1
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Wang Z, Wang Z, Wang G, Zhang Q, Wang Q, Wang W. New insight into biodegradation mechanism of phenylurea herbicides by cytochrome P450 enzymes: Successive N-demethylation mechanism. ENVIRONMENT INTERNATIONAL 2023; 182:108332. [PMID: 37988774 DOI: 10.1016/j.envint.2023.108332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 11/12/2023] [Accepted: 11/15/2023] [Indexed: 11/23/2023]
Abstract
Phenylurea herbicides (PUHs) present one of the most important herbicides, which have cause serious effects on ecological environment and humans. Nowadays enzyme strategy shows great advantages in degradation of PUHs. Here density functional theory (DFT), quantitative structure - activity relationship (QSAR) and quantum mechanics/molecular mechanics (QM/MM) approaches are used to investigate the degradation mechanism of PUHs catalyzed by P450 enzymes. Two successive N-demethylation pathways are identified and two hydrogen abstraction (H-abstraction) reaction pathways are identified as the rate-determining step through high-throughput DFT calculations. The Boltzmann-weighted average energy barrier of the second H-abstraction pathway (19.95 kcal/mol) is higher than that of the first H-abstraction pathway (16.80 kcal/mol). Two QSAR models are established to predict the energy barriers of the two H-abstraction pathways based on the quantum chemical descriptors and mordred molecular descriptors. The determination coefficient (R2) values of QSAR models are > 0.9, which reveal that the established QSAR models have great predictive capability. QM/MM calculations indicate that human P450 enzymes are more efficient in degradation of PUHs than crop and weed P450 enzymes. Correlations between energy barriers and key structural/charge parameters are revealed and key parameters that have influence on degradation efficiency of PUHs are identified. This study provides lateral insights into the biodegradation strategy and removal method of PUHs and valuable information for designing or engineering of highly efficient degradation enzymes and genetically modified crops.
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Affiliation(s)
- Zijian Wang
- Environment Research Institute, Shandong University, Qingdao 266237, PR China
| | - Zhong Wang
- Shandong Nuclear and Radiation Safety Monitoring Center, Jinan 250117, PR China
| | - Guoqiang Wang
- Environment Research Institute, Shandong University, Qingdao 266237, PR China
| | - Qingzhu Zhang
- Environment Research Institute, Shandong University, Qingdao 266237, PR China.
| | - Qiao Wang
- Environment Research Institute, Shandong University, Qingdao 266237, PR China
| | - Wenxing Wang
- Environment Research Institute, Shandong University, Qingdao 266237, PR China
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2
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Hermano Sampaio Dias A, Yadav R, Mokkawes T, Kumar A, Skaf MS, Sastri CV, Kumar D, de Visser SP. Biotransformation of Bisphenol by Human Cytochrome P450 2C9 Enzymes: A Density Functional Theory Study. Inorg Chem 2023; 62:2244-2256. [PMID: 36651185 PMCID: PMC9923688 DOI: 10.1021/acs.inorgchem.2c03984] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Bisphenol A (BPA, 2,2-bis-(4-hydroxyphenyl)propane) is used as a precursor in the synthesis of polycarbonate and epoxy plastics; however, its availability in the environment is causing toxicity as an endocrine-disrupting chemical. Metabolism of BPA and their analogues (substitutes) is generally performed by liver cytochrome P450 enzymes and often leads to a mixture of products, and some of those are toxic. To understand the product distributions of P450 activation of BPA, we have performed a computational study into the mechanisms and reactivities using large model structures of a human P450 isozyme (P450 2C9) with BPA bound. Density functional theory (DFT) calculations on mechanisms of BPA activation by a P450 compound I model were investigated, leading to a number of possible products. The substrate-binding pocket is tight, and as a consequence, aliphatic hydroxylation is not feasible as the methyl substituents of BPA cannot reach compound I well due to constraints of the substrate-binding pocket. Instead, we find low-energy pathways that are initiated with phenol hydrogen atom abstraction followed by OH rebound to the phenolic ortho- or para-position. The barriers of para-rebound are well lower in energy than those for ortho-rebound, and consequently, our P450 2C9 model predicts dominant hydroxycumyl alcohol products. The reactions proceed through two-state reactivity on competing doublet and quartet spin state surfaces. The calculations show fast and efficient substrate activation on a doublet spin state surface with a rate-determining electrophilic addition step, while the quartet spin state surface has multiple high-energy barriers that can also lead to various side products including C4-aromatic hydroxylation. This work shows that product formation is more feasible on the low spin state, while the physicochemical properties of the substrate govern barrier heights of the rate-determining step of the reaction. Finally, the importance of the second-coordination sphere is highlighted that determines the product distributions and guides the bifurcation pathways.
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Affiliation(s)
- Artur Hermano Sampaio Dias
- Manchester
Institute of Biotechnology and Department of Chemical Engineering, The University of Manchester, 131 Princess Street, ManchesterM1 7DN, United Kingdom,Center
for Computing in Engineering & Sciences, University of Campinas, Rua Josué de Castro, s/n, Campinas13083-861, Brazil
| | - Rolly Yadav
- Department
of Chemistry, Indian Institute of Technology
Guwahati, Guwahati, Assam781039, India
| | - Thirakorn Mokkawes
- Manchester
Institute of Biotechnology and Department of Chemical Engineering, The University of Manchester, 131 Princess Street, ManchesterM1 7DN, United Kingdom
| | - Asheesh Kumar
- Department
of Physics, Babasaheb Bhimrao Ambedkar University, Lucknow, Uttar Pradesh (U.P.)226025, India
| | - Munir S. Skaf
- Center
for Computing in Engineering & Sciences, University of Campinas, Rua Josué de Castro, s/n, Campinas13083-861, Brazil
| | - Chivukula V. Sastri
- Department
of Chemistry, Indian Institute of Technology
Guwahati, Guwahati, Assam781039, India,
| | - Devesh Kumar
- Department
of Physics, Siddharth University, Kapilvastu, Siddharthnagar272202, India,
| | - Sam P. de Visser
- Manchester
Institute of Biotechnology and Department of Chemical Engineering, The University of Manchester, 131 Princess Street, ManchesterM1 7DN, United Kingdom,
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3
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The Antioxidant Properties of Alfalfa (Medicago sativa L.) and Its Biochemical, Antioxidant, Anti-Inflammatory, and Pathological Effects on Nicotine-Induced Oxidative Stress in the Rat Liver. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:2691577. [PMID: 35378828 PMCID: PMC8976666 DOI: 10.1155/2022/2691577] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 03/11/2022] [Indexed: 01/08/2023]
Abstract
Medicago sativa Linn or alfalfa is a tonic plant rich in proteins, vitamins, and minerals that is used to treat many diseases due to its pharmacological properties such as anti-inflammatory and antioxidant activities. So, the aim of this study was to evaluate the efficacy of alfalfa methanolic extract (AME) on the prevention of liver damage caused by nicotine. The total phenols, flavonoids levels, and the free radical scavenging activity of its extract (IC50) were measured. In this study, 30 Wistar rats were randomly divided into 5 groups as control (untreated), N (nicotine only), T1, T2, and T3 (nicotine + AME 100, 250, and 500 mg/kg/day, respectively). AME (orally) and nicotine (intraperitoneal injection, 0.5 mg/kg/day) were then administered for 21 days. Weight gain, the liver-to-body weight ratio, liver functional enzymes, and the lipid profile were measured. Moreover, we evaluated oxidative stress, proinflammatory parameters, and histopathological changes in the liver. Total phenols, flavonoids, and IC50 were determined as
mg GAE/g,
mg QE/g, and
μg/ml, respectively. Nicotine changed the measured parameters to abnormal. AME increased weight gain, the liver-to-body weight ratio, and enzymatic antioxidant levels and decreased malondialdehyde, liver functional enzymes, and proinflammatory cytokine levels. The lipid profile and histopathological changes have also been improved by AME in a dose-dependent manner. The results showed that AME in a dose-dependent manner by improving the inflammation and oxidative damage could improve the liver damage caused by nicotine.
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Product Distributions of Cytochrome P450 OleT JE with Phenyl-Substituted Fatty Acids: A Computational Study. Int J Mol Sci 2021; 22:ijms22137172. [PMID: 34281222 PMCID: PMC8269385 DOI: 10.3390/ijms22137172] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 06/29/2021] [Accepted: 06/29/2021] [Indexed: 11/17/2022] Open
Abstract
There are two types of cytochrome P450 enzymes in nature, namely, the monooxygenases and the peroxygenases. Both enzyme classes participate in substrate biodegradation or biosynthesis reactions in nature, but the P450 monooxygenases use dioxygen, while the peroxygenases take H2O2 in their catalytic cycle instead. By contrast to the P450 monooxygenases, the P450 peroxygenases do not require an external redox partner to deliver electrons during the catalytic cycle, and also no external proton source is needed. Therefore, they are fully self-sufficient, which affords them opportunities in biotechnological applications. One specific P450 peroxygenase, namely, P450 OleTJE, reacts with long-chain linear fatty acids through oxidative decarboxylation to form hydrocarbons and, as such, has been implicated as a suitable source for the biosynthesis of biofuels. Unfortunately, the reactions were shown to produce a considerable amount of side products originating from Cα and Cβ hydroxylation and desaturation. These product distributions were found to be strongly dependent on whether the substrate had substituents on the Cα and/or Cβ atoms. To understand the bifurcation pathways of substrate activation by P450 OleTJE leading to decarboxylation, Cα hydroxylation, Cβ hydroxylation and Cα–Cβ desaturation, we performed a computational study using 3-phenylpropionate and 2-phenylbutyrate as substrates. We set up large cluster models containing the heme, the substrate and the key features of the substrate binding pocket and calculated (using density functional theory) the pathways leading to the four possible products. This work predicts that the two substrates will react with different reaction rates due to accessibility differences of the substrates to the active oxidant, and, as a consequence, these two substrates will also generate different products. This work explains how the substrate binding pocket of P450 OleTJE guides a reaction to a chemoselectivity.
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Roach S, Faponle AS, Satpathy JK, Sastri CV, de Visser SP. Substrate sulfoxidation by a biomimetic cytochrome P450 Compound I mimic: How do porphyrin and phthalocyanine equatorial ligands compare? J CHEM SCI 2021. [DOI: 10.1007/s12039-021-01917-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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6
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Lee CWZ, Mubarak MQE, Green AP, de Visser SP. How Does Replacement of the Axial Histidine Ligand in Cytochrome c Peroxidase by N δ-Methyl Histidine Affect Its Properties and Functions? A Computational Study. Int J Mol Sci 2020; 21:ijms21197133. [PMID: 32992593 PMCID: PMC7583937 DOI: 10.3390/ijms21197133] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 09/21/2020] [Accepted: 09/22/2020] [Indexed: 12/27/2022] Open
Abstract
Heme peroxidases have important functions in nature related to the detoxification of H2O2. They generally undergo a catalytic cycle where, in the first stage, the iron(III)-heme-H2O2 complex is converted into an iron(IV)-oxo-heme cation radical species called Compound I. Cytochrome c peroxidase Compound I has a unique electronic configuration among heme enzymes where a metal-based biradical is coupled to a protein radical on a nearby Trp residue. Recent work using the engineered Nδ-methyl histidine-ligated cytochrome c peroxidase highlighted changes in spectroscopic and catalytic properties upon axial ligand substitution. To understand the axial ligand effect on structure and reactivity of peroxidases and their axially Nδ-methyl histidine engineered forms, we did a computational study. We created active site cluster models of various sizes as mimics of horseradish peroxidase and cytochrome c peroxidase Compound I. Subsequently, we performed density functional theory studies on the structure and reactivity of these complexes with a model substrate (styrene). Thus, the work shows that the Nδ-methyl histidine group has little effect on the electronic configuration and structure of Compound I and little changes in bond lengths and the same orbital occupation is obtained. However, the Nδ-methyl histidine modification impacts electron transfer processes due to a change in the reduction potential and thereby influences reactivity patterns for oxygen atom transfer. As such, the substitution of the axial histidine by Nδ-methyl histidine in peroxidases slows down oxygen atom transfer to substrates and makes Compound I a weaker oxidant. These studies are in line with experimental work on Nδ-methyl histidine-ligated cytochrome c peroxidases and highlight how the hydrogen bonding network in the second coordination sphere has a major impact on the function and properties of the enzyme.
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Affiliation(s)
- Calvin W. Z. Lee
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK; (C.W.Z.L.); (M.Q.E.M.); (A.P.G.)
- Department of Chemical Engineering and Analytical Science, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - M. Qadri E. Mubarak
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK; (C.W.Z.L.); (M.Q.E.M.); (A.P.G.)
- Department of Chemical Engineering and Analytical Science, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Anthony P. Green
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK; (C.W.Z.L.); (M.Q.E.M.); (A.P.G.)
- Department of Chemistry, 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; (C.W.Z.L.); (M.Q.E.M.); (A.P.G.)
- Department of Chemical Engineering and Analytical Science, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
- Correspondence: ; Tel.: +44-161-306-4882
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7
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Jaladanki CK, Gahlawat A, Rathod G, Sandhu H, Jahan K, Bharatam PV. Mechanistic studies on the drug metabolism and toxicity originating from cytochromes P450. Drug Metab Rev 2020; 52:366-394. [DOI: 10.1080/03602532.2020.1765792] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Chaitanya K. Jaladanki
- Department of Medicinal Chemistry and Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), SAS Nagar, Punjab, India
| | - Anuj Gahlawat
- Department of Medicinal Chemistry and Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), SAS Nagar, Punjab, India
| | - Gajanan Rathod
- Department of Medicinal Chemistry and Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), SAS Nagar, Punjab, India
| | - Hardeep Sandhu
- Department of Medicinal Chemistry and Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), SAS Nagar, Punjab, India
| | - Kousar Jahan
- Department of Medicinal Chemistry and Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), SAS Nagar, Punjab, India
| | - Prasad V. Bharatam
- Department of Medicinal Chemistry and Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), SAS Nagar, Punjab, India
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8
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Lin B, Zhang H, Zheng Q. How do mutations affect the structural characteristics and substrate binding of CYP21A2? An investigation by molecular dynamics simulations. Phys Chem Chem Phys 2020; 22:8870-8877. [DOI: 10.1039/d0cp00763c] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
CYP21A2 mutations affect the activity of the protein leading to CAH disease.
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Affiliation(s)
- Baihui Lin
- Laboratory of Theoretical and Computational Chemistry
- Institute of Theoretical Chemistry
- International Joint Research Laboratory of Nano-Micro Architecture Chemistry
- Jilin University
- Changchun 130023
| | - Hongxing Zhang
- Laboratory of Theoretical and Computational Chemistry
- Institute of Theoretical Chemistry
- International Joint Research Laboratory of Nano-Micro Architecture Chemistry
- Jilin University
- Changchun 130023
| | - Qingchuan Zheng
- Laboratory of Theoretical and Computational Chemistry
- Institute of Theoretical Chemistry
- International Joint Research Laboratory of Nano-Micro Architecture Chemistry
- Jilin University
- Changchun 130023
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9
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Neves Cruz J, Santana de Oliveira M, Gomes Silva S, Pedro da Silva Souza Filho A, Santiago Pereira D, Lima E Lima AH, de Aguiar Andrade EH. Insight into the Interaction Mechanism of Nicotine, NNK, and NNN with Cytochrome P450 2A13 Based on Molecular Dynamics Simulation. J Chem Inf Model 2019; 60:766-776. [PMID: 31622091 DOI: 10.1021/acs.jcim.9b00741] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Tobacco smoke contains various cancer-causing toxic substances, including nicotine and nitrosamines 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) and N'-nitrosonornicotine (NNN). The cytochrome 2A13 is involved in nicotine metabolism and in the activation of the pro-carcinogenic agents NNK and NNN, by means of α-hydroxylation reactions. Despite the significance of cytochrome 2A13 in the biotransformation of these molecules, its conformational mechanism and the molecular basis involved in the process are not fully understood. In this study, we used molecular dynamics and principal component analysis simulations for an in-depth analysis of the essential protein motions involved in the interaction of cytochrome 2A13 with its substrates. We also evaluated the interaction of these substrates with the amino acid residues in the binding pocket of cytochrome 2A13. Furthermore, we quantified the nature of these chemical interactions from free energy calculations using the Molecular Mechanics/Generalized Born Surface Area method. The ligands remained favorably oriented toward compound I (cytochrome P450 O═FeIV state), to undergo α-hydroxylation. The hydrogen bond with asparagine 297 was essential to maintaining the substrates in a favorable catalytic orientation. The plot of first principal motion vs second principal motion revealed that the enzyme's interaction with nicotine and NNK involved different conformational subgroups, whereas the conformational subgroups in the interaction with NNN are more similar. These results provide new mechanistic insights into the mode of interaction of the substrates with the active site of cytochrome 2A13, in the presence of compound I, which is essential for α-hydroxylation.
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Affiliation(s)
- Jorddy Neves Cruz
- Adolpho Ducke Laboratory , Emílio Goeldi Paraense Museum , Belém , Pará 66040-170, Brazil.,Laboratory of Agro-Industry , Embrapa Eastern Amazon , Belém , Pará 66040-170, Brazil
| | | | - Sebastião Gomes Silva
- Adolpho Ducke Laboratory , Emílio Goeldi Paraense Museum , Belém , Pará 66040-170, Brazil
| | | | | | - Anderson Henrique Lima E Lima
- Laboratory of Planning and Development of Pharmaceuticals , Federal University of Pará , Belém , Pará 70770-901, Brazil
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10
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Rao F, Chen Z, Zhou D, Kang Y, Guo L, Xue Y. DFT investigation on the metabolic mechanisms of theophylline by cytochrome P450 monooxygenase. J Mol Graph Model 2018; 84:109-117. [PMID: 29957347 DOI: 10.1016/j.jmgm.2018.06.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Revised: 06/11/2018] [Accepted: 06/12/2018] [Indexed: 11/16/2022]
Abstract
Theophylline, one of the most commonly used bronchodilators and respiratory stimulators for the treatment of acute and chronic asthmatic conditions, can cause permanent neurological damage through chronic or excessive ingestion. In this work, DFT calculation was performed to identify the metabolic mechanisms of theophylline by cytochrome P450 (CYP450) monooxygenase. Two main metabolic pathways were investigated, namely, N1- (path A) and N3- (path B) demethylations, which proceeded through N-methyl hydroxylation followed by the decomposition of the generated carbinolamine species. N-methyl hydroxylation involved a hydrogen atom transfer (HAT) mechanism, which can be generalized as the N-demethylation mechanism of xanthine derivatives. The energy gap between the low-spin double state (LS) and the high-spin quartet state (HS) was low (<1 kcal mol-1), indicating a two-state reactivity (TSR) mechanism. The generated carbinolamine species preferred to decompose through the adjacent heteroatom (O6 for path A and O2 for path B) mediated mechanism. Path B was kinetically more feasible than path A attributed to its relatively lower activation energy. 1-Methylxanthine therefore was the energetically favorable metabolite of theophylline. The observations obtained in the work were in agreement with the experimental observation, which can offer important implications for further pharmacological and clinic studies.
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Affiliation(s)
- Fan Rao
- College of Chemistry and Chemical Engineering, Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, China West Normal University, Nanchong, 637002, China
| | - Zeqin Chen
- College of Chemistry and Chemical Engineering, Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, China West Normal University, Nanchong, 637002, China; College of Materials and Chemistry and Chemical Engineering, Chengdu University of Technology, Chengdu, 610059, China.
| | - Dagang Zhou
- College of Chemistry and Chemical Engineering, Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, China West Normal University, Nanchong, 637002, China.
| | - Yuan Kang
- College of Chemistry and Chemical Engineering, Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, China West Normal University, Nanchong, 637002, China
| | - Linfeng Guo
- College of Chemistry and Chemical Engineering, Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, China West Normal University, Nanchong, 637002, China
| | - Ying Xue
- College of Chemistry, Key Laboratory of Green Chemistry and Technology in Ministry of Education, Sichuan University, Chengdu, 610064, China
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11
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Theoretical Insights into Imidazolidine Oxidation of Imidacloprid by Cytochrome P450 3A4. J Mol Graph Model 2018; 80:173-181. [DOI: 10.1016/j.jmgm.2018.01.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 01/09/2018] [Accepted: 01/10/2018] [Indexed: 12/18/2022]
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12
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Tao J, Kang Y, Xue Z, Wang Y, Zhang Y, Chen Q, Chen Z, Xue Y. Theoretical study on the N-demethylation mechanism of theobromine catalyzed by P450 isoenzyme 1A2. J Mol Graph Model 2015. [PMID: 26218892 DOI: 10.1016/j.jmgm.2015.06.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Theobromine, a widely consumed pharmacological active substance, can cause undesirable muscle stiffness, nausea and anorexia in high doses ingestion. The main N-demethylation metabolic mechanism of theobromine catalyzed by P450 isoenzyme 1A2 (CYP1A2) has been explored in this work using the unrestricted hybrid density functional method UB3LYP in conjunction with the LACVP(Fe)/6-31G (H, C, N, O, S, Cl) basis set. Single-point calculations including empirical dispersion corrections were carried out at the higher 6-311++G** basis set. Two N-demethylation pathways were characterized, i.e., 3-N and 7-N demethylations, which involve the initial N-methyl hydroxylation to form carbinolamines and the subsequent carbinolamines decomposition to yield monomethylxanthines and formaldehydes. Our results have shown that the rate-limiting N-methyl hydroxylation occurs via a hydrogen atom transfer (HAT) mechanism, which proceeds in a spin-selective mechanism (SSM) in the gas phase. The carbinolamines generated are prone to decomposition via the contiguous heteroatom-assisted proton-transfer. Strikingly, 3-N demethylation is more favorable than 7-N demethylation due to its lower free energy barrier and 7-methylxanthine therefore is the optimum product reported for the demethylation of theobromine catalyzed by CYP1A2, which are in good agreement with the experimental observation. This work has first revealed the detail N-demethylation mechanisms of theobromine at the theoretical level. It can offer more significant information for the metabolism of purine alkaloid.
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Affiliation(s)
- Jing Tao
- College of Chemistry and Chemical Engineering, Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, China West Normal University, Nanchong 637002, People's Republic of China
| | - Yuan Kang
- College of Chemistry and Chemical Engineering, Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, China West Normal University, Nanchong 637002, People's Republic of China
| | - Zhiyu Xue
- College of Chemistry and Chemical Engineering, Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, China West Normal University, Nanchong 637002, People's Republic of China
| | - Yongting Wang
- College of Chemistry and Chemical Engineering, Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, China West Normal University, Nanchong 637002, People's Republic of China
| | - Yan Zhang
- College of Chemistry and Chemical Engineering, Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, China West Normal University, Nanchong 637002, People's Republic of China
| | - Qiu Chen
- College of Chemistry and Chemical Engineering, Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, China West Normal University, Nanchong 637002, People's Republic of China
| | - Zeqin Chen
- College of Chemistry and Chemical Engineering, Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, China West Normal University, Nanchong 637002, People's Republic of China.
| | - Ying Xue
- College of Chemistry, Key Laboratory of Green Chemistry and Technology in Ministry of Education, Sichuan University, Chengdu 610064, People's Republic of China
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13
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Cui YL, Zheng QC, Zhang JL, Xue Q, Wang Y, Zhang HX. Molecular Dynamic Investigations of the Mutational Effects on Structural Characteristics and Tunnel Geometry in CYP17A1. J Chem Inf Model 2013; 53:3308-17. [DOI: 10.1021/ci400553w] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Ying-Lu Cui
- State Key
Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, Jilin 130023, P. R. China
| | - Qing-Chuan Zheng
- State Key
Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, Jilin 130023, P. R. China
| | - Ji-Long Zhang
- State Key
Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, Jilin 130023, P. R. China
| | - Qiao Xue
- State Key
Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, Jilin 130023, P. R. China
| | - Yan Wang
- State Key
Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, Jilin 130023, P. R. China
| | - Hong-Xing Zhang
- State Key
Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, Jilin 130023, P. R. China
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14
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Liu H, Liu S, Zhang X. The substitution reaction of (CNC)Fe−2N2 with CO. J Mol Model 2013; 19:2625-33. [DOI: 10.1007/s00894-013-1797-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Accepted: 02/05/2013] [Indexed: 12/01/2022]
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15
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Li D, Huang X, Lin J, Zhan CG. Catalytic mechanism of cytochrome P450 for N-methylhydroxylation of nicotine: reaction pathways and regioselectivity of the enzymatic nicotine oxidation. Dalton Trans 2013; 42:3812-20. [PMID: 23303461 DOI: 10.1039/c2dt32106h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The fundamental reaction mechanism of cytochrome P450 2A6 (CYP2A6)-catalyzed N-methylhydroxylation of (S)-(-)-nicotine and the free energy profile have been studied by performing pseudobond first-principles quantum mechanical/molecular mechanical (QM/MM) reaction-coordinate calculations. In the CYP2A6-(S)-(-)-nicotine binding structures that allow for 5'-hydroxylation, the N-methyl group is also sufficiently close to the oxygen of Cpd I for the N-methylhydroxylation reaction to occur. It has been demonstrated that the CYP2A6-catalyzed N-methylhydroxylation reaction is a concerted process involving a hydrogen-transfer transition state on both the quartet and the doublet states. The N-methylhydroxylation reaction proceeds mainly in the doublet state, since the free energy barriers on the doublet state are lower than the corresponding ones on the quartet state. The calculated free energy barriers indicate that (S)-(-)-nicotine oxidation catalyzed by CYP2A6 proceeds with a high regioselective abstraction of the hydrogen at the 5'-position, rather than the hydrogen at the N-methyl group. The predicted regioselectivity of 93% is in agreement with the most recent experimentally reported regioselectivity of 95%. The binding mode of (S)-(-)-nicotine in the active site of CYP2A6 is an important determinant for the stereoselectivity of nicotine (S)-(-)-oxidation, whereas the regioselectivity of (S)-(-)-nicotine oxidation is determined mainly by the free energy barrier difference between the 5'-hydroxylation and N-methylhydroxylation reactions.
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Affiliation(s)
- Dongmei Li
- College of Pharmacy, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China.
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Cui YL, Zhang JL, Zheng QC, Niu RJ, Xu Y, Zhang HX, Sun CC. Structural and Dynamic Basis of Human Cytochrome P450 7B1: A Survey of Substrate Selectivity and Major Active Site Access Channels. Chemistry 2012. [DOI: 10.1002/chem.201202627] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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Kwiecień RA, Le Questel JY, Lebreton J, Delaforge M, André F, Pihan E, Roussel A, Fournial A, Paneth P, Robins RJ. Cytochrome P450-Catalyzed Degradation of Nicotine: Fundamental Parameters Determining Hydroxylation by Cytochrome P450 2A6 at the 5′-Carbon or the N-Methyl Carbon. J Phys Chem B 2012; 116:7827-40. [DOI: 10.1021/jp304276v] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Renata A. Kwiecień
- Laboratory
for the Study of Biosynthesis by Isotopic Spectroscopy, Interdisciplinary
Chemistry: Synthesis, Analysis and Modeling (CEISAM), UMR6230, University of Nantes-CNRS, 2 rue de la Houssinière,
BP 92208, F-44322 Nantes 3, France
| | - Jean-Yves Le Questel
- Laboratory
for the Study of Biosynthesis by Isotopic Spectroscopy, Interdisciplinary
Chemistry: Synthesis, Analysis and Modeling (CEISAM), UMR6230, University of Nantes-CNRS, 2 rue de la Houssinière,
BP 92208, F-44322 Nantes 3, France
| | - Jacques Lebreton
- Laboratory
for the Study of Biosynthesis by Isotopic Spectroscopy, Interdisciplinary
Chemistry: Synthesis, Analysis and Modeling (CEISAM), UMR6230, University of Nantes-CNRS, 2 rue de la Houssinière,
BP 92208, F-44322 Nantes 3, France
| | - Marcel Delaforge
- Laboratoire Stress Oxydant et Détoxication, CNRS UMR8221, iBiTec-S/SB2SM, CEA Saclay, 91191 Saclay, France
| | - François André
- Laboratoire Stress Oxydant et Détoxication, CNRS UMR8221, iBiTec-S/SB2SM, CEA Saclay, 91191 Saclay, France
| | - Emilie Pihan
- Laboratoire Stress Oxydant et Détoxication, CNRS UMR8221, iBiTec-S/SB2SM, CEA Saclay, 91191 Saclay, France
| | - Anaïs Roussel
- Laboratoire Stress Oxydant et Détoxication, CNRS UMR8221, iBiTec-S/SB2SM, CEA Saclay, 91191 Saclay, France
| | - Anaïs Fournial
- Laboratory
for the Study of Biosynthesis by Isotopic Spectroscopy, Interdisciplinary
Chemistry: Synthesis, Analysis and Modeling (CEISAM), UMR6230, University of Nantes-CNRS, 2 rue de la Houssinière,
BP 92208, F-44322 Nantes 3, France
| | - Piotr Paneth
- Laboratory for Isotope Effects
Studies, Faculty of Chemistry, Institute
of Applied Radiation Chemistry, University of Technology Lodz, Zeromskiego 116, 90-924 Łodź, Poland
| | - Richard J. Robins
- Laboratory
for the Study of Biosynthesis by Isotopic Spectroscopy, Interdisciplinary
Chemistry: Synthesis, Analysis and Modeling (CEISAM), UMR6230, University of Nantes-CNRS, 2 rue de la Houssinière,
BP 92208, F-44322 Nantes 3, France
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Li D, Wang Y, Han K. Recent density functional theory model calculations of drug metabolism by cytochrome P450. Coord Chem Rev 2012. [DOI: 10.1016/j.ccr.2012.01.016] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Kwiecień RA, Kosieradzka K, Le Questel JY, Lebreton J, Fournial A, Gentil E, Delaforge M, Paneth P, Robins RJ. Cytochrome P450 Monooxygenase-Catalyzed Ring Opening of the Bicyclic Amine, Nortropine: An Experimental and DFT Computational Study. ChemCatChem 2012. [DOI: 10.1002/cctc.201100386] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Li D, Huang X, Han K, Zhan CG. Catalytic mechanism of cytochrome P450 for 5'-hydroxylation of nicotine: fundamental reaction pathways and stereoselectivity. J Am Chem Soc 2011; 133:7416-27. [PMID: 21513309 DOI: 10.1021/ja111657j] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
A series of computational methods were used to study how cytochrome P450 2A6 (CYP2A6) interacts with (S)-(-)-nicotine, demonstrating that the dominant molecular species of (S)-(-)-nicotine in CYP2A6 active site exists in the free base state (with two conformations, SR(t) and SR(c)), despite the fact that the protonated state is dominant for the free ligand in solution. The computational results reveal that the dominant pathway of nicotine metabolism in CYP2A6 is through nicotine free base oxidation. Further, first-principles quantum mechanical/molecular mechanical free energy (QM/MM-FE) calculations were carried out to uncover the detailed reaction pathways for the CYP2A6-catalyzed nicotine 5'-hydroxylation reaction. In the determined CYP2A6-(S)-(-)-nicotine binding structures, the oxygen of Compound I (Cpd I) can abstract a hydrogen from either the trans-5'- or the cis-5'-position of (S)-(-)-nicotine. CYP2A6-catalyzed (S)-(-)-nicotine 5'-hydroxylation consists of two reaction steps, that is, the hydrogen transfer from the 5'-position of (S)-(-)-nicotine to the oxygen of Cpd I (the H-transfer step), followed by the recombination of the (S)-(-)-nicotine moiety with the iron-bound hydroxyl group to generate the 5'-hydroxynicotine product (the O-rebound step). The H-transfer step is rate-determining. The 5'-hydroxylation proceeds mainly with the stereoselective loss of the trans-5'-hydrogen, that is, the 5'-hydrogen trans to the pyridine ring. The calculated overall stereoselectivity of ∼97% favoring the trans-5'-hydroxylation is close to the observed stereoselectivity of 89-94%. This is the first time it has been demonstrated that a CYP substrate exists dominantly in one protonation state (cationic species) in solution, but uses its less-favorable protonation state (neutral free base) to perform the enzymatic reaction.
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Affiliation(s)
- Dongmei Li
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, People's Republic of China
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