject of this review, it is clear that simple trial-and-error approaches with individual substrate candidates will not be very productive in addressing questions about function. A series of liquid chromatography/mass spectrometry/informatics approaches are discussed, along with some successes with both human and bacterial P450s. Current information on what are still considered "orphan" P450s is presented. The potential for application of some of these approaches to other enzyme systems is also discussed.
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Affiliation(s)
- F Peter Guengerich
- Department of Biochemistry and Center in Molecular Toxicology, Vanderbilt University School of Medicine, 638 Robinson Research Building, 2200 Pierce Avenue, Nashville, Tennessee 37232-0146, USA.
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