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Zhang X, Feng Y, Hua Y, Zhang C, Fang B, Long X, Pan Y, Gao B, Zhang JZH, Li L, Ni H, Zhang L. Biosynthesis of eriodictyol in citrus waster by endowing P450BM3 activity of naringenin hydroxylation. Appl Microbiol Biotechnol 2024; 108:84. [PMID: 38189953 PMCID: PMC10787690 DOI: 10.1007/s00253-023-12867-9] [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: 06/20/2023] [Revised: 09/20/2023] [Accepted: 10/13/2023] [Indexed: 01/09/2024]
Abstract
The flavonoid naringenin is abundantly present in pomelo peels, and the unprocessed naringenin in wastes is not friendly for the environment once discarded directly. Fortunately, the hydroxylated product of eriodictyol from naringenin exhibits remarkable antioxidant and anticancer properties. The P450s was suggested promising for the bioconversion of the flavonoids, but less naturally existed P450s show hydroxylation activity to C3' of the naringenin. By well analyzing the catalytic mechanism and the conformations of the naringenin in P450, we proposed that the intermediate Cmpd I ((porphyrin)Fe = O) is more reasonable as key conformation for the hydrolyzation, and the distance between C3'/C5' of naringenin to the O atom of CmpdI determines the hydroxylating activity for the naringenin. Thus, the "flying kite model" that gradually drags the C-H bond of the substrate to the O atom of CmpdI was put forward for rational design. With ab initio design, we successfully endowed the self-sufficient P450-BM3 hydroxylic activity to naringenin and obtained mutant M5-5, with kcat, Km, and kcat/Km values of 230.45 min-1, 310.48 µM, and 0.742 min-1 µM-1, respectively. Furthermore, the mutant M4186 was screened with kcat/Km of 4.28-fold highly improved than the reported M13. The M4186 also exhibited 62.57% yield of eriodictyol, more suitable for the industrial application. This study provided a theoretical guide for the rational design of P450s to the nonnative compounds. KEY POINTS: •The compound I is proposed as the starting point for the rational design of the P450BM3 •"Flying kite model" is proposed based on the distance between O of Cmpd I and C3'/C5' of naringenin •Mutant M15-5 with 1.6-fold of activity than M13 was obtained by ab initio modification.
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Affiliation(s)
- Xingyi Zhang
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, 361021, China
| | - Yinghui Feng
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China
| | - Yuanzhe Hua
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, 361021, China
| | - Chuanxi Zhang
- Department of Micro/Nano Electronics, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Bohuan Fang
- Department of Micro/Nano Electronics, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiang Long
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, 361021, China
| | - Yue Pan
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China
| | - Bei Gao
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - John Z H Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, 200062, China
| | - Lijun Li
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, 361021, China
| | - Hui Ni
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, 361021, China.
| | - Lujia Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China.
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, 200062, China.
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2
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Schelvis JPM, Chen Z, Messina MA, Catalano J. Effect of CO binding to P450 BM3 F393 mutants on electron density distribution in the heme cofactor. J Inorg Biochem 2024; 259:112660. [PMID: 39002177 DOI: 10.1016/j.jinorgbio.2024.112660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 06/04/2024] [Accepted: 07/03/2024] [Indexed: 07/15/2024]
Abstract
Resonance Raman spectroscopy has been performed on a set of cytochrome P450 BM3 heme domains in which mutation of the highly conserved Phe393 induces significant variation in heme iron reduction potential. In previous work [Chen, Z., Ost, T.W.B., and Schelvis, J.P.M. (2004) Biochemistry 43, 1798-1808], a correlation between heme vinyl conformation and the heme iron reduction potential indicated a steric control by the protein over the distribution of electron density in the reduced heme cofactor. The current study aims to monitor changes in electron density on the ferrous heme cofactor following CO binding. In addition, ferric-NO complexes have been studied to investigate potential changes to the proximal Cys400 thiolate. We find that binding of CO to the ferrous heme domains results in a reorientation of the vinyl groups to a largely out-of-plane conformation, the extent of which correlates with the size of the residue at position 393. We conclude that FeII dπ back bonding to the CO ligand largely takes away the need for conjugation of the vinyl groups with the porphyrin ring to accommodate FeII dπ back bonding to the porphyrin ligand. The ferrous-CO and ferric-NO data are consistent with a small decrease in σ-electron donation from the proximal Cys400 thiolate in the F393A mutant and, to a lesser extent, the F393H mutant, potentially due to a small increase in hydrogen bonding to the proximal ligand. Phe393 seems strategically placed to preserve robust σ-electron donation to the heme iron and to fine-tune its electron density by limiting vinyl group rotation.
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Affiliation(s)
- Johannes P M Schelvis
- Department of Chemistry and Biochemistry, Montclair State University, 1 Normal Avenue, Montclair, NJ 07043, USA.
| | - Zhucheng Chen
- School of Life Sciences, Tsinghua University, Beijing, China.
| | - Marisa A Messina
- Department of Chemistry and Biochemistry, Montclair State University, 1 Normal Avenue, Montclair, NJ 07043, USA.
| | - Jaclyn Catalano
- Department of Chemistry and Biochemistry, Montclair State University, 1 Normal Avenue, Montclair, NJ 07043, USA.
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Mokhosoev IM, Astakhov DV, Terentiev AA, Moldogazieva NT. Cytochrome P450 monooxygenase systems: Diversity and plasticity for adaptive stress response. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2024; 193:19-34. [PMID: 39245215 DOI: 10.1016/j.pbiomolbio.2024.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 08/21/2024] [Accepted: 09/04/2024] [Indexed: 09/10/2024]
Abstract
Superfamily of cytochromes P450 (CYPs) is composed of heme-thiolate-containing monooxygenase enzymes, which play crucial roles in the biosynthesis, bioactivation, and detoxification of a variety of organic compounds, both endogenic and exogenic. Majority of CYP monooxygenase systems are multi-component and contain various redox partners, cofactors and auxiliary proteins, which contribute to their diversity in both prokaryotes and eukaryotes. Recent progress in bioinformatics and computational biology approaches make it possible to undertake whole-genome and phylogenetic analyses of CYPomes of a variety of organisms. Considerable variations in sequences within and between CYP families and high similarity in secondary and tertiary structures between all CYPs along with dramatic conformational changes in secondary structure elements of a substrate binding site during catalysis have been reported. This provides structural plasticity and substrate promiscuity, which underlie functional diversity of CYPs. Gene duplication and mutation events underlie CYP evolutionary diversity and emergence of novel selectable functions, which provide the involvement of CYPs in high adaptability to changing environmental conditions and dietary restrictions. In our review, we discuss the recent advancements and challenges in the elucidating the evolutionary origin and mechanisms underlying the CYP monooxygenase system diversity and plasticity. Our review is in the view of hypothesis that diversity of CYP monooxygenase systems is translated into the broad metabolic profiles, and this has been acquired during the long evolutionary time to provide structural plasticity leading to high adaptative capabilities to environmental stress conditions.
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Affiliation(s)
| | - Dmitry V Astakhov
- Department of Biochemistry, I.M. Sechenov First Moscow State Medical University (Sechenov University), 119991, Moscow, Russia
| | - Alexander A Terentiev
- Department of Biochemistry and Molecular Biology, N.I. Pirogov Russian National Research Medical University, 117997, Moscow, Russia
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4
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Costanzo A, Fata F, Freda I, De Sciscio ML, Gugole E, Bulfaro G, Di Renzo M, Barbizzi L, Exertier C, Parisi G, D'Abramo M, Vallone B, Savino C, Montemiglio LC. Binding of steroid substrates reveals the key to the productive transition of the cytochrome P450 OleP. Structure 2024; 32:1465-1476.e3. [PMID: 38971159 DOI: 10.1016/j.str.2024.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 05/08/2024] [Accepted: 06/11/2024] [Indexed: 07/08/2024]
Abstract
OleP is a bacterial cytochrome P450 involved in oleandomycin biosynthesis as it catalyzes regioselective epoxidation on macrolide intermediates. OleP has recently been reported to convert lithocholic acid (LCA) into murideoxycholic acid through a highly regioselective reaction and to unspecifically hydroxylate testosterone (TES). Since LCA and TES mainly differ by the substituent group at the C17, here we used X-ray crystallography, equilibrium binding assays, and molecular dynamics simulations to investigate the molecular basis of the diverse reactivity observed with the two steroids. We found that the differences in the structure of TES and LCA affect the capability of these molecules to directly form hydrogen bonds with N-terminal residues of OleP internal helix I. The establishment of these contacts, by promoting the bending of helix I, fosters an efficient trigger of the open-to-closed structural transition that occurs upon substrate binding to OleP and contributes to the selectivity of the subsequent monooxygenation reaction.
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Affiliation(s)
- Antonella Costanzo
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza, University of Rome, P. le Aldo Moro, 5, 00185 Rome, Italy; Takis Biotech, Via di Castel Romano 100, 00128 Rome, Italy
| | - Francesca Fata
- Institute of Molecular Biology and Pathology c/o Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza, University of Rome, National Research Council, P.le Aldo Moro, 5, 00185 Rome, Italy
| | - Ida Freda
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza, University of Rome, P. le Aldo Moro, 5, 00185 Rome, Italy
| | - Maria Laura De Sciscio
- Department of Chemistry, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy
| | - Elena Gugole
- Institute of Molecular Biology and Pathology c/o Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza, University of Rome, National Research Council, P.le Aldo Moro, 5, 00185 Rome, Italy
| | - Giovanni Bulfaro
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza, University of Rome, P. le Aldo Moro, 5, 00185 Rome, Italy; Takis Biotech, Via di Castel Romano 100, 00128 Rome, Italy
| | - Matteo Di Renzo
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza, University of Rome, P. le Aldo Moro, 5, 00185 Rome, Italy
| | - Luca Barbizzi
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza, University of Rome, P. le Aldo Moro, 5, 00185 Rome, Italy
| | - Cécile Exertier
- Institute of Molecular Biology and Pathology c/o Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza, University of Rome, National Research Council, P.le Aldo Moro, 5, 00185 Rome, Italy
| | - Giacomo Parisi
- Department of Basic and Applied Sciences for Engineering (SBAI), Sapienza, University of Rome, Via Antonio Scarpa, 16, 00161 Rome, Italy
| | - Marco D'Abramo
- Department of Chemistry, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy
| | - Beatrice Vallone
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza, University of Rome, P. le Aldo Moro, 5, 00185 Rome, Italy; Institute of Molecular Biology and Pathology c/o Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza, University of Rome, National Research Council, P.le Aldo Moro, 5, 00185 Rome, Italy.
| | - Carmelinda Savino
- Institute of Molecular Biology and Pathology c/o Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza, University of Rome, National Research Council, P.le Aldo Moro, 5, 00185 Rome, Italy.
| | - Linda Celeste Montemiglio
- Institute of Molecular Biology and Pathology c/o Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza, University of Rome, National Research Council, P.le Aldo Moro, 5, 00185 Rome, Italy.
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5
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Lee JHZ, Bruning JB, Bell SG. An In Crystallo Reaction with an Engineered Cytochrome P450 Peroxygenase. Chemistry 2024; 30:e202303335. [PMID: 37971151 DOI: 10.1002/chem.202303335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/10/2023] [Accepted: 11/16/2023] [Indexed: 11/19/2023]
Abstract
The cytochrome P450 monooxygenases (CYPs) are a class of heme-thiolate enzymes that insert oxygen into unactivated C-H bonds. These enzymes can be converted into peroxygenases via protein engineering, which enables their activity to occur using hydrogen peroxide (H2 O2 ) without the requirement for additional nicotinamide co-factors or partner proteins. Here, we demonstrate that soaking crystals of an engineered P450 peroxygenase with H2 O2 enables the enzymatic reaction to occur within the crystal. Crystals of the designed P450 peroxygenase, the T252E mutant of CYP199A4, in complex with 4-methoxybenzoic acid were soaked with different concentrations of H2 O2 for varying times to initiate the in crystallo O-demethylation reaction. Crystal structures of T252E-CYP199A4 showed a distinct loss of electron density that was consistent with the O-demethylated metabolite, 4-hydroxybenzoic acid. A new X-ray crystal structure of this enzyme with the 4-hydroxybenzoic acid product was obtained to enable comparison alongside the existing substrate-bound structure. The visualisation of enzymatic catalysis in action is challenging in structural biology and the ability to initiate the reactions of P450 enzymes, in crystallo by simply soaking crystals with H2 O2 will enable new structural biology methods and techniques to be applied to study their mechanism of action.
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Affiliation(s)
- Joel H Z Lee
- Department of Chemistry, University of Adelaide, Adelaide, SA 5005, Australia
| | - John B Bruning
- School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Stephen G Bell
- Department of Chemistry, University of Adelaide, Adelaide, SA 5005, Australia
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6
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Mokkawes T, De Visser T, Cao Y, De Visser SP. Melatonin Activation by Human Cytochrome P450 Enzymes: A Comparison between Different Isozymes. Molecules 2023; 28:6961. [PMID: 37836804 PMCID: PMC10574541 DOI: 10.3390/molecules28196961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 09/30/2023] [Accepted: 10/02/2023] [Indexed: 10/15/2023] Open
Abstract
Cytochrome P450 enzymes in the human body play a pivotal role in both the biosynthesis and the degradation of the hormone melatonin. Melatonin plays a key role in circadian rhythms in the body, but its concentration is also linked to mood fluctuations as well as emotional well-being. In the present study, we present a computational analysis of the binding and activation of melatonin by various P450 isozymes that are known to yield different products and product distributions. In particular, the P450 isozymes 1A1, 1A2, and 1B1 generally react with melatonin to provide dominant aromatic hydroxylation at the C6-position, whereas the P450 2C19 isozyme mostly provides O-demethylation products. To gain insight into the origin of these product distributions of the P450 isozymes, we performed a comprehensive computational study of P450 2C19 isozymes and compared our work with previous studies on alternative isozymes. The work covers molecular mechanics, molecular dynamics and quantum mechanics approaches. Our work highlights major differences in the size and shape of the substrate binding pocket amongst the different P450 isozymes. Consequently, substrate binding and positioning in the active site varies substantially within the P450 isozymes. Thus, in P450 2C19, the substrate is oriented with its methoxy group pointing towards the heme, and therefore reacts favorably through hydrogen atom abstraction, leading to the production of O-demethylation products. On the other hand, the substrate-binding pockets in P450 1A1, 1A2, and 1B1 are tighter, direct the methoxy group away from the heme, and consequently activate an alternative site and lead to aromatic hydroxylation instead.
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Affiliation(s)
| | | | | | - Sam P. De Visser
- Department of Chemical Engineering, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
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7
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Nagel R, Alexander L, Stewart C, Peters R. Dual factors required for cytochrome-P450-mediated hydrocarbon ring contraction in bacterial gibberellin phytohormone biosynthesis. Proc Natl Acad Sci U S A 2023; 120:e2221549120. [PMID: 37339230 PMCID: PMC10293830 DOI: 10.1073/pnas.2221549120] [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: 12/19/2022] [Accepted: 05/02/2023] [Indexed: 06/22/2023] Open
Abstract
Cytochromes P450 (CYPs) are heme-thiolate monooxygenases that prototypically catalyze the insertion of oxygen into unactivated C-H bonds but are capable of mediating more complex reactions. One of the most remarked-upon alternative reactions occurs during biosynthesis of the gibberellin A (GA) phytohormones, involving hydrocarbon ring contraction with coupled aldehyde extrusion of ent-kaurenoic acid to form the first gibberellin intermediate. While the unusual nature of this reaction has long been noted, its mechanistic basis has remained opaque. Building on identification of the relevant CYP114 from bacterial GA biosynthesis, detailed structure-function studies are reported here, including development of in vitro assays as well as crystallographic analyses both in the absence and presence of substrate. These structures provided insight into enzymatic catalysis of this unusual reaction, as exemplified by identification of a key role for the "missing" acid from an otherwise highly conserved acid-alcohol pair of residues. Notably, the results demonstrate that ring contraction requires dual factors, both the use of a dedicated ferredoxin and absence of the otherwise conserved acidic residue, with exclusion of either limiting turnover to just the initiating and more straightforward hydroxylation. The results provide detailed insight into the enzymatic structure-function relationships underlying this fascinating reaction and support the use of a semipinacol mechanism for the unusual ring contraction reaction.
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Affiliation(s)
- Raimund Nagel
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA50011
| | - Liza E. Alexander
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA50011
| | - Charles E. Stewart
- Macromolecular X-ray Crystallography Facility, Iowa State University, Ames, IA50011
| | - Reuben J. Peters
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA50011
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8
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Hagen WR. The Development of Tungsten Biochemistry-A Personal Recollection. Molecules 2023; 28:molecules28104017. [PMID: 37241758 DOI: 10.3390/molecules28104017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 04/27/2023] [Accepted: 05/08/2023] [Indexed: 05/28/2023] Open
Abstract
The development of tungsten biochemistry is sketched from the viewpoint of personal participation. Following its identification as a bio-element, a catalogue of genes, enzymes, and reactions was built up. EPR spectroscopic monitoring of redox states was, and remains, a prominent tool in attempts to understand tungstopterin-based catalysis. A paucity of pre-steady-state data remains a hindrance to overcome to this day. Tungstate transport systems have been characterized and found to be very specific for W over Mo. Additional selectivity is presented by the biosynthetic machinery for tungstopterin enzymes. Metallomics analysis of hyperthermophilic archaeon Pyrococcus furiosus indicates a comprehensive inventory of tungsten proteins.
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Affiliation(s)
- Wilfred R Hagen
- Department of Biotechnology, Delft University of Technology, Building 58, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
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9
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Mohamed H, Ghith A, Bell SG. The binding of nitrogen-donor ligands to the ferric and ferrous forms of cytochrome P450 enzymes. J Inorg Biochem 2023; 242:112168. [PMID: 36870164 DOI: 10.1016/j.jinorgbio.2023.112168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/24/2023] [Accepted: 02/21/2023] [Indexed: 02/27/2023]
Abstract
The cytochrome P450 superfamily of heme-thiolate monooxygenase enzymes can catalyse various oxidation reactions. The addition of a substrate or an inhibitor ligand induces changes in the absorption spectrum of these enzymes and UV-visible (UV-vis) absorbance spectroscopy is the most common and readily available technique used to interrogate their heme and active site environment. Nitrogen-containing ligands can inhibit the catalytic cycle of heme enzymes by interacting with the heme. Here we evaluate the binding of imidazole and pyridine-based ligands to the ferric and ferrous forms of a selection of bacterial cytochrome P450 enzymes using UV-visible absorbance spectroscopy. The majority of these ligands interact with the heme as one would expect for type II nitrogen directly coordinated to a ferric heme-thiolate species. However, the spectroscopic changes observed in the ligand-bound ferrous forms indicated differences in the heme environment across these P450 enzyme/ligand combinations. Multiple species were observed in the UV-vis spectra of the ferrous ligand-bound P450s. None of the enzymes gave rise to the isolation of a single species with a Soret band at ∼442-447 nm, indicative of a 6-coordinate ferrous thiolate species with a nitrogen-donor ligand. A ferrous species with Soret band at ∼427 nm coupled with an α-band of increased intensity was observed with the imidazole ligands. With some enzyme-ligand combinations reduction resulted in breaking of the iron‑nitrogen bond yielding a 5-coordinate high-spin ferrous species. In other instances, the ferrous form was readily oxidised back to the ferric form on addition of the ligand.
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Affiliation(s)
- Hebatalla Mohamed
- Department of Chemistry, University Adelaide, Adelaide, SA 5005, Australia
| | - Amna Ghith
- Department of Chemistry, University Adelaide, Adelaide, SA 5005, Australia
| | - Stephen G Bell
- Department of Chemistry, University Adelaide, Adelaide, SA 5005, Australia.
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10
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Denison M, Ahrens JJ, Dunbar MN, Warmahaye H, Majeed A, Turro C, Kocarek TA, Sevrioukova IF, Kodanko JJ. Dynamic Ir(III) Photosensors for the Major Human Drug-Metabolizing Enzyme Cytochrome P450 3A4. Inorg Chem 2023; 62:3305-3320. [PMID: 36758158 PMCID: PMC10268476 DOI: 10.1021/acs.inorgchem.3c00059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Probing the activity of cytochrome P450 3A4 (CYP3A4) is critical for monitoring the metabolism of pharmaceuticals and identifying drug-drug interactions. A library of Ir(III) probes that detect occupancy of the CYP3A4 active site were synthesized and characterized. These probes show selectivity for CYP3A4 inhibition, low cellular toxicity, Kd values as low as 9 nM, and are highly emissive with lifetimes up to 3.8 μs in cell growth media under aerobic conditions. These long emission lifetimes allow for time-resolved gating to distinguish probe from background autofluorescence from growth media and live cells. X-ray crystallographic analysis revealed structure-activity relationships and the preference or indifference of CYP3A4 toward resolved stereoisomers. Ir(III)-based probes show emission quenching upon CYP3A4 binding, then emission increases following displacement with CYP3A4 inhibitors or substrates. Importantly, the lead probes inhibit the activity of CYP3A4 at concentrations as low as 300 nM in CYP3A4-overexpressing HepG2 cells that accurately mimic human hepatic drug metabolism. Thus, the Ir(III)-based agents show promise as novel chemical tools for monitoring CYP3A4 active site occupancy in a high-throughput manner to gain insight into drug metabolism and drug-drug interactions.
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Affiliation(s)
- Madeline Denison
- Department of Chemistry, Wayne State University, 5101 Cass Ave, Detroit, Michigan 48202, United States
| | - Justin J Ahrens
- Department of Chemistry, Wayne State University, 5101 Cass Ave, Detroit, Michigan 48202, United States
| | - Marilyn N Dunbar
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Habon Warmahaye
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Aliza Majeed
- Institute of Environmental Health Sciences, Wayne State University, 6135 Woodward Avenue, Integrative Biosciences Center, Room 2126, Detroit, Michigan 48202, United States
| | - Claudia Turro
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Thomas A Kocarek
- Institute of Environmental Health Sciences, Wayne State University, 6135 Woodward Avenue, Integrative Biosciences Center, Room 2126, Detroit, Michigan 48202, United States
| | - Irina F Sevrioukova
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697, United States
| | - Jeremy J Kodanko
- Department of Chemistry, Wayne State University, 5101 Cass Ave, Detroit, Michigan 48202, United States
- Barbara Ann Karmanos Cancer Institute, Detroit, Michigan 48201, United States
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11
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Mokkawes T, de Visser SP. Melatonin Activation by Cytochrome P450 Isozymes: How Does CYP1A2 Compare to CYP1A1? Int J Mol Sci 2023; 24:3651. [PMID: 36835057 PMCID: PMC9959256 DOI: 10.3390/ijms24043651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/09/2023] [Accepted: 02/09/2023] [Indexed: 02/16/2023] Open
Abstract
Cytochrome P450 enzymes are versatile enzymes found in most biosystems that catalyze mono-oxygenation reactions as a means of biosynthesis and biodegradation steps. In the liver, they metabolize xenobiotics, but there are a range of isozymes with differences in three-dimensional structure and protein chain. Consequently, the various P450 isozymes react with substrates differently and give varying product distributions. To understand how melatonin is activated by the P450s in the liver, we did a thorough molecular dynamics and quantum mechanics study on cytochrome P450 1A2 activation of melatonin forming 6-hydroxymelatonin and N-acetylserotonin products through aromatic hydroxylation and O-demethylation pathways, respectively. We started from crystal structure coordinates and docked substrate into the model, and obtained ten strong binding conformations with the substrate in the active site. Subsequently, for each of the ten substrate orientations, long (up to 1 μs) molecular dynamics simulations were run. We then analyzed the orientations of the substrate with respect to the heme for all snapshots. Interestingly, the shortest distance does not correspond to the group that is expected to be activated. However, the substrate positioning gives insight into the protein residues it interacts with. Thereafter, quantum chemical cluster models were created and the substrate hydroxylation pathways calculated with density functional theory. These relative barrier heights confirm the experimental product distributions and highlight why certain products are obtained. We make a detailed comparison with previous results on CYP1A1 and identify their reactivity differences with melatonin.
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Affiliation(s)
- Thirakorn Mokkawes
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
- Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Sam P. de Visser
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
- Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
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12
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Hachey AC, Fenton AD, Heidary DK, Glazer EC. Design of Cytochrome P450 1B1 Inhibitors via a Scaffold-Hopping Approach. J Med Chem 2023; 66:398-412. [PMID: 36520541 DOI: 10.1021/acs.jmedchem.2c01368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Cytochrome P450 1B1 (CYP1B1) is a potential drug target in cancer research that is overexpressed in several solid tumors but is present only at low levels in healthy tissues. Its expression is associated with resistance to common chemotherapeutics, while inhibitors restore efficacy to these drugs in model systems. The majority of CYP1B1 inhibitors are derived from a limited number of scaffolds, and few have achieved outstanding selectivity against other human CYPs, which could impede clinical development. This study explores a new chemical space for CYP1B1 inhibitors using a scaffold-hopping approach and establishes 2,4-diarylthiazoles as a promising framework for further development. From a small library, compound 15 emerged as the lead, with picomolar CYP1B1 inhibition, and over 19,000-fold selectivity against its relative, CYP1A1. To investigate the activity of 15, molecular dynamics, optical spectroscopy, point mutations, and traditional structure-activity relationships were employed and revealed key interactions important for the development of CYP1B1 inhibitors.
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Affiliation(s)
- Austin C Hachey
- Department of Chemistry, University of Kentucky, 505 Rose Street, Lexington, Kentucky40506, United States
| | - Alexander D Fenton
- Department of Chemistry, University of Kentucky, 505 Rose Street, Lexington, Kentucky40506, United States
| | - David K Heidary
- Department of Chemistry, University of Kentucky, 505 Rose Street, Lexington, Kentucky40506, United States
| | - Edith C Glazer
- Department of Chemistry, University of Kentucky, 505 Rose Street, Lexington, Kentucky40506, United States
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13
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Collins DP, Johnson E, Coulter ED, Beharry Z, Ballou DP, Dawson JH. Caught in the act: Monitoring OO bond cleavage in Acylperoxoferric cytochrome P450cam to form compound I in real time. J Inorg Biochem 2022; 236:111949. [PMID: 36028338 DOI: 10.1016/j.jinorgbio.2022.111949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 07/25/2022] [Indexed: 12/15/2022]
Abstract
While monitoring the reaction of ferric cytochrome P450cam (Cyp101) with substituted peroxybenzoic acids using rapid-scanning, stopped-flow (RSSF) spectroscopy, an intermediate appears en route to formation of the high-valent moiety known as Compound I [Fe(IV)=O/porphyrin radical cation] that is thought to be the key catalytic species for O-atom transfer to substrate. We have previously suggested (Spolitak, T., Dawson, J.H., Ballou, D.P., J. Biol. Chem.2005, 280, 20,300-20,309) that this species is an acylperoxo-ferric heme adduct that subsequently undergoes OO bond cleavage to generate Compound I. Singular value decomposition analysis of the RSSF data for formation of this intermediate shows that the energy of its Soret absorption peak is sensitive to the electron donor properties of the aryl substituents on the peracid. A linear Hammett correlation plot is seen for the energy of the Soret absorption peak vs. the Hammett σ constant. This correlation requires that the aryl substituents remain as part of the ligand bound to the heme iron, providing direct evidence that the adduct is indeed a ferric acylperoxo derivative. Linear Hammett correlation plots are also seen for both the rate of formation of the intermediate as well as for its conversion to Compound I. It is proposed that the electron donating/withdrawing properties of the aryl-bound substituents affect the electrophilic nature for binding substrate, changing the observed rate of formation for the acylperoxo intermediate, as well as the propensity and stability of the substituted benzoic acid to serve as the leaving group during OO bond cleavage yielding Compound I.
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Affiliation(s)
- Daniel P Collins
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Emily Johnson
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Eric D Coulter
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Zanna Beharry
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - David P Ballou
- Department of Biological Chemistry, Medical School, University of Michigan, Ann Arbor, MI 48109, USA.
| | - John H Dawson
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA.
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14
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Subedi P, Do H, Lee JH, Oh TJ. Crystal Structure and Biochemical Analysis of a Cytochrome P450 CYP101D5 from Sphingomonas echinoides. Int J Mol Sci 2022; 23:ijms232113317. [PMID: 36362105 PMCID: PMC9655578 DOI: 10.3390/ijms232113317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 10/28/2022] [Accepted: 10/30/2022] [Indexed: 11/06/2022] Open
Abstract
Cytochrome P450 enzymes (CYPs) are heme-containing enzymes that catalyze hydroxylation with a variety of biological molecules. Despite their diverse activity and substrates, the structures of CYPs are limited to a tertiary structure that is similar across all the enzymes. It has been presumed that CYPs overcome substrate selectivity with highly flexible loops and divergent sequences around the substrate entrance region. Here, we report the newly identified CYP101D5 from Sphingomonas echinoides. CYP101D5 catalyzes the hydroxylation of β-ionone and flavonoids, including naringenin and apigenin, and causes the dehydrogenation of α-ionone. A structural investigation and comparison with other CYP101 families indicated that spatial constraints at the substrate-recognition site originate from the B/C loop. Furthermore, charge distribution at the substrate binding site may be important for substrate selectivity and the preference for CYP101D5.
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Affiliation(s)
- Pradeep Subedi
- Department of Life Science and Biochemical Engineering, Graduate School, Sun Moon University, Asan 31460, Korea
| | - Hackwon Do
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Korea
- Department of Polar Sciences, University of Science and Technology, Incheon 21990, Korea
| | - Jun Hyuck Lee
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Korea
- Department of Polar Sciences, University of Science and Technology, Incheon 21990, Korea
- Correspondence: (J.H.L.); (T.-J.O.); Tel.: +82-32-760-5555 (J.H.L.); +82-41-530-2677 (T.-J.O.); Fax: +82-32-760-5509 (J.H.L.); +82-41-530-2279 (T.-J.O.)
| | - Tae-Jin Oh
- Department of Life Science and Biochemical Engineering, Graduate School, Sun Moon University, Asan 31460, Korea
- Genome-Based BioIT Convergence Institute, Asan 31460, Korea
- Department of Pharmaceutical Engineering and Biotechnology, Sun Moon University, Asan 31460, Korea
- Correspondence: (J.H.L.); (T.-J.O.); Tel.: +82-32-760-5555 (J.H.L.); +82-41-530-2677 (T.-J.O.); Fax: +82-32-760-5509 (J.H.L.); +82-41-530-2279 (T.-J.O.)
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15
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Liao L, Li Y, Bi X, Xiong B, Wang X, Deng H, Zhang M, Sun G, Jin Z, Huang Z, Wang Z. Transcriptome analysis of Harumi tangor fruits: Insights into interstock-mediated fruit quality. FRONTIERS IN PLANT SCIENCE 2022; 13:995913. [PMID: 36311145 PMCID: PMC9608513 DOI: 10.3389/fpls.2022.995913] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 09/30/2022] [Indexed: 05/27/2023]
Abstract
Harumi tangor fruit with Ponkan as an interstock contains significantly higher levels of total soluble solids compared to Harumi tangor fruit cv.with no interstock. Transcriptome analysis of two graft combinations (Harumi/Hongjv (HP) and cv. cv.Harumi/Ponkan/Hongjv (HPP)) was conducted to identify the genes related to use of the Ponkan interstock. Soluble sugars and organic acids were also measured in the two graft combinations. The results showed that the contents of sucrose, glucose, and fructose were higher in the fruits of HPP than in those of HP; additionally, the titratable acid levels were lower in grafts with interstocks than in grafts without interstocks. Transcriptome analysis of HPP and HP citrus revealed that the interstock regulated auxin and ethylene signals, sugar and energy metabolism, and cell wall metabolism. Trend and Venn analyses suggested that genes related to carbohydrate-, energy-, and hormone-metabolic activities were more abundant in HPP plants than in HP plants during different periods. Moreover, weighted gene co-expression network analysis demonstrated that carbohydrates, hormones, cell wall, and transcription factors may be critical for interstock-mediated citrus fruit development and ripening. The contents of ethylene, auxin, cytokinin, transcription factors, starch, sucrose, glucose, fructose, and total sugar in HPP plants differed considerably than those in HP fruits. Interstocks may help to regulate the early ripening and quality of citrus fruit through the above-mentioned pathways. These findings provide information on the effects of interstock on plant growth and development.
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Affiliation(s)
- Ling Liao
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Yunjie Li
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Xiaoyi Bi
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Bo Xiong
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Xun Wang
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Honghong Deng
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Mingfei Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Guochao Sun
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Zhenghua Jin
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Zehao Huang
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Zhihui Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
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16
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Engineering of Microbial Substrate Promiscuous CYP105A5 for Improving the Flavonoid Hydroxylation. Catalysts 2022. [DOI: 10.3390/catal12101157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Bacterial cytochrome P450 (CYP) enzymes are versatile biocatalysts that are responsible for the biotransformation of diverse endogenous substances. CYP105A5 from Streptomyces sp. showed substrate flexibility with different flavonoids and was able to catalyze O-demethylation of biochanin A, regioselective C3′-hydroxylation of daidzein, genistein, and naringenin, and additional C8-hydroxylation for daidzein using heterologous redox partners putidaredoxin and putidaredoxin reductase. By rational design of substrate-binding pocket based on experimental data, homology modeling, and molecular docking analysis, we enhanced the product formation rate of flavonoids. The double mutant L100A/I302A and L100A/I408N exhibited greatly enhanced in vivo conversion rates for flavonoid hydroxylation. Particularly, the L100A/I302A mutant’s kcat/Km values and in vivo conversion rate increased by 1.68-fold and 2.57-fold, respectively, for naringenin. Overall, our result might facilitate the potential use of CYP105A5 for future modification and application in whole-cell biocatalysts for the production of valuable polyphenols.
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17
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Dos Santos KF, Materón EM, Oliveira ON. Influence of cytochrome P450 3A4 and membrane lipid composition on doxorubicin activity. Colloids Surf B Biointerfaces 2022; 220:112886. [PMID: 36183636 DOI: 10.1016/j.colsurfb.2022.112886] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/30/2022] [Accepted: 09/25/2022] [Indexed: 11/28/2022]
Abstract
Drug resistance is known to depend on the interactions with cell membranes and other molecules such as human cytochromes P450 (CYPs) which are anchored on the endoplasmic reticulum (ER) membrane and involved in the metabolism of anticancer drugs. In this study, we determined the influence from cytochrome P450 3A4 (CYP3A4) on the interaction between the drug doxorubicin (DOX) and Langmuir monolayers mimicking cell membranes. The lipid composition was varied by changing the relative concentrations of cholesterol (Chol), 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), 1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine (DPPE), and L-α-phosphatidylinositol (PI). Three compositions were studied in detail which represented a healthy cell membrane and cancerous cell membranes. DOX induced an expansion in the surface pressure isotherms for all monolayers, with stronger effect for the composition of cancerous cell with a high Chol content, thus confirming the relevance of lipid composition. This effect decreased considerably when CYP3A4 was incorporated with the formation of CYP3A4-DOX complexes, according to results from polarization-modulated infrared reflection absorption spectroscopy (PM-IRRAS) measurements. Taken together, these results support the hypothesis of CYP3A4 being involved in drug resistance, which may be exploited to design strategies to enhance chemotherapy efficacy.
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Affiliation(s)
- Kevin F Dos Santos
- São Carlos Institute of Physics, University of São Paulo, São Carlos, SP, Brazil
| | - Elsa M Materón
- São Carlos Institute of Physics, University of São Paulo, São Carlos, SP, Brazil
| | - Osvaldo N Oliveira
- São Carlos Institute of Physics, University of São Paulo, São Carlos, SP, Brazil.
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18
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Meng S, Ji Y, Liu L, Davari MD, Schwaneberg U. Modulating the Coupling Efficiency of P450 BM3 by Controlling Water Diffusion through Access Tunnel Engineering. CHEMSUSCHEM 2022; 15:e202102434. [PMID: 34936208 PMCID: PMC9302676 DOI: 10.1002/cssc.202102434] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/19/2021] [Indexed: 06/03/2023]
Abstract
Cytochromes P450 have gained much interest for their broad substrate scope in the catalysis of oxidation reactions for pharmaceuticals, plastics, and hormones. However, achieving high coupling efficiency by the engineering of P450s is still a big challenge. The presence of extra water around the active site is deemed to be related to uncoupling. In this study, the access tunnels of P450 BM3 from Bacillus megaterium are engineered to control water access from bulk solvent to the active site. Nine residues located in tunnels are investigated by site-saturation mutagenesis to reduce water diffusion, thereby improving the coupling efficiency. The recombined variant N319L/T411V/T436A shows improved coupling efficiency (from 31.2 % to 52.6 %). Tunnel polarity analysis and molecular dynamics simulation further indicate that reduced water molecules around the active site lead to higher coupling efficiency. Overall, this study provides valuable insight on improving coupling efficiency by controlling water diffusion through tunnel engineering.
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Affiliation(s)
- Shuaiqi Meng
- Institute of BiotechnologyRWTH Aachen UniversityWorringerweg 352074AachenGermany
| | - Yu Ji
- Institute of BiotechnologyRWTH Aachen UniversityWorringerweg 352074AachenGermany
| | - Luo Liu
- Beijing Bioprocess Key LaboratoryBeijing University of Chemical TechnologyBeisanhuan East Road 15Beijing10029P. R. China
| | - Mehdi D. Davari
- Department of Bioorganic ChemistryLeibniz Institute of Plant BiochemistryWeinberg 306120HalleGermany
| | - Ulrich Schwaneberg
- Institute of BiotechnologyRWTH Aachen UniversityWorringerweg 352074AachenGermany
- DWI-Leibniz Institute for Interactive MaterialsForckenbeckstraße 5052074AachenGermany
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19
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Yang J, Qi Y, Blodgett JAV, Wencewicz TA. Multifunctional P450 Monooxygenase CftA Diversifies the Clifednamide Pool through Tandem C-H Bond Activations. JOURNAL OF NATURAL PRODUCTS 2022; 85:47-55. [PMID: 35086337 DOI: 10.1021/acs.jnatprod.1c00606] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Polycyclic tetramate macrolactams (PTMs) are a class of structurally complex hybrid polyketide-nonribosomal peptide (PK-NRP) natural products produced by diverse bacteria. Several PTMs display pharmaceutically interesting bioactivities, and the early stages of PTM biosynthesis involving polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) enzymology are well studied. However, the timing and mechanisms of post PKS-NRPS oxidations by P450 monooxygenases encoded in PTM biosynthetic gene clusters (BGCs) remain poorly characterized. Here we demonstrate that CftA, encoded in clifednamide-type PTM BGCs, is a multifunctional P450 monooxygenase capable of converting the C29-C30 ethyl side chain of ikarugamycin to either a C29-C30 methyl ketone or a C29-C30 hydroxymethyl ketone through C-H bond activation, resulting in the formation of clifednamide A or clifednamide C, respectively. We also report the complete structure of clifednamide C solved via multidimensional NMR (COSY, HSQC, HMBC, NOESY, and TOCSY) using material purified from an engineered Streptomyces strain optimized for production. Finally, the in vitro reconstitution of recombinant CftA catalytic activity revealed the oxidation cascade for sequential conversion of ikarugamycin to clifednamide A and clifednamide C. Our findings confirm prior genetics-based predictions on the origins of clifednamide complexity via P450s encoded in PTM BGCs and place CftA into a growing group of multifunctional P450s that tailor PTM natural products through late-stage regioselective C-H bond activation.
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Affiliation(s)
- Jinping Yang
- Department of Chemistry, Washington University in St. Louis, One Brookings Drive, St. Louis, Missouri 63130, United States
| | - Yunci Qi
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, Missouri 63130, United States
| | - Joshua A V Blodgett
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, Missouri 63130, United States
| | - Timothy A Wencewicz
- Department of Chemistry, Washington University in St. Louis, One Brookings Drive, St. Louis, Missouri 63130, United States
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20
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Podgorski MN, Coleman T, Giang PD, Wang CR, Bruning JB, Bernhardt PV, De Voss JJ, Bell SG. To Be, or Not to Be, an Inhibitor: A Comparison of Azole Interactions with and Oxidation by a Cytochrome P450 Enzyme. Inorg Chem 2022; 61:236-245. [PMID: 34910500 DOI: 10.1021/acs.inorgchem.1c02786] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The cytochrome P450 (CYP) superfamily of heme monooxygenases is involved in a range of important chemical biotransformations across nature. Azole-containing molecules have been developed as drugs that bind to the heme center of these enzymes, inhibiting their function. The optical spectrum of CYP enzymes after the addition of these inhibitors is used to assess how the molecules bind. Here we use the bacterial CYP199A4 enzyme, from Rhodopseudomonas palustris HaA2, to compare how imidazolyl and triazolyl inhibitors bind to ferric and ferrous heme. 4-(Imidazol-1-yl)benzoic acid induced a red shift in the Soret wavelength (424 nm) in the ferric enzyme along with an increase and a decrease in the intensities of the δ and α bands, respectively. 4-(1H-1,2,4-Triazol-1-yl)benzoic acid binds to CYP199A4 with a 10-fold lower affinity and induces a smaller red shift in the Soret band. The crystal structures of CYP199A4 with these two inhibitors confirmed that these differences in the optical spectra were due to coordination of the imidazolyl ligand to the ferric Fe, but the triazolyl inhibitor interacts with, rather than displaces, the ferric aqua ligand. Additional water molecules were present in the active site of 4-(1H-1,2,4-triazol-1-yl)benzoic acid-bound CYP199A4. The space required to accommodate these additional water molecules in the active site necessitates changes in the position of the hydrophobic phenylalanine 298 residue. Upon reduction of the heme, the imidazole-based inhibitor Fe-N ligation was not retained. A 5-coordinate heme was also the predominant species in 4-(1H-1,2,4-triazol-1-yl)benzoic acid-bound ferrous CYP199A4, but there was an obvious shoulder at 447 nm indicative of some degree of Fe-N coordination. Rather than inhibit CYP199A4, 4-(imidazol-1-yl)benzoic acid was a substrate and was oxidized to generate a metabolite derived from ring opening of the imidazolyl ring: 4-[[2-(formylamino)acetyl]amino]benzoic acid.
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Affiliation(s)
- Matthew N Podgorski
- Department of Chemistry, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Tom Coleman
- Department of Chemistry, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Peter D Giang
- School of Chemistry and Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
| | - C Ruth Wang
- Department of Chemistry, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - John B Bruning
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Paul V Bernhardt
- School of Chemistry and Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
| | - James J De Voss
- School of Chemistry and Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Stephen G Bell
- Department of Chemistry, University of Adelaide, Adelaide, South Australia 5005, Australia
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21
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Subedi P, Kim KH, Hong YS, Lee JH, Oh TJ. Enzymatic Characterization and Comparison of Two Steroid Hydroxylases CYP154C3-1 and CYP154C3-2 from Streptomyces Species. J Microbiol Biotechnol 2021; 31:464-474. [PMID: 33397832 PMCID: PMC9705902 DOI: 10.4014/jmb.2010.10020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 12/15/2020] [Accepted: 12/31/2020] [Indexed: 12/15/2022]
Abstract
Bacterial cytochrome P450 (CYP) enzymes are responsible for the hydroxylation of diverse endogenous substances with a heme molecule used as a cofactor. This study characterized two CYP154C3 proteins from Streptomyces sp. W2061 (CYP154C3-1) and Streptomyces sp. KCCM40643 (CYP154C3-2). The enzymatic activity assays of both CYPs conducted using heterologous redox partners' putidaredoxin and putidaredoxin reductase showed substrate flexibility with different steroids and exhibited interesting product formation patterns. The enzymatic characterization revealed good activity over a pH range of 7.0 to 7.8 and the optimal temperature range for activity was 30 to 37°C. The major product was the C16-hydroxylated product and the kinetic profiles and patterns of the generated hydroxylated products differed between the two enzymes. Both enzymes showed a higher affinity toward progesterone, with CYP154C3-1 demonstrating slightly higher activity than CYP154C3-2 for most of the substrates. Oxidizing agents (diacetoxyiodo) benzene (PIDA) and hydrogen peroxide (H2O2) were also utilized to actively support the redox reactions, with optimum conversion achieved at concentrations of 3 mM and 65 mM, respectively. The oxidizing agents affected the product distribution, influencing the type and selectivity of the CYP-catalyzed reaction. Additionally, CYP154C3s also catalyzed the C-C bond cleavage of steroids. Therefore, CYP154C3s may be a good candidate for the production of modified steroids for various biological uses.
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Affiliation(s)
- Pradeep Subedi
- Department of Life Science and Biochemical Engineering, Sunmoon University, Asan 31460, Republic of Korea
| | - Ki-Hwa Kim
- Department of Life Science and Biochemical Engineering, Sunmoon University, Asan 31460, Republic of Korea
| | - Young-Soo Hong
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Ochang-eup, Chungbuk 28116, Republic of Korea
| | - Joo-Ho Lee
- Genome-Based BioIT Convergence Institute, Asan 31460, Republic of Korea
| | - Tae-Jin Oh
- Department of Life Science and Biochemical Engineering, Sunmoon University, Asan 31460, Republic of Korea,Genome-Based BioIT Convergence Institute, Asan 31460, Republic of Korea,Department of BT-Convergent Pharmaceutical Engineering, Sunmoon University, Asan 31460, Republic of Korea,Corresponding author Phone: +82-41-530-2677 Fax: +82-41-530-2279 E-mail:
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22
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Liu Y, Denisov IG, Sligar SG, Kincaid JR. Substrate-Specific Allosteric Effects on the Enhancement of CYP17A1 Lyase Efficiency by Cytochrome b5. J Am Chem Soc 2021; 143:3729-3733. [PMID: 33656879 DOI: 10.1021/jacs.1c00581] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
CYP17A1 is an essential human steroidogenic enzyme, which catalyzes two sequential reactions leading to the formation of androstenedione from progesterone and dehydroepiandrosterone from pregnenolone. The second reaction is the C17-C20 bond scission, which is strongly dependent on the presence of cytochrome b5 and displays a heretofore unexplained more pronounced acceleration when 17OH-progesteone (17OH-PROG) is a substrate. The origin of the stimulating effect of cytochrome b5 on C-C bond scission catalyzed by CYP17A1 is still debated as mostly due to either the acceleration of the electron transfer to the P450 oxy complex or allosteric effects of cytochrome b5 favoring active site conformations that promote lyase activity. Using resonance Raman spectroscopy, we compared the effect of Mn-substituted cytochrome b5 (Mn-Cytb5) on the oxy complex of CYP17A1 with both proteins co-incorporated in lipid nanodiscs. For CYP17A1 with 17OH-PROG, a characteristic shift of the Fe-O mode is observed in the presence of Mn-b5, indicating reorientation of a hydrogen bond between the 17OH group of the substrate from the terminal to the proximal oxygen atom of the Fe-O-O moiety, a configuration favorable for the lyase catalysis. For 17OH-pregnenolone, no such shift is observed, the favorable H-bonding orientation being present even without Mn-Cytb5. These new data provide a precise allosteric interpretation for the more pronounced acceleration seen for the 17OH-PROG substrate.
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Affiliation(s)
- Yilin Liu
- Department of Chemistry, Marquette University, 1414W Clybourn Street, Milwaukee, Wisconsin 53233, United States
| | | | | | - James R Kincaid
- Department of Chemistry, Marquette University, 1414W Clybourn Street, Milwaukee, Wisconsin 53233, United States
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23
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Hong YH, Jang Y, Ezhov R, Seo MS, Lee YM, Pandey B, Hong S, Pushkar Y, Fukuzumi S, Nam W. A Highly Reactive Chromium(V)–Oxo TAML Cation Radical Complex in Electron Transfer and Oxygen Atom Transfer Reactions. ACS Catal 2021. [DOI: 10.1021/acscatal.1c00079] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Young Hyun Hong
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
| | - Yuri Jang
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
| | - Roman Ezhov
- Department of Physics and Astronomy, Purdue University 525 Northwestern Avenue, West Lafayette, Indiana 47907, United States
| | - Mi Sook Seo
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
| | - Yong-Min Lee
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
| | - Bhawana Pandey
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
| | - Seungwoo Hong
- Department of Chemistry, Sookmyung Women’s University, Seoul 04310, Korea
| | - Yulia Pushkar
- Department of Physics and Astronomy, Purdue University 525 Northwestern Avenue, West Lafayette, Indiana 47907, United States
| | - Shunichi Fukuzumi
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
| | - Wonwoo Nam
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
- School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi’an, People’s Republic of China
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24
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Zhao X, Li X, Wang S, Yang Z, Liu H, Xu S. Cadmium exposure induces mitochondrial pathway apoptosis in swine myocardium through xenobiotic receptors-mediated CYP450s activation. J Inorg Biochem 2021; 217:111361. [PMID: 33581611 DOI: 10.1016/j.jinorgbio.2021.111361] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/12/2021] [Accepted: 01/16/2021] [Indexed: 12/20/2022]
Abstract
Cadmium (Cd) pollution has become an important public and environmental health issue. Xenobiotic receptors (XRs, aryl hydrocarbon receptor, AHR; constitutive androstane receptor, CAR; pregnane X receptor, PXR) modulate downstream cytochrome P450 enzymes (CYP450s) expression to metabolize xenobiotics and environmental contaminants. However, the underlying mechanisms of cardiotoxicity induced by Cd(II) in swine and the roles of XRs and CYP450s remain poorly understood. In this study, the cardiotoxicity of Cd(II) was investigated by establishing a Cd(II)-exposed swine model (CdCl2, 20 mg Cd/Kg diet). Terminal-deoxynucleotidyl transferase mediated nick end labeling (TUNEL) assay and transmission electron microscope were used to observe the apoptosis. Antioxidant capacity was evaluated by free radicals contents and antioxidant enzymes activities. RT-PCR and western blot were used to measure the expression of XRs, CYP450s and apoptosis-related genes. Our results revealed that Cd(II) exposure activated the XRs and increased the CYP450s expression, contributing to the production of reactive oxygen species (ROS). Cd(II) exposure restrained the antioxidant capacity, causing oxidative stress. Moreover, mitogen-activated protein kinase (MAPK) pathway including c-Jun N-terminal kinase (JNK), extracellular signal-regulated kinase (ERK) and P38 mitogen-activated protein kinase (P38) was activated, triggering the mitochondrial apoptotic pathway. In brief, we concluded that Cd(II) caused mitochondrial pathway apoptosis in swine myocardium via the oxidative stress-MAPK pathway, and XRs-mediated CYP450s expression might participate in this process through promoting the ROS.
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Affiliation(s)
- Xia Zhao
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Xiaojing Li
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Shengchen Wang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Zijiang Yang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Honggui Liu
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China.
| | - Shiwen Xu
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China.
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25
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Miyagawa K, Isobe H, Shoji M, Kawakami T, Yamanaka S, Yamaguchi K. A three states model for hydrogen abstraction reactions with the cytochrome P450 compound I is revisited. Isolobal and isospin analogy among Fe(IV)=O, O = O and O. J Photochem Photobiol A Chem 2021. [DOI: 10.1016/j.jphotochem.2020.112902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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26
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Nguyen KT, Nguyen NL, Milhim M, Nguyen VT, Lai THN, Nguyen HH, Le TTX, Phan TTM, Bernhardt R. Characterization of a thermophilic cytochrome P450 of the CYP203A subfamily from Binh Chau hot spring in Vietnam. FEBS Open Bio 2020; 11:124-132. [PMID: 33176055 PMCID: PMC7780096 DOI: 10.1002/2211-5463.13033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/29/2020] [Accepted: 11/09/2020] [Indexed: 12/18/2022] Open
Abstract
Cytochromes P450 (CYPs or P450s) comprise a superfamily of heme-containing monooxygenases that are involved in a variety of biological processes. CYPs have broad utilities in industry, but most exhibit low thermostability, limiting their use on an industrial scale. Highly thermostable enzymes can be obtained from thermophiles in geothermal areas, including hot springs, offshore oil-producing wells and volcanoes. Here, we report the identification of a gene encoding for a thermophilic CYP from the Binh Chau hot spring metagenomic database, which was designated as P450-T2. The deduced amino acid sequence showed the highest identity of 73.15% with CYP203A1 of Rhodopseudomonas palustris, supporting that P450-T2 is a member of the CYP203A subfamily. Recombinant protein expression yielded 541 nm. The optimal temperature and pH of P450-T2 were 50 °C and 8.0, respectively. The half-life of P450-T2 was 50.2 min at 50 °C, and its melting temperature was 56.80 ± 0.08 °C. It was found to accept electrons from all tested redox partners systems, with BmCPR-Fdx2 being the most effective partner. Screening for putative substrates revealed binding of phenolic compounds, such as l-mimosine and emodin, suggesting a potential application of this new thermophilic P450 in the production of the corresponding hydroxylated products.
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Affiliation(s)
- Kim-Thoa Nguyen
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam.,Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Ngoc-Lan Nguyen
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam.,Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Mohammed Milhim
- Department of Biochemistry, Saarland University, Saarbrucken, Germany
| | - Van-Tung Nguyen
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam.,Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Thi-Hong-Nhung Lai
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Huy-Hoang Nguyen
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam.,Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Thi-Thanh-Xuan Le
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Thi-Tuyet-Minh Phan
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Rita Bernhardt
- Department of Biochemistry, Saarland University, Saarbrucken, Germany
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27
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Rimal H, Subedi P, Kim KH, Park H, Lee JH, Oh TJ. Characterization of CYP125A13, the First Steroid C-27 Monooxygenase from Streptomyces peucetius ATCC27952. J Microbiol Biotechnol 2020; 30:1750-1759. [PMID: 32958729 PMCID: PMC9728343 DOI: 10.4014/jmb.2007.07004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 09/08/2020] [Accepted: 09/11/2020] [Indexed: 12/15/2022]
Abstract
The characterization of cytochrome P450 CYP125A13 from Streptomyces peucetius was conducted using cholesterol as the sole substrate. The in vitro enzymatic assay utilizing putidaredoxin and putidaredoxin reductase from Pseudomonas putida revealed that CYP125A13 bound cholesterol and hydroxylated it. The calculated KD value, catalytic conversion rates, and Km value were 56.92 ± 11.28 μM, 1.95 nmol min-1 nmol-1, and 11.3 ± 2.8 μM, respectively. Gas chromatography-mass spectrometry (GC-MS) analysis showed that carbon 27 of the cholesterol side-chain was hydroxylated, characterizing CYP125A13 as steroid C27-hydroxylase. The homology modeling and docking results also revealed the binding of cholesterol to the active site, facilitated by the hydrophobic amino acids and position of the C27-methyl group near heme. This orientation was favorable for the hydroxylation of the C27-methyl group, supporting the in vitro analysis. This was the first reported case of the hydroxylation of cholesterol at the C-27 position by Streptomyces P450. This study also established the catalytic function of CYP125A13 and provides a solid basis for further studies related to the catabolic potential of Streptomyces species.
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Affiliation(s)
- Hemraj Rimal
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan 3460, Republic of Korea
| | - Pradeep Subedi
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan 3460, Republic of Korea
| | - Ki -Hwa Kim
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan 3460, Republic of Korea
| | - Hyun Park
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 0841, Republic of Korea
| | - Jun Hyuck Lee
- Unit of Research for Practical Application, Korea Polar Research Institute, Incheon 21990, Republic of Korea,Department of Polar Sciences, University of Science and Technology, Incheon 21990, Republic of Korea,Corresponding author J.H.Lee Phone: +82-32-760-5555 E-mail:
| | - Tae-Jin Oh
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan 3460, Republic of Korea,Genome-based BioIT Convergence Institute, Asan 31460, Republic of Korea,Department of Pharmaceutical Engineering and Biotechnology, SunMoon University, Asan 3140, Republic of Korea,T-J.Oh Phone: +82-41-530-2677 E-mail:
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28
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Liu Y, Denisov IG, Grinkova YV, Sligar SG, Kincaid JR. P450 CYP17A1 Variant with a Disordered Proton Shuttle Assembly Retains Peroxo‐Mediated Lyase Efficiency. Chemistry 2020; 26:16846-16852. [DOI: 10.1002/chem.202003181] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Indexed: 11/07/2022]
Affiliation(s)
- Yilin Liu
- Department of Chemistry Marquette University 1414W Clybourn Street Milwaukee WI 53233 USA
| | - Ilia G. Denisov
- Departments of Biochemistry and Chemistry University of Illinois 116 Morrill Hall 505 S. Goodwin Avenue Urbana IL 61801 USA
| | - Yelena V. Grinkova
- Departments of Biochemistry and Chemistry University of Illinois 116 Morrill Hall 505 S. Goodwin Avenue Urbana IL 61801 USA
| | - Stephen G. Sligar
- Departments of Biochemistry and Chemistry University of Illinois 116 Morrill Hall 505 S. Goodwin Avenue Urbana IL 61801 USA
| | - James R. Kincaid
- Department of Chemistry Marquette University 1414W Clybourn Street Milwaukee WI 53233 USA
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29
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Masamrekh RA, Filippova TA, Sherbakov KA, Veselovsky AV, Shumyantseva VV, Kuzikov AV. Interactions of galeterone and its 3-keto-Δ4 metabolite (D4G) with one of the key enzymes of corticosteroid biosynthesis - steroid 21-monooxygenase (CYP21A2). Fundam Clin Pharmacol 2020; 35:423-431. [PMID: 33012006 DOI: 10.1111/fcp.12607] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/11/2020] [Accepted: 09/28/2020] [Indexed: 11/30/2022]
Abstract
We have investigated interactions of galeterone and its pharmacologically active metabolite - 3-keto-Δ4-galeterone (D4G) - with one of the key enzymes of corticosteroid biosynthesis - steroid 21-monooxygenase (CYP21A2). It was shown by absorption spectroscopy that both compounds induce type I spectral changes of CYP21A2. Spectral dissociation constants (KS ) of complexes of CYP21A2 with galeterone or D4G were calculated as 3.1 ± 0.7 μm and 4.6 ± 0.4 μm, respectively. It was predicted by molecular docking that both ligands similarly bind to the active site of CYP21A2. We have revealed using reconstituted monooxygenase system that galeterone is a competitive inhibitor of CYP21A2 with the inhibition constant (Ki ) value of 12 ± 3 μm, while D4G at the concentrations of 10 and 25 μm does not inhibit the enzyme. Summarizing, based on the in vitro analyses we detected inhibition of CYP21A2 by galeterone and lack of the influence of D4G on this enzyme.
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Affiliation(s)
- Rami A Masamrekh
- Pirogov Russian National Research Medical University, Ostrovitianov Street, 1, Moscow, 117997, Russia.,Institute of Biomedical Chemistry, Pogodinskaya Street, 10, Build 8, Moscow, 119121, Russia
| | - Tatiana A Filippova
- Pirogov Russian National Research Medical University, Ostrovitianov Street, 1, Moscow, 117997, Russia.,Institute of Biomedical Chemistry, Pogodinskaya Street, 10, Build 8, Moscow, 119121, Russia
| | - Kirill A Sherbakov
- Institute of Biomedical Chemistry, Pogodinskaya Street, 10, Build 8, Moscow, 119121, Russia
| | - Alexander V Veselovsky
- Institute of Biomedical Chemistry, Pogodinskaya Street, 10, Build 8, Moscow, 119121, Russia
| | - Victoria V Shumyantseva
- Pirogov Russian National Research Medical University, Ostrovitianov Street, 1, Moscow, 117997, Russia.,Institute of Biomedical Chemistry, Pogodinskaya Street, 10, Build 8, Moscow, 119121, Russia
| | - Alexey V Kuzikov
- Pirogov Russian National Research Medical University, Ostrovitianov Street, 1, Moscow, 117997, Russia.,Institute of Biomedical Chemistry, Pogodinskaya Street, 10, Build 8, Moscow, 119121, Russia
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30
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A Novel Thermostable Cytochrome P450 from Sequence-Based Metagenomics of Binh Chau Hot Spring as a Promising Catalyst for Testosterone Conversion. Catalysts 2020. [DOI: 10.3390/catal10091083] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Biotechnological applications of cytochromes P450 show difficulties, such as low activity, thermal and/or solvent instability, narrow substrate specificity and redox partner dependence. In an attempt to overcome these limitations, an exploitation of novel thermophilic P450 enzymes from nature via uncultured approaches is desirable due to their great advantages that can resolve nearly all mentioned impediments. From the metagenomics library of the Binh Chau hot spring, an open reading frame (ORF) encoding a thermostable cytochrome P450—designated as P450-T3—which shared 66.6% amino acid sequence identity with CYP109C2 of Sorangium cellulosum So ce56 was selected for further identification and characterization. The ORF was synthesized artificially and heterologously expressed in Escherichia coli C43(DE3) using the pET17b system. The purified enzyme had a molecular weight of approximately 43 kDa. The melting temperature of the purified enzyme was 76.2 °C and its apparent half-life at 60 °C was 38.7 min. Redox partner screening revealed that P450-T3 was reduced well by the mammalian AdR-Adx4-108 and the yeast Arh1-Etp1 redox partners. Lauric acid, palmitic acid, embelin, retinoic acid (all-trans) and retinoic acid (13-cis) demonstrated binding to P450-T3. Interestingly, P450-T3 also bound and converted testosterone. Overall, P450-T3 might become a good candidate for biocatalytic applications on a larger scale.
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31
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Synthesis, Optimization, Antifungal Activity, Selectivity, and CYP51 Binding of New 2-Aryl-3-azolyl-1-indolyl-propan-2-ols. Pharmaceuticals (Basel) 2020; 13:ph13080186. [PMID: 32784450 PMCID: PMC7464559 DOI: 10.3390/ph13080186] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 07/29/2020] [Accepted: 08/05/2020] [Indexed: 12/14/2022] Open
Abstract
A series of 2-aryl-3-azolyl-1-indolyl-propan-2-ols was designed as new analogs of fluconazole (FLC) by replacing one of its two triazole moieties by an indole scaffold. Two different chemical approaches were then developed. The first one, in seven steps, involved the synthesis of the key intermediate 1-(1H-benzotriazol-1-yl)methyl-1H-indole and the final opening of oxiranes by imidazole or 1H-1,2,4-triazole. The second route allowed access to the target compounds in only three steps, this time with the ring opening by indole and analogs. Twenty azole derivatives were tested against Candida albicans and other Candida species. The enantiomers of the best anti-Candida compound, 2-(2,4-dichlorophenyl)-3-(1H-indol-1-yl)-1-(1H-1,2,4-triazol-1-yl)-propan-2-ol (8g), were analyzed by X-ray diffraction to determine their absolute configuration. The (−)-8g enantiomer (Minimum inhibitory concentration (MIC) = IC80 = 0.000256 µg/mL on C. albicans CA98001) was found with the S-absolute configuration. In contrast the (+)-8g enantiomer was found with the R-absolute configuration (MIC = 0.023 µg/mL on C. albicans CA98001). By comparison, the MIC value for FLC was determined as 0.020 µg/mL for the same clinical isolate. Additionally, molecular docking calculations and molecular dynamics simulations were carried out using a crystal structure of Candida albicans lanosterol 14α-demethylase (CaCYP51). The (−)-(S)-8g enantiomer aligned with the positioning of posaconazole within both the heme and access channel binding sites, which was consistent with its biological results. All target compounds have been also studied against human fetal lung fibroblast (MRC-5) cells. Finally, the selectivity of four compounds on a panel of human P450-dependent enzymes (CYP19, CYP17, CYP26A1, CYP11B1, and CYP11B2) was investigated.
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32
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Usai R, Kaluka D, Mak PJ, Liu Y, Kincaid JR. Resonance Raman spectroscopic studies of peroxo and hydroperoxo intermediates in lauric acid (LA)-bound cytochrome P450 119. J Inorg Biochem 2020; 208:111084. [PMID: 32470906 DOI: 10.1016/j.jinorgbio.2020.111084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 03/07/2020] [Accepted: 03/29/2020] [Indexed: 11/30/2022]
Abstract
Cytochromes P450 bind and cleave dioxygen to generate a potent intermediate compound I, capable of hydroxylating inert hydrocarbon substrates. Cytochrome P450 119, a bacterial cytochrome P450 that serves as a good model system for the study of the intermediate states in the P450 catalytic cycle. CYP119 is found in high temperature and sulfur rich environments. Though the natural substrate and redox partner are still unknown, a potential application of such thermophilic P450s is utilizing them as biocatalysts in biotechnological industry; e.g., the synthesis of organic compounds otherwise requiring hostile environments like extremes of pH or temperature. In the present work the oxygenated complex of this enzyme bound to lauric acid, a surrogate substrate known to have a good binding affinity, was studied by a combination of cryoradiolysis and resonance Raman spectroscopy, to trap and characterize active site structures of the key fleeting enzymatic intermediates, including the peroxo and hydroperoxo species.
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Affiliation(s)
- Remigio Usai
- Department of Chemistry, Marquette University, P.O. Box 1881, Milwaukee, WI 53201-1881, United States
| | - Daniel Kaluka
- Department of Chemistry, Marquette University, P.O. Box 1881, Milwaukee, WI 53201-1881, United States
| | - Piotr J Mak
- Department of Chemistry, Marquette University, P.O. Box 1881, Milwaukee, WI 53201-1881, United States
| | - Yilin Liu
- Department of Chemistry, Marquette University, P.O. Box 1881, Milwaukee, WI 53201-1881, United States
| | - James R Kincaid
- Department of Chemistry, Marquette University, P.O. Box 1881, Milwaukee, WI 53201-1881, United States.
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33
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Moldogazieva NT, Mokhosoev IM, Mel'nikova TI, Zavadskiy SP, Kuz'menko AN, Terentiev AA. Dual Character of Reactive Oxygen, Nitrogen, and Halogen Species: Endogenous Sources, Interconversions and Neutralization. BIOCHEMISTRY (MOSCOW) 2020; 85:S56-S78. [PMID: 32087054 DOI: 10.1134/s0006297920140047] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Oxidative stress resulting from accumulation of reactive oxygen, nitrogen, and halogen species (ROS, RNS, and RHS, respectively) causes the damage of cells and biomolecules. However, over the long evolutionary time, living organisms have developed the mechanisms for adaptation to oxidative stress conditions including the activity of the antioxidant system (AOS), which maintains low intracellular levels of RONS (ROS and RNS) and RHS. Moreover, living organisms have adapted to use low concentrations of these electrophiles for the regulation of cell functions through the reversible post-translational chemical modifications of redox-sensitive amino acid residues in intracellular effectors of signal transduction pathways (protein kinases and protein phosphatases), transcription factors, etc. An important fine-tuning mechanism that ensures involvement of RONS and RHS in the regulation of physiological processes is interconversion between different reactive species. This review focuses on the complex networks of interacting RONS and RHS types and their endogenous sources, such as NOX family of NADPH oxidases, complexes I and III of the mitochondrial electron transport chain, NO synthases, cytochrome P450-containing monooxygenase system, xanthine oxidoreductase, and myeloperoxidases. We highlight that kinetic parameters of reactions involving RONS and RHS determine the effects of these reactive species on cell functions. We also describe the functioning of enzymatic and non-enzymatic AOS components and the mechanisms of RONS and RHS scavenging under physiological conditions. We believe that analysis of interactions between RONS and relationships between different endogenous sources of these compounds will contribute to better understanding of their role in the maintenance of cell redox homeostasis as well as initiation and progression of diseases.
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Affiliation(s)
- N T Moldogazieva
- Sechenov First Moscow State Medical University, Moscow, 119991, Russia.
| | - I M Mokhosoev
- Pirogov Russian National Research Medical University, Moscow, 117997, Russia.
| | - T I Mel'nikova
- Sechenov First Moscow State Medical University, Moscow, 119991, Russia
| | - S P Zavadskiy
- Sechenov First Moscow State Medical University, Moscow, 119991, Russia
| | - A N Kuz'menko
- Sechenov First Moscow State Medical University, Moscow, 119991, Russia
| | - A A Terentiev
- Pirogov Russian National Research Medical University, Moscow, 117997, Russia
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34
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Brezny AC, Johnson SI, Raugei S, Mayer JM. Selectivity-Determining Steps in O 2 Reduction Catalyzed by Iron(tetramesitylporphyrin). J Am Chem Soc 2020; 142:4108-4113. [PMID: 32064870 PMCID: PMC7266133 DOI: 10.1021/jacs.9b13654] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The oxygen reduction reaction (ORR) is the cathode reaction in fuel cells and its selectivity for water over hydrogen peroxide production is important for these technologies. Iron porphyrin catalysts have long been studied for the ORR, but the origins of their selectivity are not well understood because the selectivity-determining step(s) usually occur after the rate-determining step. We report here the effects of acid concentration, as well as other solution conditions such as acid pKa, on the H2O2/H2O selectivity in electrocatalytic ORR by iron(tetramesitylporphyrin) (Fe(TMP)) in DMF. The results show that selectivity reflects a kinetic competition in which the dependence on [HX] is one order greater for the production of H2O than H2O2. Based on such experimental results and computational studies, we propose that the selectivity is governed by competition between protonation of the hydroperoxo intermediate, FeIII(TMP)(OOH), to produce water versus dissociation of the HOO- ligand to yield H2O2. The data rule out a bifurcation based on the regioselectivity of protonation of the hydroperoxide, as suggested in the enzymatic systems. Furthermore, the analysis developed in this report should be generally valuable to the study of selectivity in other multi-proton/multi-electron electrocatalytic reactions.
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Affiliation(s)
- Anna C. Brezny
- Department of Chemistry, Yale University, New Haven, Connecticut 06520
| | - Samantha I. Johnson
- Center for Molecular Electrocatalysis, Pacific Northwest National Laboratory, Richland, Washington 99352
| | - Simone Raugei
- Center for Molecular Electrocatalysis, Pacific Northwest National Laboratory, Richland, Washington 99352
| | - James M. Mayer
- Department of Chemistry, Yale University, New Haven, Connecticut 06520
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35
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Podgorski MN, Harbort JS, Coleman T, Stok JE, Yorke JA, Wong LL, Bruning JB, Bernhardt PV, De Voss JJ, Harmer JR, Bell SG. Biophysical Techniques for Distinguishing Ligand Binding Modes in Cytochrome P450 Monooxygenases. Biochemistry 2020; 59:1038-1050. [PMID: 32058707 DOI: 10.1021/acs.biochem.0c00027] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The cytochrome P450 superfamily of heme monooxygenases catalyzes important chemical reactions across nature. The changes in the optical spectra of these enzymes, induced by the addition of substrates or inhibitors, are critical for assessing how these molecules bind to the P450, enhancing or inhibiting the catalytic cycle. Here we use the bacterial CYP199A4 enzyme (Uniprot entry Q2IUO2), from Rhodopseudomonas palustris HaA2, and a range of substituted benzoic acids to investigate different binding modes. 4-Methoxybenzoic acid elicits an archetypal type I spectral response due to a ≥95% switch from the low- to high-spin state with concomitant dissociation of the sixth aqua ligand. 4-(Pyridin-3-yl)- and 4-(pyridin-2-yl)benzoic acid induced different type II ultraviolet-visible (UV-vis) spectral responses in CYP199A4. The former induced a greater red shift in the Soret wavelength (424 nm vs 422 nm) along with a larger overall absorbance change and other differences in the α-, β-, and δ-bands. There were also variations in the ferrous UV-vis spectra of these two substrate-bound forms with a spectrum indicative of Fe-N bond formation with 4-(pyridin-3-yl)benzoic acid. The crystal structures of CYP199A4, with the pyridinyl compounds bound, revealed that while the nitrogen of 4-(pyridin-3-yl)benzoic acid is coordinated to the heme, with 4-(pyridin-2-yl)benzoic acid an aqua ligand remains. Continuous wave and pulse electron paramagnetic resonance data in frozen solution revealed that the substrates are bound in the active site in a form consistent with the crystal structures. The redox potential of each CYP199A4-substrate combination was measured, allowing correlation among binding modes, spectroscopic properties, and the observed biochemical activity.
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Affiliation(s)
- Matthew N Podgorski
- Department of Chemistry, University of Adelaide, Adelaide, SA 5005, Australia
| | - Joshua S Harbort
- Center for Advanced Imaging, University of Queensland, Brisbane, QLD 4072, Australia
| | - Tom Coleman
- Department of Chemistry, University of Adelaide, Adelaide, SA 5005, Australia
| | - Jeanette E Stok
- School of Chemistry and Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
| | - Jake A Yorke
- Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, U.K
| | - Luet-Lok Wong
- Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, U.K
| | - John B Bruning
- School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Paul V Bernhardt
- School of Chemistry and Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
| | - James J De Voss
- School of Chemistry and Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
| | - Jeffrey R Harmer
- Center for Advanced Imaging, University of Queensland, Brisbane, QLD 4072, Australia
| | - Stephen G Bell
- Department of Chemistry, University of Adelaide, Adelaide, SA 5005, Australia
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36
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Wright WC, Chenge J, Wang J, Girvan HM, Yang L, Chai SC, Huber AD, Wu J, Oladimeji PO, Munro AW, Chen T. Clobetasol Propionate Is a Heme-Mediated Selective Inhibitor of Human Cytochrome P450 3A5. J Med Chem 2020; 63:1415-1433. [PMID: 31965799 PMCID: PMC7087482 DOI: 10.1021/acs.jmedchem.9b02067] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The human cytochrome P450 (CYP) enzymes CYP3A4 and CYP3A5 metabolize most drugs and have high similarities in their structure and substrate preference. Whereas CYP3A4 is predominantly expressed in the liver, CYP3A5 is upregulated in cancer, contributing to drug resistance. Selective inhibitors of CYP3A5 are, therefore, critical to validating it as a therapeutic target. Here we report clobetasol propionate (clobetasol) as a potent and selective CYP3A5 inhibitor identified by high-throughput screening using enzymatic and cell-based assays. Molecular dynamics simulations suggest a close proximity of clobetasol to the heme in CYP3A5 but not in CYP3A4. UV-visible spectroscopy and electron paramagnetic resonance analyses confirmed the formation of an inhibitory type I heme-clobetasol complex in CYP3A5 but not in CYP3A4, thus explaining the CYP3A5 selectivity of clobetasol. Our results provide a structural basis for selective CYP3A5 inhibition, along with mechanistic insights, and highlight clobetasol as an important chemical tool for target validation.
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Affiliation(s)
- William C. Wright
- Department of Chemical Biology and Therapeutics, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105-3678, USA
- Integrated Biomedical Sciences Program, University of
Tennessee Health Science Center, Memphis, Tennessee 38163, USA
| | - Jude Chenge
- Department of Chemical Biology and Therapeutics, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105-3678, USA
| | - Jingheng Wang
- Department of Chemical Biology and Therapeutics, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105-3678, USA
| | - Hazel M. Girvan
- Manchester Institute of Biotechnology, School of Natural
Sciences, Department of Chemistry, The University of Manchester, Manchester, M1 7DN,
UK
| | - Lei Yang
- Department of Chemical Biology and Therapeutics, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105-3678, USA
| | - Sergio C. Chai
- Department of Chemical Biology and Therapeutics, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105-3678, USA
| | - Andrew D. Huber
- Department of Chemical Biology and Therapeutics, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105-3678, USA
| | - Jing Wu
- Department of Chemical Biology and Therapeutics, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105-3678, USA
| | - Peter O. Oladimeji
- Department of Chemical Biology and Therapeutics, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105-3678, USA
| | - Andrew W. Munro
- Manchester Institute of Biotechnology, School of Natural
Sciences, Department of Chemistry, The University of Manchester, Manchester, M1 7DN,
UK
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105-3678, USA
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Zorrilla S, Mónico A, Duarte S, Rivas G, Pérez-Sala D, Pajares MA. Integrated approaches to unravel the impact of protein lipoxidation on macromolecular interactions. Free Radic Biol Med 2019; 144:203-217. [PMID: 30991143 DOI: 10.1016/j.freeradbiomed.2019.04.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 04/03/2019] [Accepted: 04/10/2019] [Indexed: 12/13/2022]
Abstract
Protein modification by lipid derived reactive species, or lipoxidation, is increased during oxidative stress, a common feature observed in many pathological conditions. Biochemical and functional consequences of lipoxidation include changes in the conformation and assembly of the target proteins, altered recognition of ligands and/or cofactors, changes in the interactions with DNA or in protein-protein interactions, modifications in membrane partitioning and binding and/or subcellular localization. These changes may impact, directly or indirectly, signaling pathways involved in the activation of cell defense mechanisms, but when these are overwhelmed they may lead to pathological outcomes. Mass spectrometry provides state of the art approaches for the identification and characterization of lipoxidized proteins/residues and the modifying species. Nevertheless, understanding the complexity of the functional effects of protein lipoxidation requires the use of additional methodologies. Herein, biochemical and biophysical methods used to detect and measure functional effects of protein lipoxidation at different levels of complexity, from in vitro and reconstituted cell-like systems to cells, are reviewed, focusing especially on macromolecular interactions. Knowledge generated through innovative and complementary technologies will contribute to comprehend the role of lipoxidation in pathophysiology and, ultimately, its potential as target for therapeutic intervention.
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Affiliation(s)
- Silvia Zorrilla
- Dept. of Structural and Chemical Biology, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain.
| | - Andreia Mónico
- Dept. of Structural and Chemical Biology, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Sofia Duarte
- Dept. of Structural and Chemical Biology, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Germán Rivas
- Dept. of Structural and Chemical Biology, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Dolores Pérez-Sala
- Dept. of Structural and Chemical Biology, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - María A Pajares
- Dept. of Structural and Chemical Biology, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain.
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Masamrekh RA, Kuzikov AV, Haurychenka YI, Shcherbakov KA, Veselovsky AV, Filimonov DA, Dmitriev AV, Zavialova MG, Gilep AA, Shkel TV, Strushkevich NV, Usanov SA, Archakov AI, Shumyantseva VV. In vitro
interactions of abiraterone, erythromycin, and CYP3A4: implications for drug–drug interactions. Fundam Clin Pharmacol 2019; 34:120-130. [DOI: 10.1111/fcp.12497] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 06/12/2019] [Accepted: 07/04/2019] [Indexed: 02/06/2023]
Affiliation(s)
- Rami A. Masamrekh
- Institute of Biomedical Chemistry Pogodinskaya Street, 10, Build 8 Moscow 119121 Russia
- Pirogov Russian National Research Medical University Ostrovityanova Street, 1 Moscow 117997 Russia
| | - Alexey V. Kuzikov
- Institute of Biomedical Chemistry Pogodinskaya Street, 10, Build 8 Moscow 119121 Russia
- Pirogov Russian National Research Medical University Ostrovityanova Street, 1 Moscow 117997 Russia
| | - Yaraslau I. Haurychenka
- Pirogov Russian National Research Medical University Ostrovityanova Street, 1 Moscow 117997 Russia
| | - Kirill A. Shcherbakov
- Institute of Biomedical Chemistry Pogodinskaya Street, 10, Build 8 Moscow 119121 Russia
| | | | - Dmitrii A. Filimonov
- Institute of Biomedical Chemistry Pogodinskaya Street, 10, Build 8 Moscow 119121 Russia
| | - Alexander V. Dmitriev
- Institute of Biomedical Chemistry Pogodinskaya Street, 10, Build 8 Moscow 119121 Russia
| | - Maria G. Zavialova
- Institute of Biomedical Chemistry Pogodinskaya Street, 10, Build 8 Moscow 119121 Russia
| | - Andrei A. Gilep
- Institute of Bioorganic Chemistry NASB 5 Academician V.F. Kuprevich Street, Build 2 Minsk BY‐220141 Belarus
| | - Tatsiana V. Shkel
- Institute of Bioorganic Chemistry NASB 5 Academician V.F. Kuprevich Street, Build 2 Minsk BY‐220141 Belarus
| | - Natallia V. Strushkevich
- Institute of Bioorganic Chemistry NASB 5 Academician V.F. Kuprevich Street, Build 2 Minsk BY‐220141 Belarus
| | - Sergey A. Usanov
- Institute of Bioorganic Chemistry NASB 5 Academician V.F. Kuprevich Street, Build 2 Minsk BY‐220141 Belarus
| | - Alexander I. Archakov
- Institute of Biomedical Chemistry Pogodinskaya Street, 10, Build 8 Moscow 119121 Russia
- Pirogov Russian National Research Medical University Ostrovityanova Street, 1 Moscow 117997 Russia
| | - Victoria V. Shumyantseva
- Institute of Biomedical Chemistry Pogodinskaya Street, 10, Build 8 Moscow 119121 Russia
- Pirogov Russian National Research Medical University Ostrovityanova Street, 1 Moscow 117997 Russia
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Erdogan H. One small step for cytochrome P450 in its catalytic cycle, one giant leap for enzymology. J PORPHYR PHTHALOCYA 2019. [DOI: 10.1142/s1088424619300040] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The intermediates operating in the cytochrome P450 catalytic cycle have been investigated for more than half a century, fascinating many enzymologists. Each intermediate has its unique role to carry out diverse oxidations. Natural time course of the catalytic cycle is quite fast, hence, not all of the reactive intermediates could be isolated during physiological catalysis. Different high-valent iron intermediates have been proposed as primary oxidants: the candidates are compound 0 (Cpd 0, [FeOOH][Formula: see text]P450) and compound I (Cpd I, Fe(IV)[Formula: see text]O por[Formula: see text]P450). Among them, the role of Cpd I in hydroxylation is fairly well understood due the discovery of the peroxide shunt. This review endeavors to put the outstanding research efforts conducted to isolate and characterize the intermediates together. In addition to spectral features of each intermediate in the catalytic cycle, the oxidizing powers of Cpd 0 and Cpd I will be discussed along with most recent scientific findings.
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Affiliation(s)
- Huriye Erdogan
- Department of Chemistry, Gebze Technical University, Gebze, 41400, Kocaeli, Turkey
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40
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Zhang X, Dong J, Wu H, Zhang H, Zhang J, Ma E. Knockdown of cytochrome P450 CYP6 family genes increases susceptibility to carbamates and pyrethroids in the migratory locust, Locusta migratoria. CHEMOSPHERE 2019; 223:48-57. [PMID: 30763915 DOI: 10.1016/j.chemosphere.2019.02.011] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 02/02/2019] [Accepted: 02/04/2019] [Indexed: 06/09/2023]
Abstract
Insect cytochrome P450 monooxygenase (CYP) plays a key role in the detoxification of insecticides. In this study, four cDNA sequences of CYP6 genes were identified and characterized. Transcription levels of LmCYP6HC1 and LmCYP6HCL1 were high in first- and fourth-instar nymph stages, respectively. LmCYP6HN1 was primarily expressed in the egg to third-instar nymph stages, while LmCYP6HQ1 was predominantly expressed in the stages from fourth-instar nymph to the adult. The four CYP6 genes were predominantly distributed in the antenna, brain, fat body, integument, and hemolymph. Piperonyl butoxide exposure inhibited total CYP activity and synergized the toxicity of carbamates and pyrethroids. Knockdown of LmCYP6HL1, LmCYP6HN1, and LmCYP6HQ1 increased nymph mortality following exposure to carbaryl, and silencing of LmCYP6HC1, LmCYP6HL1, LmCYP6HN1, and LmCYP6HQ1 comprehensively raised nymph mortality following exposure to fluvalinate. Knockdown of LmCYP6HL1 or LmCYP6HN1 significantly increased nymph mortality following exposure to cypermethrin or fenvalerate, respectively. These results suggest that the CYP6 family plays a key role in determining the susceptibility of Locusta migratoria to both carbamates and pyrethroids.
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Affiliation(s)
- Xueyao Zhang
- Institute of Applied Biology, Shanxi University, Taiyuan, Shanxi, China
| | - Jie Dong
- Institute of Applied Biology, Shanxi University, Taiyuan, Shanxi, China
| | - Haihua Wu
- Institute of Applied Biology, Shanxi University, Taiyuan, Shanxi, China
| | - Haihan Zhang
- Key Laboratory of Northwest Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an, 710055, China
| | - Jianzhen Zhang
- Institute of Applied Biology, Shanxi University, Taiyuan, Shanxi, China.
| | - Enbo Ma
- Institute of Applied Biology, Shanxi University, Taiyuan, Shanxi, China.
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41
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Jiang G, Zhang Y, Powell MM, Hylton SM, Hiller NW, Loria R, Ding Y. A Promiscuous Cytochrome P450 Hydroxylates Aliphatic and Aromatic C-H Bonds of Aromatic 2,5-Diketopiperazines. Chembiochem 2019; 20:1068-1077. [PMID: 30604585 PMCID: PMC8162728 DOI: 10.1002/cbic.201800736] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Indexed: 11/06/2022]
Abstract
Cytochrome P450 enzymes generally functionalize inert C-H bonds, and thus, they are important biocatalysts for chemical synthesis. However, enzymes that catalyze both aliphatic and aromatic hydroxylation in the same biotransformation process have rarely been reported. A recent biochemical study demonstrated the P450 TxtC for the biosynthesis of herbicidal thaxtomins as the first example of this unique type of enzyme. Herein, the detailed characterization of substrate requirements and biocatalytic applications of TxtC are reported. The results reveal the importance of N-methylation of the thaxtomin diketopiperazine (DKP) core on enzyme reactions and demonstrate the tolerance of the enzyme to modifications on the indole and phenyl moieties of its substrates. Furthermore, hydroxylated, methylated, aromatic DKPs are synthesized through a biocatalytic route comprising TxtC and the promiscuous N-methyltransferase Amir_4628; thus providing a basis for the broad application of this unique P450.
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Affiliation(s)
- Guangde Jiang
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, FL, 32610, USA
| | - Yi Zhang
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, FL, 32610, USA
| | - Magan M Powell
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, FL, 32610, USA
| | - Sarah M Hylton
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, FL, 32610, USA
| | - Nicholas W Hiller
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, FL, 32610, USA
| | - Rosemary Loria
- Department of Plant Pathology, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, 32611, USA
| | - Yousong Ding
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, FL, 32610, USA
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Szaleniec M, Wojtkiewicz AM, Bernhardt R, Borowski T, Donova M. Bacterial steroid hydroxylases: enzyme classes, their functions and comparison of their catalytic mechanisms. Appl Microbiol Biotechnol 2018; 102:8153-8171. [PMID: 30032434 PMCID: PMC6153880 DOI: 10.1007/s00253-018-9239-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 07/10/2018] [Accepted: 07/10/2018] [Indexed: 12/22/2022]
Abstract
The steroid superfamily includes a wide range of compounds that are essential for living organisms of the animal and plant kingdoms. Structural modifications of steroids highly affect their biological activity. In this review, we focus on hydroxylation of steroids by bacterial hydroxylases, which take part in steroid catabolic pathways and play an important role in steroid degradation. We compare three distinct classes of metalloenzymes responsible for aerobic or anaerobic hydroxylation of steroids, namely: cytochrome P450, Rieske-type monooxygenase 3-ketosteroid 9α-hydroxylase, and molybdenum-containing steroid C25 dehydrogenases. We analyze the available literature data on reactivity, regioselectivity, and potential application of these enzymes in organic synthesis of hydroxysteroids. Moreover, we describe mechanistic hypotheses proposed for all three classes of enzymes along with experimental and theoretical evidences, which have provided grounds for their formulation. In case of the 3-ketosteroid 9α-hydroxylase, such a mechanistic hypothesis is formulated for the first time in the literature based on studies conducted for other Rieske monooxygenases. Finally, we provide comparative analysis of similarities and differences in the reaction mechanisms utilized by bacterial steroid hydroxylases.
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Affiliation(s)
- Maciej Szaleniec
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239, Kraków, Poland.
| | - Agnieszka M Wojtkiewicz
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239, Kraków, Poland
| | - Rita Bernhardt
- Lehrstuhl für Biochemie, Universität des Saarlandes, Campus B2 2, 66123, Saarbrücken, Germany
| | - Tomasz Borowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239, Kraków, Poland
| | - Marina Donova
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Oblast, 142290, Russia
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Kuzikov AV, Masamrekh RA, Archakov AI, Shumyantseva VV. Methods for Determination of Functional Activity of Cytochrome P450 Isoenzymes. BIOCHEMISTRY MOSCOW-SUPPLEMENT SERIES B-BIOMEDICAL CHEMISTRY 2018. [DOI: 10.1134/s1990750818030046] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Fukuzumi S, Lee YM, Ahn HS, Nam W. Mechanisms of catalytic reduction of CO 2 with heme and nonheme metal complexes. Chem Sci 2018; 9:6017-6034. [PMID: 30090295 PMCID: PMC6053956 DOI: 10.1039/c8sc02220h] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Accepted: 06/26/2018] [Indexed: 11/21/2022] Open
Abstract
The catalytic conversion of CO2 into valuable chemicals and fuels has attracted increasing attention, providing a promising route for mitigating the greenhouse effect of CO2 and also meeting the global energy demand. Among many homogeneous and heterogeneous catalysts for CO2 reduction, this mini-review is focused on heme and nonheme metal complexes that act as effective catalysts for the electrocatalytic and photocatalytic reduction of CO2. Because metalloporphyrinoids show strong absorption in the visible region, which is sensitive to the oxidation states of the metals and ligands, they are suited for the detection of reactive intermediates in the catalytic CO2 reduction cycle by electronic absorption spectroscopy. The first part of this review deals with the catalytic mechanism for the one-electron reduction of CO2 to oxalic acid with heme and nonheme metal complexes, with an emphasis on how the formation of highly energetic CO2˙ is avoided. Then, the catalytic mechanism of two-electron reduction of CO2 to produce CO and H2O is compared with that to produce HCOOH. The effect of metals and ligands of the heme and nonheme complexes on the CO or HCOOH product selectivity is also discussed. The catalytic mechanisms of multi-electron reduction of CO2 to methanol (six-electron reduced product) and methane (eight-electron reduced product) are also discussed for both electrocatalytic and photocatalytic systems.
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Affiliation(s)
- Shunichi Fukuzumi
- Department of Chemistry and Nano Science , Ewha Womans University , Seoul 03760 , Korea . ; ;
- Graduate School of Science and Engineering , Meijo University , Nagoya , Aichi 468-8502 , Japan
| | - Yong-Min Lee
- Department of Chemistry and Nano Science , Ewha Womans University , Seoul 03760 , Korea . ; ;
- Research Institute for Basic Sciences , Ewha Womans University , Seoul 03760 , Korea
| | - Hyun S Ahn
- Department of Chemistry , Yonsei University , Seoul 03722 , Korea .
| | - Wonwoo Nam
- Department of Chemistry and Nano Science , Ewha Womans University , Seoul 03760 , Korea . ; ;
- School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710119 , P. R. China
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Increased Phenacetin Oxidation upon the L382V Substitution in Cytochrome P450 1A2 is Associated with Altered Substrate Binding Orientation. Int J Mol Sci 2018; 19:ijms19061580. [PMID: 29799514 PMCID: PMC6032418 DOI: 10.3390/ijms19061580] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 05/23/2018] [Accepted: 05/23/2018] [Indexed: 11/22/2022] Open
Abstract
Leucine382 of cytochrome P450 1A2 (CYP1A2) plays an important role in binding and O-dealkylation of phenacetin, with the L382V mutation increasing substrate oxidation (Huang and Szklarz, 2010, Drug Metab. Dispos. 38:1039–1045). This was attributed to altered substrate binding orientation, but no direct experimental evidence had been available. Therefore, in the current studies, we employed nuclear magnetic resonance (NMR) longitudinal (T1) relaxation measurements to investigate phenacetin binding orientations within the active site of CYP1A2 wild type (WT) and mutants. Paramagnetic relaxation time (T1P) for each proton of phenacetin was calculated from the T1 value obtained from the enzymes in ferric and ferrous-CO state in the presence of phenacetin, and used to model the orientation of phenacetin in the active site. All aromatic protons of phenacetin were nearly equidistant from the heme iron (6.34–8.03 Å). In contrast, the distance between the proton of the –OCH2– group, which is abstracted during phenacetin oxidation, and the heme iron, was much shorter in the L382V (5.93 Å) and L382V/N312L (5.96 Å) mutants compared to the N312L mutant (7.84 Å) and the wild type enzyme (6.55 Å), consistent with modeling results. These studies provide direct evidence for the molecular mechanism underlying increased oxidation of phenacetin upon the L382V mutation.
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Kuzikov AV, Masamrekh RA, Archakov AI, Shumyantseva VV. [Methods for determining of cytochrome P450 isozymes functional activity]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2018; 64:149-168. [PMID: 29723145 DOI: 10.18097/pbmc20186402149] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The review is dedicated to modern methods and technologies for determining of cytochrome P450 isozymes functional activity, such as absorbance and fluorescent spectroscopy, electron paramagnetic resonance (EPR), nuclear magnetic resonance (NMR), Raman, Mossbauer, and X-ray spectroscopy, surface plasmon resonance (SPR), atomic force microscopy (AFM). Methods of molecular genetic analysis were reviewed from personalized medicine point of view. The use of chromate-mass-spectrometric methods for cytochrome P450-dependent catalytic reactions' products was discussed. The review covers modern electrochemical systems based on cytochrome P450 isozymes for their catalytic activity analysis, their use in practice and further development perspectives for experimental pharmacology, biotechnology and translational medicine.
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Affiliation(s)
- A V Kuzikov
- Institute of Biomedical Chemistry, Moscow, Russia; Pirogov Russian National Research Medical University (RNRMU), Moscow, Russia
| | - R A Masamrekh
- Institute of Biomedical Chemistry, Moscow, Russia; Pirogov Russian National Research Medical University (RNRMU), Moscow, Russia
| | - A I Archakov
- Institute of Biomedical Chemistry, Moscow, Russia; Pirogov Russian National Research Medical University (RNRMU), Moscow, Russia
| | - V V Shumyantseva
- Institute of Biomedical Chemistry, Moscow, Russia; Pirogov Russian National Research Medical University (RNRMU), Moscow, Russia
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Production of 1-Dodecanol, 1-Tetradecanol, and 1,12-Dodecanediol through Whole-Cell Biotransformation in Escherichia coli. Appl Environ Microbiol 2018; 84:AEM.01806-17. [PMID: 29180361 DOI: 10.1128/aem.01806-17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 11/16/2017] [Indexed: 12/18/2022] Open
Abstract
Medium- and long-chain 1-alkanol and α,ω-alkanediols are used in personal care products, in industrial lubricants, and as precursors for polymers synthesized for medical applications. The industrial production of α,ω-alkanediols by alkane hydroxylation primarily occurs at high temperature and pressure using heavy metal catalysts. However, bioproduction has recently emerged as a more economical and environmentally friendly alternative. Among alkane monooxygenases, CYP153A from Marinobacter aquaeolei VT8 (CYP153A M.aq ; the strain is also known as Marinobacter hydrocarbonoclasticus VT8) possesses low overoxidation activity and high regioselectivity and thus has great potential for use in terminal hydroxylation. However, the application of CYP153A M.aq is limited because it is encoded by a dysfunctional operon. In this study, we demonstrated that the operon regulator AlkR M.aq is functional, can be induced by alkanes of various lengths, and does not suffer from product inhibition. Additionally, we identified a transposon insertion in the CYP153A M.aq operon. When the transposon was removed, the expression of the operon genes could be induced by alkanes, and the alkanes could then be oxyfunctionalized by the resulting proteins. To increase the accessibility of medium- and long-chain alkanes, we coexpressed a tunable alkane facilitator (AlkL) from Pseudomonas putida GPo1. Using a recombinant Escherichia coli strain, we produced 1.5 g/liter 1-dodecanol in 20 h and 2 g/liter 1-tetradecanol in 50 h by adding dodecane and tetradecane, respectively. Furthermore, in 68 h, we generated 3.76 g/liter of 1,12-dodecanediol by adding a dodecane-1-dodecanol substrate mixture. This study reports a very efficient method of producing C12/C14 alkanols and C12 1,12-alkanediol by whole-cell biotransformation.IMPORTANCE To produce terminally hydroxylated medium- to long-chain alkane compounds by whole-cell biotransformation, substrate permeability, enzymatic activity, and the control of overoxidability should be considered. Due to difficulties in production, small amounts of 1-dodecanol, 1-tetradecanol, and 1,12-dodecanediol are typically produced. In this study, we identified an alkane-inducible monooxygenase operon that can efficiently catalyze the conversion of alkane to 1-alkanol with no detection of the overoxidation product. By coexpressing an alkane membrane facilitator, high levels of 1-dodecanol, 1-tetradecanol, and 1,12-dodecanediol could be generated. This study is significant for the bioproduction of medium- and long-chain 1-alkanol and α,ω-alkanediols.
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