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Di Nardo G, Gilardi G. Optimization of the bacterial cytochrome P450 BM3 system for the production of human drug metabolites. Int J Mol Sci 2012; 13:15901-24. [PMID: 23443101 PMCID: PMC3546669 DOI: 10.3390/ijms131215901] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Revised: 11/01/2012] [Accepted: 11/13/2012] [Indexed: 12/28/2022] Open
Abstract
Drug metabolism in human liver is a process involving many different enzymes. Among them, a number of cytochromes P450 isoforms catalyze the oxidation of most of the drugs commercially available. Each P450 isoform acts on more than one drug, and one drug may be oxidized by more than one enzyme. As a result, multiple products may be obtained from the same drug, and as the metabolites can be biologically active and may cause adverse drug reactions (ADRs), the metabolic profile of a new drug has to be known before this can be commercialized. Therefore, the metabolites of a certain drug must be identified, synthesized and tested for toxicity. Their synthesis must be in sufficient quantities to be used for metabolic tests. This review focuses on the progresses done in the field of the optimization of a bacterial self-sufficient and efficient cytochrome P450, P450 BM3 from Bacillus megaterium, used for the production of metabolites of human enzymes. The progress made in the improvement of its catalytic performance towards drugs, the substitution of the costly NADPH cofactor and its immobilization and scale-up of the process for industrial application are reported.
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Affiliation(s)
- Giovanna Di Nardo
- Department of Life Sciences and Systems Biology, University of Torino, via Accademia Albertina 13, 10123 Torino, Italy; E-Mail:
| | - Gianfranco Gilardi
- Department of Life Sciences and Systems Biology, University of Torino, via Accademia Albertina 13, 10123 Torino, Italy; E-Mail:
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52
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Choi KY, Jung E, Jung DH, An BR, Pandey BP, Yun H, Sung C, Park HY, Kim BG. Engineering of daidzein 3'-hydroxylase P450 enzyme into catalytically self-sufficient cytochrome P450. Microb Cell Fact 2012; 11:81. [PMID: 22697884 PMCID: PMC3434051 DOI: 10.1186/1475-2859-11-81] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Accepted: 05/16/2012] [Indexed: 11/10/2022] Open
Abstract
A cytochrome P450 (CYP) enzyme, 3’-daidzein hydroxylase, CYP105D7 (3’-DH), responsible for daidzein hydroxylation at the 3’-position, was recently reported. CYP105D7 (3’-DH) is a class I type of CYP that requires electrons provided through electron transfer proteins such as ferredoxin and ferredoxin reductase. Presently, we constructed an artificial CYP in order to develop a reaction host for the production of a hydroxylated product. Fusion-mediated construction with the reductase domain from self-sufficient CYP102D1 was done to increase electron transfer efficiency and coupling with the oxidative process. An artificial self-sufficient daidzein hydroxylase (3’-ASDH) displayed distinct spectral properties of both flavoprotein and CYP. The fusion enzyme catalyzed hydroxylation of daidzein more efficiently, with a kcat/Km value of 16.8 μM-1 min-1, which was about 24-fold higher than that of the 3’-DH-camA/B reconstituted enzyme. Finally, a recombinant Streptomyces avermitilis host for the expression of 3’-ASDH and production of the hydroxylated product was developed. The conversion that was attained (34.6%) was 5.2-fold higher than that of the wild-type.
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Affiliation(s)
- Kwon-Young Choi
- School of Chemical and Biological Engineering, Institute of Bioengineering, Seoul National University, Seoul, South Korea
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53
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Kaspera R, Sahele T, Lakatos K, Totah RA. Cytochrome P450BM-3 reduces aldehydes to alcohols through a direct hydride transfer. Biochem Biophys Res Commun 2012; 418:464-8. [PMID: 22281497 DOI: 10.1016/j.bbrc.2012.01.040] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Accepted: 01/09/2012] [Indexed: 12/15/2022]
Abstract
Cytochrome P450BM-3 catalyzed the reduction of lipophilic aldehydes to alcohols efficiently. A k(cat) of ∼25 min(-1) was obtained for the reduction of methoxy benzaldehyde with wild type P450BM-3 protein which was higher than in the isolated reductase domain (BMR) alone and increased in specific P450-domain variants. The reduction was caused by a direct hydride transfer from preferentially R-NADP(2)H to the carbonyl moiety of the substrate. Weak substrate-P450-binding of the aldehyde, turnover with the reductase domain alone, a deuterium incorporation in the product from NADP(2)H but not D(2)O, and no inhibition by imidazole suggests the reductase domain of P450BM-3 as the potential catalytic site. However, increased aldehyde reduction by P450 domain variants (P450BM-3 F87A T268A) may involve allosteric or redox mechanistic interactions between heme and reductase domains. This is a novel reduction of aldehydes by P450BM-3 involving a direct hydride transfer and could have implications for the metabolism of endogenous substrates or xenobiotics.
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Affiliation(s)
- Rüdiger Kaspera
- Department of Medicinal Chemistry, University of Washington, Box 357610, Seattle, WA 98195-7610, USA
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54
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Robin A, Köhler V, Jones A, Ali A, Kelly PP, O'Reilly E, Turner NJ, Flitsch SL. Chimeric self-sufficient P450cam-RhFRed biocatalysts with broad substrate scope. Beilstein J Org Chem 2011; 7:1494-8. [PMID: 22238522 PMCID: PMC3252848 DOI: 10.3762/bjoc.7.173] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Accepted: 10/19/2011] [Indexed: 12/31/2022] Open
Abstract
A high-throughput screening protocol for evaluating chimeric, self-sufficient P450 biocatalysts and their mutants against a panel of substrates was developed, leading to the identification of a number of novel biooxidation activities.
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Affiliation(s)
- Aélig Robin
- School of Chemistry & Manchester Interdisciplinary Biocentre (MIB), University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
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55
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Bright TV, Clark BR, O’Brien E, Murphy CD. Bacterial production of hydroxylated and amidated metabolites of flurbiprofen. ACTA ACUST UNITED AC 2011. [DOI: 10.1016/j.molcatb.2011.05.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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56
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Hunter D, Behrendorff J, Johnston W, Hayes P, Huang W, Bonn B, Hayes M, De Voss J, Gillam E. Facile production of minor metabolites for drug development using a CYP3A shuffled library. Metab Eng 2011; 13:682-93. [DOI: 10.1016/j.ymben.2011.09.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Revised: 06/08/2011] [Accepted: 09/07/2011] [Indexed: 10/17/2022]
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57
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Abstract
P450(BM3) (CYP102A1), a fatty acid hydroxylase from Bacillus megaterium, has been extensively studied over a period of almost forty years. The enzyme has been redesigned to catalyse the oxidation of non-natural substrates as diverse as pharmaceuticals, terpenes and gaseous alkanes using a variety of engineering strategies. Crystal structures have provided a basis for several of the catalytic effects brought about by mutagenesis, while changes to reduction potentials, inter-domain electron transfer rates and catalytic parameters have yielded functional insights. Areas of active research interest include drug metabolite production, the development of process-scale techniques, unravelling general mechanistic aspects of P450 chemistry, methane oxidation, and improving selectivity control to allow the synthesis of fine chemicals. This review draws together the disparate research themes and places them in a historical context with the aim of creating a resource that can be used as a gateway to the field.
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Affiliation(s)
- Christopher J C Whitehouse
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford OX1 3QR, UK
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Rea V, Dragovic S, Boerma JS, de Kanter FJJ, Vermeulen NPE, Commandeur JNM. Role of Residue 87 in the Activity and Regioselectivity of Clozapine Metabolism by Drug-Metabolizing CYP102A1 M11H: Application for Structural Characterization of Clozapine GSH Conjugates. Drug Metab Dispos 2011; 39:2411-20. [DOI: 10.1124/dmd.111.041046] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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60
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Rentmeister A, Brown TR, Snow CD, Carbone MN, Arnold FH. Engineered Bacterial Mimics of Human Drug Metabolizing Enzyme CYP2C9. ChemCatChem 2011. [DOI: 10.1002/cctc.201000452] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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61
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Kang JY, Kim SY, Kim D, Kim DH, Shin SM, Park SH, Kim KH, Jung HC, Pan JG, Joung YH, Chi YT, Chae HZ, Ahn T, Yun CH. Characterization of diverse natural variants of CYP102A1 found within a species of Bacillus megaterium. AMB Express 2011; 1:1. [PMID: 21906327 PMCID: PMC3159907 DOI: 10.1186/2191-0855-1-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Accepted: 03/28/2011] [Indexed: 12/03/2022] Open
Abstract
An extreme diversity of substrates and catalytic reactions of cytochrome P450 (P450) enzymes is considered to be the consequence of evolutionary adaptation driven by different metabolic or environmental demands. Here we report the presence of numerous natural variants of P450 BM3 (CYP102A1) within a species of Bacillus megaterium. Extensive amino acid substitutions (up to 5% of the total 1049 amino acid residues) were identified from the variants. Phylogenetic analyses suggest that this P450 gene evolve more rapidly than the rRNA gene locus. It was found that key catalytic residues in the substrate channel and active site are retained. Although there were no apparent variations in hydroxylation activity towards myristic acid (C14) and palmitic acid (C16), the hydroxylation rates of lauric acid (C12) by the variants varied in the range of >25-fold. Interestingly, catalytic activities of the variants are promiscuous towards non-natural substrates including human P450 substrates. It can be suggested that CYP102A1 variants can acquire new catalytic activities through site-specific mutations distal to the active site.
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62
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Non-covalent modification of the active site of cytochrome P450 for inverting the stereoselectivity of monooxygenation. Tetrahedron Lett 2011. [DOI: 10.1016/j.tetlet.2010.11.048] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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63
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Marvalin C, Azerad R. Microbial production of phase I and phase II metabolites of propranolol. Xenobiotica 2010; 41:175-86. [PMID: 21110747 DOI: 10.3109/00498254.2010.535219] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
1. The production in multimilligram amounts of 4- and 5-hydroxylated metabolites of (R)- or (S)-propranolol by biotransformation with two fungal strains, an Absidia sp. M50002 and a Cunninghamella sp. M50036, was carried out, starting from either the racemic drug or pure enantiomers. 2. While both enantiomers of propranolol were hydroxylated in the 5-position by incubation with strain M50002, the strain M50036 operated a chiral discrimination, resulting in the exclusive formation of the 4-hydroxy-(R)-enantiomer. 3. In addition, a Streptomyces sp. strain M52104, isolated from a soil sample, was selected for the high-yield regioselective β-glucuronidation of propranolol and its 4- and 5-hydroxylated derivatives. 4. NMR and mass spectroscopic data have been extensively used for the unambiguous characterization of 4- and 5-hydroxylated and glucuronidated derivatives, all of them corresponding to the major animal and human metabolites of propranolol, a typical substrate of CYP2D6.
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Affiliation(s)
- Cyrille Marvalin
- Bertin-Pharma, 10bis avenue Ampère, Zone d'activités du Pas du Lac, Montigny-le-Bretonneux, France
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64
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Kim KH, Kang JY, Kim DH, Park SH, Park SH, Kim D, Park KD, Lee YJ, Jung HC, Pan JG, Ahn T, Yun CH. Generation of Human Chiral Metabolites of Simvastatin and Lovastatin by Bacterial CYP102A1 Mutants. Drug Metab Dispos 2010; 39:140-50. [DOI: 10.1124/dmd.110.036392] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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65
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Rabe KS, Erkelenz M, Kiko K, Niemeyer CM. Peroxidase activity of bacterial cytochrome P450 enzymes: Modulation by fatty acids and organic solvents. Biotechnol J 2010; 5:891-9. [DOI: 10.1002/biot.201000028] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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66
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Aromatic C–H bond hydroxylation by P450 peroxygenases: a facile colorimetric assay for monooxygenation activities of enzymes based on Russig’s blue formation. J Biol Inorg Chem 2010; 15:1109-15. [DOI: 10.1007/s00775-010-0671-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2009] [Accepted: 04/27/2010] [Indexed: 10/19/2022]
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67
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Kim DH, Kim KH, Kim D, Jung HC, Pan JG, Chi YT, Ahn T, Yun CH. Oxidation of human cytochrome P450 1A2 substrates by Bacillus megaterium cytochrome P450 BM3. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.molcatb.2010.01.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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68
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Park SH, Kim DH, Kim D, Kim DH, Jung HC, Pan JG, Ahn T, Kim D, Yun CH. Engineering Bacterial Cytochrome P450 (P450) BM3 into a Prototype with Human P450 Enzyme Activity Using Indigo Formation. Drug Metab Dispos 2010; 38:732-9. [DOI: 10.1124/dmd.109.030759] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
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69
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Kim DH, Ahn T, Jung HC, Pan JG, Yun CH. Generation of the Human Metabolite Piceatannol from the Anticancer-Preventive Agent Resveratrol by Bacterial Cytochrome P450 BM3. Drug Metab Dispos 2009; 37:932-6. [DOI: 10.1124/dmd.108.026484] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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70
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Chen HC, Swenson RP. Effect of the Insertion of a Glycine Residue into the Loop Spanning Residues 536-541 on the Semiquinone State and Redox Properties of the Flavin Mononucleotide-Binding Domain of Flavocytochrome P450BM-3 from Bacillus megaterium. Biochemistry 2009; 47:13788-99. [PMID: 19055322 DOI: 10.1021/bi800954h] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Despite sharing sequence and structural similarities with other diflavin reductases such as NADPH-cytochrome P450 reductase (CPR) and nitric oxide synthase, flavocytochrome P450BM-3 displays some unique redox and electron transferring properties, including the inability to thermodynamically stabilize the neutral semiquinone (SQ) state of the flavin mononucleotide (FMN) cofactor. Rather, the anionic SQ species is only transiently formed during rapid reduction. Why is this? The absence of a conserved glycine residue and, as a consequence, the shorter and less flexible cofactor-binding loop in P450BM-3 represents a notable difference from other diflavin reductases and the structurally related flavodoxin. This difference may facilitate the formation of a strong hydrogen bond between backbone amide NH group of Asn537 and N5 of the oxidized FMN, an interaction not found in the other proteins. In the flavodoxin, the conserved glycine residue plays a crucial role in a redox-linked conformational change that contributes to the thermodynamic stabilization of the neutral SQ species of the FMN through the formation of a hydrogen bond with the N5H group of the flavin. In this study, a glycine residue was inserted after Tyr536 in the loop within the isolated FMN-binding domain as well as the diflavin reductase domain of P450BM-3, a position equivalent to Gly141 in human CPR. As a result, the insertion variant was observed to accumulate the neutral form of the FMN SQ species much like CPR. The midpoint potential for the SQ/HQ couple decreased by 68 mV, while that for the OX/SQ couple remained unchanged. (15)N NMR data provide evidence of the disruption of the hydrogen bond between the backbone amide group of Asn537 and the N5 atom in the oxidized state of the FMN. Molecular models suggest that the neutral FMN SQ could be stabilized through hydrogen bonding with the backbone carbonyl group of the inserted glycine residue in a manner similar to that of CPR and the flavodoxin. The insertion of the glycine at the same location within the diflavin domain resulted in a purified protein that retained nearly stoichiometric levels of bound FAD but tended to lose the FMN cofactor. This preparation retained one-third of the ferricyanide reductase activity but <1% of the cytochrome c reductase activity of the wild type. However, the insertion variant reconstituted with FMN regained nearly half of the wild-type cytochrome c reductase activity. These results demonstrate the importance of the unique structural characteristics of the shorter loop in P450BM-3 in establishing the unique redox properties of the FMN in this protein but not its general cytochrome reductase activity.
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Affiliation(s)
- Huai-Chun Chen
- Department of Biochemistry and Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210
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71
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Kim DH, Kim KH, Kim DH, Liu KH, Jung HC, Pan JG, Yun CH. Generation of Human Metabolites of 7-Ethoxycoumarin by Bacterial Cytochrome P450 BM3. Drug Metab Dispos 2008; 36:2166-70. [DOI: 10.1124/dmd.108.021220] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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72
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Rabe KS, Gandubert VJ, Spengler M, Erkelenz M, Niemeyer CM. Engineering and assaying of cytochrome P450 biocatalysts. Anal Bioanal Chem 2008; 392:1059-73. [PMID: 18622752 DOI: 10.1007/s00216-008-2248-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2008] [Revised: 06/11/2008] [Accepted: 06/12/2008] [Indexed: 11/29/2022]
Abstract
Cytochrome P450s constitute a highly fascinating superfamily of enzymes which catalyze a broad range of reactions. They are essential for drug metabolism and promise industrial applications in biotechnology and biosensing. The constant search for cytochrome P450 enzymes with enhanced catalytic performances has generated a large body of research. This review will concentrate on two key aspects related to the identification and improvement of cytochrome P450 biocatalysts, namely the engineering and assaying of these enzymes. To this end, recent advances in cytochrome P450 development are reported and commonly used screening methods are surveyed.
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Affiliation(s)
- Kersten S Rabe
- Fakultät für Chemie, Biologisch-Chemische Mikrostrukturtechnik, Technische Universität Dortmund, Otto-Hahn-Strabetae 6, 44227, Dortmund, Germany
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73
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Haines DC, Chen B, Tomchick DR, Bondlela M, Hegde A, Machius M, Peterson JA. Crystal structure of inhibitor-bound P450BM-3 reveals open conformation of substrate access channel. Biochemistry 2008; 47:3662-70. [PMID: 18298086 DOI: 10.1021/bi7023964] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
P450BM-3 is an extensively studied P450 cytochrome that is naturally fused to a cytochrome P450 reductase domain. Crystal structures of the heme domain of this enzyme have previously generated many insights into features of P450 structure, substrate binding specificity, and conformational changes that occur on substrate binding. Although many P450s are inhibited by imidazole, this compound does not effectively inhibit P450BM-3. Omega-imidazolyl fatty acids have previously been found to be weak inhibitors of the enzyme and show some unusual cooperativity with the substrate lauric acid. We set out to improve the properties of these inhibitors by attaching the omega-imidazolyl fatty acid to the nitrogen of an amino acid group, a tactic that we used previously to increase the potency of substrates. The resulting inhibitors were significantly more potent than their parent compounds lacking the amino acid group. A crystal structure of one of the new inhibitors bound to the heme domain of P450BM-3 reveals that the mode of interaction of the amino acid group with the enzyme is different from that previously observed for acyl amino acid substrates. Further, required movements of residues in the active site to accommodate the imidazole group provide an explanation for the low affinity of imidazole itself. Finally, the previously observed cooperativity with lauric acid is explained by a surprisingly open substrate-access channel lined with hydrophobic residues that could potentially accommodate lauric acid in addition to the inhibitor itself.
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Affiliation(s)
- Donovan C Haines
- Department of Chemistry, The University of Texas at Dallas, Dallas, Texas 75083-0688, USA
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Affiliation(s)
- Elizabeth M. J. Gillam
- School of Biomedical Sciences, The University of Queensland, St. Lucia, Brisbane, Australia 4072
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