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Feng S, Zheng Q. Mechanism of 7H-Dibenzo[c,g]carbazole metabolism in cytochrome P450 1A1: Insights from computational studies. JOURNAL OF HAZARDOUS MATERIALS 2024; 476:134933. [PMID: 38925058 DOI: 10.1016/j.jhazmat.2024.134933] [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: 01/10/2024] [Revised: 06/01/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024]
Abstract
7H-Dibenzo[c,g]carbazole (DBC) is a prevalent environmental contaminant that induces tumorigenesis in several experimental animals. Recently, it has been utilized to develop high-performance solar cells and organic phosphorescent materials. It is imperative to strengthen investigations of DBC metabolism to understand its potential risks to human health. In this study, human CYP1A1 was employed as the metabolic enzyme to investigate the metabolic mechanism of DBC by molecular docking, molecular dynamics (MD) simulation, and quantum mechanical (QM) calculation. The results indicate that DBC binds to CYP1A1 in two modes (mode 1 and mode 2) mainly through nonpolar solvation energies (ΔGnonpolar). The formation of the two binding modes is attributed to the anchoring effect of the hydrogen bond formed by DBC with Asp320 (mode 1) or Ser116 (mode 2). Mode 1 is a "reactive" conformation, while mode 2 is not considered a "reactive" conformation. C5 is identified as the dominant site, and the pyrrole nitrogen cannot participate in the metabolism. DBC is metabolized mainly by a distinct electrophilic addition-rearrangement mechanism, with an energy barrier of 21.74 kcal/mol. The results provide meaningful insights into the biometabolic process of DBC and contribute to understanding its environmental effects and health risks.
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Affiliation(s)
- Shi Feng
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130023, China
| | - Qingchuan Zheng
- School of Pharmaceutical Sciences, Jilin University, Changchun 130021, China; Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130023, China.
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2
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Rojas-Vargas J, Rebollar EA, Sanchez-Flores A, Pardo-López L. A comparative genomic study of a hydrocarbon-degrading marine bacterial consortium. PLoS One 2024; 19:e0303363. [PMID: 39116055 PMCID: PMC11309472 DOI: 10.1371/journal.pone.0303363] [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] [Received: 11/21/2023] [Accepted: 04/23/2024] [Indexed: 08/10/2024] Open
Abstract
Ocean oil pollution has a large impact on the environment and the health of living organisms. Bioremediation cleaning strategies are promising eco-friendly alternatives for tackling this problem. Previously, we designed and reported a hydrocarbon (HC) degrading microbial consortium of four marine strains belonging to the species Alloalcanivorax xenomutans, Halopseudomonas aestusnigri, Paenarthrobacter sp., and Pseudomonas aeruginosa. However, the knowledge about the metabolic potential of this bacterial consortium for HC bioremediation is not yet well understood. Here, we analyzed the complete genomes of these marine bacterial strains accompanied by a phylogenetic reconstruction along with 138 bacterial strains. Synteny between complete genomes of the same species or genus, revealed high conservation among strains of the same species, covering over 91% of their genomic sequences. Functional predictions highlighted a high abundance of genes related to HC degradation, which may result in functional redundancy within the consortium; however, unique and complete gene clusters linked to aromatic degradation were found in the four genomes, suggesting substrate specialization. Pangenome gain and loss analysis of genes involved in HC degradation provided insights into the evolutionary history of these capabilities, shedding light on the acquisition and loss of relevant genes related to alkane and aromatic degradation. Our work, including comparative genomic analyses, identification of secondary metabolites, and prediction of HC-degrading genes, enhances our understanding of the functional diversity and ecological roles of these marine bacteria in crude oil-contaminated marine environments and contributes to the applied knowledge of bioremediation.
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Affiliation(s)
- Jorge Rojas-Vargas
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Eria A. Rebollar
- Programa de Microbiología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Alejandro Sanchez-Flores
- Instituto de Biotecnología, Unidad Universitaria de Secuenciación Masiva y Bioinformática, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Liliana Pardo-López
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
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3
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Wang J, Yuan H, Wang H, Wang J, Geng Y, Zhang Y, He Z. Enantioselective bioaccumulation, biotransformation and spatial distribution of chiral fungicide difenoconazole in earthworms (Eisenia fetida). CHEMOSPHERE 2024; 361:142404. [PMID: 38782131 DOI: 10.1016/j.chemosphere.2024.142404] [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: 03/25/2024] [Revised: 05/12/2024] [Accepted: 05/20/2024] [Indexed: 05/25/2024]
Abstract
The enantioselective environmental behavior of difenoconazole, a widely utilized triazole fungicide commonly detected in agricultural soils, has yet to be comprehensively explored within the earthworm-soil system. To address this research gap, we investigated the bioaccumulation and elimination kinetics, degradation pathways, biotransformation mechanisms, spatial distribution, and toxicity of chiral difenoconazole. The four stereoisomers of difenoconazole were baseline separated and analyzed using SFC-MS/MS. Pronounced enantioselectivity was observed during the uptake phase, with earthworms exhibiting a preference for (2R,4R)-difenoconazole and (2R,4S)-difenoconazole. A total of five transformation products (TPs) were detected and identified using UHPLC-QTOF/MS in the earthworm-soil system. Four of the TPs were detected in both earthworm and soil, and one TP was produced only in eaerthwroms. Hydrolysis and hydroxylation were the primary transformation pathways of difenoconazole in both earthworms and soil. Furthermore, a chiral TP, 3-chloro, 4-hydroxy difenoconazole, was generated with significant enantioselectivity, and molecular docking results indicate the greater catalytic bioactivity of (2R,4R)- and (2R,4S)-difenoconazole, leading to the preferential formation of their corresponding hydroxylated TPs. Furthermore, Mass Spectrometry Imaging (MSI) was applied for the first time to explore the spatial distribution of difenoconazole and the TPs in earthworms, and the "secretory zone" was found to be the dominant region to uptake and biodegrade difenoconazole. ECOSAR predictions highlighted the potentially hazardous impact of most difenoconazole TPs on aquatic ecosystems. These findings are important for understanding the environmental fate of difenoconazole, evaluating environmental risks, and offering valuable insights for guiding scientific bioremediation efforts.
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Affiliation(s)
- Jiafu Wang
- Key Laboratory for Environmental Factors Control of Agro-product Quality Safety, Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, PR China.
| | - Haiyue Yuan
- Key Laboratory for Environmental Factors Control of Agro-product Quality Safety, Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, PR China
| | - Hao Wang
- Key Laboratory for Environmental Factors Control of Agro-product Quality Safety, Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, PR China
| | - Jishi Wang
- Key Laboratory for Environmental Factors Control of Agro-product Quality Safety, Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, PR China
| | - Yue Geng
- Key Laboratory for Environmental Factors Control of Agro-product Quality Safety, Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, PR China
| | - Yanwei Zhang
- Key Laboratory for Environmental Factors Control of Agro-product Quality Safety, Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, PR China
| | - Zeying He
- Key Laboratory for Environmental Factors Control of Agro-product Quality Safety, Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, PR China.
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4
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Yue D, Hirao H. Mechanism of Selective Aromatic Hydroxylation in the Metabolic Transformation of Paclitaxel Catalyzed by Human CYP3A4. J Chem Inf Model 2023; 63:7826-7836. [PMID: 38039955 DOI: 10.1021/acs.jcim.3c01630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2023]
Abstract
Paclitaxel (PTX) is heralded as one of the most successful natural-product drugs for the treatment of refractory cancers. In humans, the hepatic metabolic transformation of PTX is primarily mediated by two cytochrome P450 enzymes (P450s): CYP3A4 and CYP2C8. The impact of P450 metabolism on the anticancer effectiveness of PTX is significant. However, the precise mechanism underlying selective P450-catalyzed reactions in PTX metabolism remains elusive. To address this knowledge gap, we conducted molecular docking and molecular dynamics simulations using multiple crystal structures of CYP3A4, which originally contained other ligands. These methods enabled us to determine the most plausible binding structure of PTX within the enzyme. By further employing hybrid quantum mechanics and molecular mechanics calculations, we successfully identified two primary pathways for the reaction between compound I (Cpd I) of CYP3A4 and PTX. One of these pathways involves the formation of an epoxide, while the other proceeds through a ketone intermediate.
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Affiliation(s)
- Dongxiao Yue
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, P. R. China
| | - Hajime Hirao
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, P. R. China
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5
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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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6
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Monika, Kumar M, Somi, Sarkar A, Gupta MK, Ansari A. Theoretical study of the formation of metal-oxo species of the first transition series with the ligand 14-TMC: driving factors of the "Oxo Wall". Dalton Trans 2023; 52:14160-14169. [PMID: 37750348 DOI: 10.1039/d3dt02109b] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
Terminal metal-oxo species of the early transition metal series are well known, whereas those for the late transition series are rare, and this is related to the "Oxo Wall". Here, we have undertaken a theoretical study on the formation of metal-oxo species from the metal hydroperoxo species of the 3d series (Cr, Mn, Fe, Co, Ni, and Cu) with the ligand 14-TMC (1,4,8,11-tetramethyl-1,4,8,11-tetraazacyclotetradecane) via O⋯O bond cleavage. DFT calculations reveal that the barrier for O⋯O bond cleavage is higher with the late transition metals (Co, Ni, and Cu) than the early transition metals (Cr, Mn, and Fe), and the formed late metal-oxo species are also thermodynamically less stable. The higher barrier may be due to electronic repulsion because of the pairing of d electrons. In the late transition metal series, the electron goes into an antibonding orbital, which decreases the bond order and hence decreases the possibility of metal-oxo formation. Computed structural parameters and spin densities suggest that valence tautomerism occurs in the late transition metal-oxo species which remain as a metal-oxyl. Our findings support the concept of the "Oxo Wall".
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Affiliation(s)
- Monika
- Department of Chemistry, Central University of Haryana, Mahendergarh-123031, Haryana, India.
| | - Manjeet Kumar
- Department of Chemistry, Central University of Haryana, Mahendergarh-123031, Haryana, India.
| | - Somi
- Department of Chemistry, Central University of Haryana, Mahendergarh-123031, Haryana, India.
| | - Arup Sarkar
- Department of Chemistry, The University of Chicago 5735 South Ellis Avenue, Chicago, IL 60637, USA
| | - Manoj Kumar Gupta
- Department of Chemistry, Central University of Haryana, Mahendergarh-123031, Haryana, India.
| | - Azaj Ansari
- Department of Chemistry, Central University of Haryana, Mahendergarh-123031, Haryana, India.
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7
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Podgorski MN, Keto AB, Coleman T, Bruning JB, De Voss JJ, Krenske EH, Bell SG. The Oxidation of Oxygen and Sulfur-Containing Heterocycles by Cytochrome P450 Enzymes. Chemistry 2023; 29:e202301371. [PMID: 37338048 DOI: 10.1002/chem.202301371] [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: 04/30/2023] [Revised: 06/12/2023] [Accepted: 06/20/2023] [Indexed: 06/21/2023]
Abstract
The cytochrome P450 (CYP) superfamily of monooxygenase enzymes play important roles in the metabolism of molecules which contain heterocyclic, aromatic functional groups. Here we study how oxygen- and sulfur-containing heterocyclic groups interact with and are oxidized using the bacterial enzyme CYP199A4. This enzyme oxidized both 4-(thiophen-2-yl)benzoic acid and 4-(thiophen-3-yl)benzoic acid almost exclusively via sulfoxidation. The thiophene oxides produced were activated towards Diels-Alder dimerization after sulfoxidation, forming dimeric metabolites. Despite X-ray crystal structures demonstrating that the aromatic carbon atoms of the thiophene ring were located closer to the heme than the sulfur, sulfoxidation was still favoured with 4-(thiophen-3-yl)benzoic acid. These results highlight a preference of this cytochrome P450 enzyme for sulfoxidation over aromatic hydroxylation. Calculations predict a strong preference for homodimerization of the enantiomers of the thiophene oxides and the formation of a single major product, in broad agreement with the experimental data. 4-(Furan-2-yl)benzoic acid was oxidized to 4-(4'-hydroxybutanoyl)benzoic acid using a whole-cell system. This reaction proceeded via a γ-keto-α,β-unsaturated aldehyde species which could be trapped in vitro using semicarbazide to generate a pyridazine species. The combination of the enzyme structures, the biochemical data and theoretical calculations provides detailed insight into the formation of the metabolites formed from these heterocyclic compounds.
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Affiliation(s)
- Matthew N Podgorski
- Department of Chemistry, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Angus B Keto
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Qld, 4072, Australia
| | - Tom Coleman
- Department of Chemistry, University of Adelaide, Adelaide, SA, 5005, Australia
| | - John B Bruning
- School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - James J De Voss
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Qld, 4072, Australia
| | - Elizabeth H Krenske
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Qld, 4072, Australia
| | - Stephen G Bell
- Department of Chemistry, University of Adelaide, Adelaide, SA, 5005, Australia
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8
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Tu HF, Jeandin A, Bon C, Brocklehurst C, Lima F, Suero MG. Late-Stage Aryl C-H Bond Cyclopropenylation with Cyclopropenium Cations. Angew Chem Int Ed Engl 2023; 62:e202308379. [PMID: 37459194 DOI: 10.1002/anie.202308379] [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: 06/14/2023] [Accepted: 07/17/2023] [Indexed: 07/29/2023]
Abstract
Herein, we disclose the first regio-, site- and chemoselective late-stage (hetero)aryl C-H bond cyclopropenylation with cyclopropenium cations (CPCs). The process is fast, operationally simple and shows an excellent functional group tolerance in densely-functionalized drug molecules, natural products, agrochemicals and fluorescent dyes. Moreover, we discovered that the installation of the cyclopropene ring in drug molecules could not only be used to shield against metabolic instability but also as a synthetic tool to reach medicinally-relevant sp3 -rich scaffolds exploiting the highly-strained nature of the cyclopropene ring with known transformations.
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Affiliation(s)
- Hang-Fei Tu
- Institute of Chemical Research of Catalonia (ICIQ-CERCA), Barcelona Institute of Science and Technology, Av. Països Catalans, 16, 43007, Tarragona, Spain
| | - Aliénor Jeandin
- Institute of Chemical Research of Catalonia (ICIQ-CERCA), Barcelona Institute of Science and Technology, Av. Països Catalans, 16, 43007, Tarragona, Spain
- Departament de Química Analítica i Química Orgánica, Universitat Rovira i Virgili, Calle Marcel.lí Domingo, 1, 43007, Tarragona, Spain
| | - Corentin Bon
- Global Discovery Chemistry, Novartis Institutes of BioMedical Research, 4056, Basel, Switzerland
| | - Cara Brocklehurst
- Global Discovery Chemistry, Novartis Institutes of BioMedical Research, 4056, Basel, Switzerland
| | - Fabio Lima
- Global Discovery Chemistry, Novartis Institutes of BioMedical Research, 4056, Basel, Switzerland
| | - Marcos G Suero
- Institute of Chemical Research of Catalonia (ICIQ-CERCA), Barcelona Institute of Science and Technology, Av. Països Catalans, 16, 43007, Tarragona, Spain
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9
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Hou Z, Li Y, Zheng M, Liu X, Zhang Q, Wang W. Regioselective oxidation of heterocyclic aromatic hydrocarbons catalyzed by cytochrome P450: A case study of carbazole. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 258:114964. [PMID: 37121081 DOI: 10.1016/j.ecoenv.2023.114964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 04/11/2023] [Accepted: 04/26/2023] [Indexed: 05/22/2023]
Abstract
Recently there are increasing interests in accurately evaluating the health effects of heterocyclic PAHs. However, the activation mechanism and possible metabolites of heterocyclic PAHs catalyzed by human CYP1A1 is still elusive to a great extent. Here, leveraged to high level QM/MM calculations, the corresponding activation pathways of a representative heterocyclic PAHs, carbazole, were systematically explored. The first stage is electrophilic addition or hydrogen abstraction from N-H group. Electrophilic addition was evidenced to be more feasible and regioselectivity at C3 and C4 sites were identified. Correlations between energy barriers and key structural/electrostatic parameters reveal that O-Cα distance and Fe-O-Cα angle are the main origin for the catalytic regioselectivity. Electrophilic addition was determined as the rate-determining step and the subsequent possible reactions include epoxidation, NIH shift (the hydrogen migration from the site of hydroxylation to the adjacent carbon) and proton shuttle. The corresponding products are epoxides, ketones and hydroxylated carbazoles, respectively. The main metabolites (hydroxylated carbazoles) are estimated to be more toxic than carbazole. The regioselectivity of carbazole activated by CYP1A1 is different from the environmental processes (gas and aqueous phase). Collectively, these results will inform the in-depth understanding the metabolic processes of heterocyclic PAHs and aid the accurate evaluation of their health effects.
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Affiliation(s)
- Zexi Hou
- Environment Research Institute, Shandong University, Qingdao 266237, PR China
| | - Yanwei Li
- Environment Research Institute, Shandong University, Qingdao 266237, PR China; Shenzhen Research Institute, Shandong University, Shenzhen 518057, PR China.
| | - Mingna Zheng
- Environment Research Institute, Shandong University, Qingdao 266237, PR China
| | - Xinning Liu
- Environment Research Institute, Shandong University, Qingdao 266237, PR China
| | - Qingzhu Zhang
- Environment Research Institute, Shandong University, Qingdao 266237, PR China
| | - Wenxing Wang
- Environment Research Institute, Shandong University, Qingdao 266237, PR China
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10
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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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11
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Reliably assessing the electronic structure of cytochrome P450 on today's classical computers and tomorrow's quantum computers. Proc Natl Acad Sci U S A 2022; 119:e2203533119. [PMID: 36095200 PMCID: PMC9499570 DOI: 10.1073/pnas.2203533119] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Chemical simulation is one of the most promising applications for future quantum computers. It is thought that quantum computers may enable accurate simulation for complex molecules that are otherwise impossible to simulate classically; that is, it displays quantum advantage. To better understand quantum advantage in chemical simulation, we explore what quantum and classical resources are required to simulate a series of pharmaceutically relevant molecules. Using classical methods, we show that reliable classical simulation of these molecules requires significant resources and therefore is a promising candidate for quantum simulation. We estimate the quantum resources, both in overall simulation time and the size. The insights from this study pave the way for future quantum simulation of complex molecules. An accurate assessment of how quantum computers can be used for chemical simulation, especially their potential computational advantages, provides important context on how to deploy these future devices. To perform this assessment reliably, quantum resource estimates must be coupled with classical computations attempting to answer relevant chemical questions and to define the classical algorithms simulation frontier. Herein, we explore the quantum computation and classical computation resources required to assess the electronic structure of cytochrome P450 enzymes (CYPs) and thus define a classical–quantum advantage boundary. This is accomplished by analyzing the convergence of density matrix renormalization group plus n-electron valence state perturbation theory (DMRG+NEVPT2) and coupled-cluster singles doubles with noniterative triples [CCSD(T)] calculations for spin gaps in models of the CYP catalytic cycle that indicate multireference character. The quantum resources required to perform phase estimation using qubitized quantum walks are calculated for the same systems. Compilation into the surface code provides runtime estimates to compare directly to DMRG runtimes and to evaluate potential quantum advantage. Both classical and quantum resource estimates suggest that simulation of CYP models at scales large enough to balance dynamic and multiconfigurational electron correlation has the potential to be a quantum advantage problem and emphasizes the important interplay between classical computations and quantum algorithms development for chemical simulation.
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12
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Zhou J, Zhang X, Li Y, Feng S, Zhang Q, Wang W. Endocrine-disrupting metabolic activation of 2-nitrofluorene catalyzed by human cytochrome P450 1A1: A QM/MM approach. ENVIRONMENT INTERNATIONAL 2022; 166:107355. [PMID: 35751956 DOI: 10.1016/j.envint.2022.107355] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 05/25/2022] [Accepted: 06/14/2022] [Indexed: 06/15/2023]
Abstract
Nitropolycyclic aromatic hydrocarbons (NPAHs) present one of the most important airborne pollutants. Recent studies have shown that one of the most abundant NPAHs, 2-Nitrofluorene (NF), was supposed to be converted to endocrine-disrupting metabolites by cytochrome P450 1A1 (CYP1A1) in human cells. However, the mechanism is still largely unexplored. Here the metabolic activation and transformation mechanism of NF catalyzed by CYP1A1 were systematically studied with the aid of Molecular Dynamics, Density Functional Theory and Quantum Mechanics/Molecular Mechanics techniques. We evidence that CYP1A1 can activate NF through two elementary processes: (i) electrophilic addition (12.4 kcal·mol-1) or hydrogen abstraction (38.2 kcal·mol-1) and (ii) epoxidation (5.9 and 8.7 kcal·mol-1) or NIH shift (12.5 and 14.9 kcal·mol-1) or proton shuttle (12.1 kcal·mol-1). Electrophilic addition was found to be the rate-determining step while epoxidation rather than NIH shift or proton shuttle is the more feasible pathway after electrophilic addition. Metabolites 6,7-epoxide-2-nitrofluorene and 7,8-epoxide-2-nitrofluorene were identified as the major epoxidation products. Epoxides are unstable and easy to react with hydrated hydrogen ions and hydroxyls to produce endocrine disrupter 7-hydroxy-2-nitrofluorene. Toxic analysis shows that some of the metabolites are more toxic to model aquatic organisms (e.g. Green algea) than NF. Binding affinity analysis to human sex hormone binding globulin reveals that NF metabolites all have endocrine-disrupting potential. This study provides a comprehensive understanding on the biotransformation process of NF and may aid future studies on various NPAHs activation catalyzed by human P450 enzyme.
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Affiliation(s)
- Junhua Zhou
- Environment Research Institute, Shandong University, Qingdao 266237, PR China; School of Environmental Science and Engineering, Shandong University, Qingdao 266237, PR China
| | - Xin Zhang
- Environment Research Institute, Shandong University, Qingdao 266237, PR China; School of Environmental Science and Engineering, Shandong University, Qingdao 266237, PR China
| | - Yanwei Li
- Environment Research Institute, Shandong University, Qingdao 266237, PR China.
| | - Shanshan Feng
- Environment Research Institute, Shandong University, Qingdao 266237, PR China
| | - Qingzhu Zhang
- Environment Research Institute, Shandong University, Qingdao 266237, PR China
| | - Wenxing Wang
- Environment Research Institute, Shandong University, Qingdao 266237, PR China
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13
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Dutra M, McElhenney S, Manley O, Makris T, Rassolov V, Garashchuk S. Modeling the Ligand Effect on the Structure of CYP 450 Within the Density Functional Theory. J Phys Chem A 2022; 126:2818-2824. [PMID: 35500128 DOI: 10.1021/acs.jpca.2c01783] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An improved understanding of the P450 structure is relevant to the development of biomimetic catalysts and inhibitors for controlled CH-bond activation, an outstanding challenge of synthetic chemistry. Motivated by the experimental findings of an unusually short Fe-S bond of 2.18 Å for the wild-type (WT) OleT P450 decarboxylase relative to a cysteine pocket mutant form (A369P), a computational model that captures the effect of the thiolate axial ligand on the iron-sulfur distance is presented. With the computational efficiency and streamlined analysis in mind, this model combines a cluster representation of the enzyme─40-110 atoms, depending on the heme and ligand truncation level─with a density functional theory (DFT) description of the electronic structure (ES) and is calibrated against the experimental data. The optimized Fe-S distances show a difference of 0.25 Å between the low and high spin states, in agreement with the crystallographic structures of the OleT WT and mutant forms. We speculate that this difference is attributable to the packing of the ligand; the mutant is bulkier due to an alanine-to-proline replacement, meaning that it is excluded from the energetically favored low-spin minimum because of steric constraints. The presence of pure spin-state pairs and the intersection of the low/high spin states for the enzyme model is indicative of the limitations of single-reference ES methods in such systems and emphasizes the significance of using the proper state when modeling the hydrogen atom transfer (HAT) reaction catalyzed by OleT. At the same time, the correct characterization of both the short and long Fe-S bonds within a small DFT-based model of 42 atoms paves the way for quantum dynamics modeling of the HAT step, which initiates the OleT decarboxylation reaction.
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Affiliation(s)
- Matthew Dutra
- Department of Chemistry & Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Shannon McElhenney
- Department of Chemistry & Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Olivia Manley
- Department of Molecular & Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27607, United States
| | - Tom Makris
- Department of Molecular & Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27607, United States
| | - Vitaly Rassolov
- Department of Chemistry & Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Sophya Garashchuk
- Department of Chemistry & Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
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14
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Monika, Ansari A. Effect of the ring size of TMC ligands in controlling C-H bond activation by metal-superoxo species. Dalton Trans 2022; 51:5878-5889. [PMID: 35347335 DOI: 10.1039/d2dt00491g] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Metal-superoxo species play a very important role in many metal-mediated catalytic transformation reactions. Their catalytic reactivity is affected by many factors such as the nature of metal ions and ring size of ligands. Herein, for the first time, we report DFT calculations on the electronic structures of a series of metal-superoxo species (M = V, Cr, Mn, Fe, and Co) with two ring size ligands, i.e., 13-TMC/14-TMC, and a detailed mechanistic study on the C-H bond activation of cyclohexa-1,4-diene followed by the effect of the ring size of ligands. Our DFT results showed that the electron density at the distal oxygen plays an important role in C-H bond activation. By computing the energetics of C-H bond activation and mapping the potential energy surface, it was found that the initial hydrogen abstraction is the rate-determining step with both TMC rings and all the studied metal-superoxo species. The significant electron density at the cyclohex-1,4-diene carbon indicates that the reaction proceeds via the proton-coupled electron transfer mechanism. By mapping the potential energy surfaces, we found that the 13-TMC ligated superoxo with the anti-isomer are more reactive than the 14-TMC superoxo species except for the iron-superoxo species where the 14-TMC ligated superoxo species is more reactive i.e. smaller ring size TMC is more reactive towards C-H bond activation. This is also supported by the structural correlation, i.e., the greater contraction in the smaller ring results in the metal being pushed out of plane along the z-axis, which reduces the steric hindrance. Thus, the ring size can help in designing catalysts with better efficiency for catalytic reactions.
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Affiliation(s)
- Monika
- Department of Chemistry, Central University of Haryana, India, 123031.
| | - Azaj Ansari
- Department of Chemistry, Central University of Haryana, India, 123031.
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15
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Zhang S, Li X, Wang Y, Wei J, Zhang X, Liu Y. Computational Study of the Peroxygenase Mechanism Catalyzed by Hemoglobin Dehaloperoxidase Involved in the Degradation of Chlorophenols. Inorg Chem 2022; 61:2628-2639. [PMID: 35080380 DOI: 10.1021/acs.inorgchem.1c03721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The biochemical evidence showed that hemoglobin dehaloperoxidase (DHP B) from Amphitrite Ornata is a multifunctional hemoprotein that catalyzes both dehalogenation and hydroxylation of halophenols via the peroxidase and peroxygenase mechanism, respectively, which sets the basis for the degradation of halophenols. In the peroxygenase mechanism, the reaction was previously suggested to be triggered either by the hydrogen atom abstraction by the Fe═O center or by the proton abstraction by His55. To illuminate the peroxygenase mechanism of DHP B at the atomistic level, on the basis of the high-resolution crystal structure, computational models were constructed, and a series of quantum mechanical/molecular mechanical calculations have been performed. According to the calculation results, the pathway (Path a) initiated by the H-abstraction by the Fe═O center is feasible. In another pathway (Path b), His55 can abstract the proton from the hydroxyl group of the substrate (4-Cl-o-cresol) to initiate the reaction; however, its feasibility depends on the prior electron transfer from the substrate to the porphyrin group. The rate-limiting step of Path a is the OH-rebound, which corresponds to an energy barrier of 14.7 kcal/mol at the quartet state. His55 acts as an acid-base catalyst and directly involves in the catalysis. Our mutant study indicates that His55 can be replaced by other titratable residues. These findings may provide useful information for further understanding of the catalytic reaction of DHP B and for the design of enzymes in the degradation of pollutants, in particular, halophenols.
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Affiliation(s)
- Shiqing Zhang
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Xinyi Li
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Yijing Wang
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Jingjing Wei
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Xue Zhang
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Yongjun Liu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
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16
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Coleman T, Kirk AM, Lee JHZ, Doherty DZ, Bruning JB, Krenske EH, De Voss JJ, Bell SG. Different Geometric Requirements for Cytochrome P450-Catalyzed Aliphatic Versus Aromatic Hydroxylation Results in Chemoselective Oxidation. ACS Catal 2022. [DOI: 10.1021/acscatal.1c05483] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Tom Coleman
- Department of Chemistry, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Alicia M. Kirk
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Joel H. Z. Lee
- Department of Chemistry, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Daniel Z. Doherty
- 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
| | - Elizabeth H. Krenske
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - James J. De Voss
- School of Chemistry and Molecular Biosciences, 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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17
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Wu X, Chen Y, Wang X, Wei W, Liang Y. Origin of Site Selectivity in Toluene Hydroxylation by Cytochrome P450 Enzymes. J Org Chem 2021; 86:13768-13773. [PMID: 34533309 DOI: 10.1021/acs.joc.1c01295] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Computational studies are utilized to reveal factors that determine the site selectivity in toluene hydroxylation by cytochrome P450 enzymes (CYPs). The DFT-computed inherent barriers suggest that the priority of product formation is in the order of benzyl alcohol > ortho- ≈ para- > meta-cresol. However, the specific size and shape of the cavities at the active sites of different CYPs dramatically affect the binding orientation of toluene, and thus, the site selectivity can be reordered.
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Affiliation(s)
- Xuan Wu
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023,China
| | - Yu Chen
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023,China
| | - Xin Wang
- Henan-Macquarie University Joint Centre for Biomedical Innovation, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Wanqing Wei
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023,China
| | - Yong Liang
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023,China
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18
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Tian G, Hao G, Chen X, Liu Y. Tyrosyl Radical-Mediated Sequential Oxidative Decarboxylation of Coproporphyrinogen III through PCET: Theoretical Insights into the Mechanism of Coproheme Decarboxylase ChdC. Inorg Chem 2021; 60:13539-13549. [PMID: 34382397 DOI: 10.1021/acs.inorgchem.1c01864] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The peroxide-dependent coproheme decarboxylase ChdC from Geobacillus stearothermophilus catalyzes two key steps in the synthesis of heme b, i.e., two sequential oxidative decarboxylations of coproporphyrinogen III (coproheme III) at propionate groups P2 and P4. In the binding site of coproheme III, P2 and P4 are anchored by different residues (Tyr144, Arg217, and Ser222 for P2 and Tyr113, Lys148, and Trp156 for P4); however, strong experimental evidence supports that the generated Tyr144 radical acts as an unique intermediary for hydrogen atom transfer (HAT) from both reactive propionates. So far, the reaction details are still unclear. Herein, we carried out quantum mechanics/molecular mechanics calculations to explore the decarboxylation mechanism of coproheme III. In our calculations, the coproheme Cpd I, Fe(IV) = O coupled to a porphyrin radical cation (por•+) with four propionate groups, was used as a reactant model. Our calculations reveal that Tyr144 is directly involved in the decarboxylation of propionate group P2. First, the proton-coupled electron transfer (PCET) occurs from Tyr144 to P2, generating a Tyr144 radical, which then abstracts a hydrogen atom from the Cβ of P2. The β-H extraction was calculated to be the rate-limiting step of decarboxylation. It is the porphyrin radical cation (por•+) that makes the PCET from Tyr144 to P2 to be quite easy to initiate the decarboxylation. Finally, the electron transfers from the Cβ• through the porphyrin to the iron center, leading to the decarboxylation of P2. Importantly, the decarboxylation of P4 mediated by Lys148 was calculated to be very difficult, which suggests that after the P2 decarboxylation, the generated harderoheme III intermediate should rebind or rotate in the active site so that the propionate P4 occupies the binding site of P2, and Tyr144 again mediates the decarboxylation of P4. Thus, our calculations support the fact that Tyr144 is responsible for the decarboxylation of both P2 and P4.
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Affiliation(s)
- Ge Tian
- School of Life Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, Shandong 271000, China.,School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Gangping Hao
- School of Life Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, Shandong 271000, China
| | - Xiaohua Chen
- National-Municipal Joint Engineering Laboratory for Chemical Process Intensification and Reaction, School of Chemistry and Chemical Engineering, Chongqing University, Chongqing 401331, China
| | - Yongjun Liu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
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19
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Zhang R, Li P, Shi X, Zhang R, Wang J, Li Y, Zhang Q, Wang W. Insights into the metabolic mechanism of PBDEs catalyzed by cytochrome P450 enzyme 3A4: A QM/MM study. CHEMOSPHERE 2021; 278:130430. [PMID: 33836398 DOI: 10.1016/j.chemosphere.2021.130430] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 03/24/2021] [Accepted: 03/27/2021] [Indexed: 06/12/2023]
Abstract
Elucidating the metabolic mechanism and the derivatives of polybrominated diphenyl ethers (PBDEs) is significant to risk assessment. This study delineated the metabolic mechanism of 2,2',4,4'-tetrabromodiphenyl ether (BDE-47) catalyzed by P450 enzymes using a combination of molecular dynamic (MD), quantum mechanics/molecular mechanics (QM/MM) and density functional theory (DFT). The calculation results reveal that the electrophilic addition is the main pathway for the biotransformation of BDE-47 catalyzed by P450 enzymes. 6-hydroxy-2,2',4,4'-tetrabromodiphenyl ether (6-OH-BDE-47) is a more kinetically preferable product than 5-hydroxy-2,2',4,4'-tetrabromodiphenyl ether (5-OH-BDE-47). Electrophilic addition reaction can lead to the formation of polybrominated dibenzo-p-dioxins and dibenzofurans (PBDD/Fs). The ecotoxicity assessment indicates that the final products of BDE-47 are still toxic to aquatic organisms, but the solubility increase of the hydroxylated products can accelerate their excretion from the body. We expect that the established metabolic mechanism and the derivatives will be used to predict the biotransformation of other PBDE congeners catalyzed by P450 enzymes in human livers.
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Affiliation(s)
- Ruiming Zhang
- Environment Research Institute, Shandong University, Qingdao, 266237, PR China
| | - Pengfei Li
- Shandong Academy for Environmental Planning, Jinan, 250014, PR China
| | - Xiangli Shi
- College of Geography and Environment, Shandong Normal University, Jinan, 250014, PR China
| | - Ruiying Zhang
- Environment Research Institute, Shandong University, Qingdao, 266237, PR China
| | - Junjie Wang
- Environment Research Institute, Shandong University, Qingdao, 266237, PR China
| | - Yanwei Li
- Environment Research Institute, Shandong University, Qingdao, 266237, PR China
| | - Qingzhu Zhang
- Environment Research Institute, Shandong University, Qingdao, 266237, PR China.
| | - Wenxing Wang
- Environment Research Institute, Shandong University, Qingdao, 266237, PR China
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20
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Chen H, Zhou A, Sun D, Zhao Y, Wang Y. Theoretical Investigation on the Elusive Reaction Mechanism of Spirooxindole Formation Mediated by Cytochrome P450s: A Nascent Feasible Charge-Shift C-O Bond Makes a Difference. J Phys Chem B 2021; 125:8419-8430. [PMID: 34313131 DOI: 10.1021/acs.jpcb.1c04088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Spirooxindoles are pivotal biofunctional groups widely distributed in natural products and clinic drugs. However, construction of such subtle chiral skeletons is a long-standing challenge to both organic and bioengineering scientists. The knowledge of enzymatic spirooxindole formation in nature may inspire rational design of new catalysts. To this end, we presented a theoretical investigation on the elusive mechanism of the spiro-ring formation at the 3-position of oxindole mediated by cytochrome P450 enzymes (P450). Our calculated results demonstrated that the electrophilic attack of CpdI, the active species of P450, to the substrate, shows regioselectivity, i.e., the attack at the C9 position forms a tetrahedral intermediate involving an unusual feasible charge-shift C9δ+-Oδ- bond, while the attack at the C1 position forms an epoxide intermediate. The predominant route is the first route with the charge-shift bonding intermediate due to holding a relatively lower barrier by >5 kcal mol-1 than the epoxide route, which fits the experimental observations. Such a delocalized charge-shift bond facilitates the formation of a spiro-ring mainly through elongation of the C1-C9 bond to eliminate the aromatization of the tricyclic beta-carboline. Our theoretical results shed profound mechanistic insights for the first time into the elusive spirooxindole formation mediated by P450s.
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Affiliation(s)
- Huanhuan Chen
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, Zhejiang, China.,Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo 315211, Zhejiang, China
| | - Anran Zhou
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, Zhejiang, China.,Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo 315211, Zhejiang, China
| | - Dongru Sun
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, Zhejiang, China.,Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo 315211, Zhejiang, China
| | - Yufen Zhao
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, Zhejiang, China.,Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo 315211, Zhejiang, China
| | - Yong Wang
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, Zhejiang, China.,Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo 315211, Zhejiang, China
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21
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Jin L, Wang Q, Chen X, Liu N, Fang X, Yang YF, She YB. Computational Studies on the Mechanism and Origin of the Different Regioselectivities of Manganese Porphyrin-Catalyzed C-H Bond Hydroxylation and Amidation of Equilenin Acetate. J Org Chem 2020; 85:14879-14889. [PMID: 33225704 DOI: 10.1021/acs.joc.0c01444] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The manganese porphyrin-catalyzed C-H bond hydroxylation and amidation of equilenin acetate developed by Breslow and his co-worker have been investigated with density functional theory (DFT) calculations. The hydroxylation of C(sp2)-H bond of equilenin acetate leading to the 6-hydroxylated product is more favorable than the hydroxylation of C(sp3)-H bond of equilenin acetate, leading to the 11β-hydroxylation product. The computational results suggest that the C(sp2)-H bond hydroxylation of equilenin acetate undergoes an oxygen-atom-transfer mechanism, which is more favorable than the C(sp3)-H bond hydroxylation undergoing the hydrogen-atom-abstraction/oxygen-rebound (HAA/OR) mechanism by 1.6 kcal/mol. That is why, the 6-hydroxylated product is the major product and the 11β-hydroxylated product is the minor product. In contrast, the 11β-amidated product is the only observed product in manganese porphyrin-catalyzed amidation reaction. The benzylic amidation undergoes a hydrogen-atom-abstraction/nitrogen-rebound (HAA/NR) mechanism, in which hydrogen atom abstraction is followed by nitrogen rebound, leading to the 11β-amidated product. The benzylic C(sp3)-H bond amidation at the C-11 position is more favorable than aromatic amidation at the C-6 position by 4.9 kcal/mol. Therefore, the DFT computational results are consistent with the experiments that manganese porphyrin-catalyzed C-H bond hydroxylation and amidation of equilenin acetate have different regioselectivities.
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Affiliation(s)
- Liyuan Jin
- College of Chemical Engineering, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China
| | - Qunmin Wang
- College of Chemical Engineering, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China
| | - Xiahe Chen
- College of Chemical Engineering, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China
| | - Ning Liu
- College of Chemical Engineering, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China
| | - Xiaoli Fang
- College of Chemical Engineering, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China
| | - Yun-Fang Yang
- College of Chemical Engineering, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China
| | - Yuan-Bin She
- College of Chemical Engineering, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China
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22
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Zhang C, Crawford JJ, Landry ML, Chen H, Kenny JR, Khojasteh SC, Lee W, Ma S, Young WB. Strategies to Mitigate the Bioactivation of Aryl Amines. Chem Res Toxicol 2020; 33:1950-1959. [PMID: 32508087 DOI: 10.1021/acs.chemrestox.0c00138] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The bioactivation of xenobiotics to yield reactive metabolites can lead to tolerability and toxicity concerns within a drug discovery program. Development of strategies for mitigating the metabolic liability of commonly encountered toxicophores, such as anilines, relies on an understanding of the relative tendency of these functionalities to undergo bioactivation. In this report, we present the first systematic study of the structure-activity relationships of the bioactivation of aryl amine fragments (molecular weight < 250 Da) using a glutathione (GSH) trapping assay in the presence of human liver microsomes and the reduced form of nicotinamide adenine dinucleotide phosphate. This study demonstrates that conversion of anilines to nitrogen-containing heteroarylamines results in a lower abundance of GSH conjugates in the order phenyl > pyrimidine ≈ pyridine > pyridazine. Introduction of electron-withdrawing functionality on the aromatic ring had a less pronounced effect on the extent of GSH conjugation. Examination of more drug-like compounds sourced from in-house drug discovery programs revealed similar trends in bioactivation between matched pairs containing (hetero)aryl amines. This study provides medicinal chemists with insights and qualitative guidance for the minimization of risks related to aryl amine metabolism.
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Affiliation(s)
- Chenghong Zhang
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - James J Crawford
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Matthew L Landry
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Huifen Chen
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Jane R Kenny
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - S Cyrus Khojasteh
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Wendy Lee
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Shuguang Ma
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Wendy B Young
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
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23
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Wen J, Chennamadhavuni D, Morel SR, Hadden MK. Truncated Itraconazole Analogues Exhibiting Potent Anti-Hedgehog Activity and Improved Drug-like Properties. ACS Med Chem Lett 2019; 10:1290-1295. [PMID: 31531199 DOI: 10.1021/acsmedchemlett.9b00188] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 08/23/2019] [Indexed: 02/06/2023] Open
Abstract
We conducted a structure-activity relationship study to explore simplified analogues of the itraconazole (ITZ) scaffold for their ability to inhibit the hedgehog (Hh) signaling pathway. These analogues were based on exploring the effects of chemical modifications to the linker and triazolone/side chain region of ITZ. Analogue 11 was identified as the most potent compound in our first generation, with an IC50 value of 81 nM in a murine Hh-dependent basal cell carcinoma. Metabolic identification studies led us to identify truncated piperazine (26) as the major metabolite in human liver microsomes (HLMs) and an improved Hh pathway inhibitor (IC50 = 22 nM). This work verifies that continued truncation of the ITZ scaffold is a practical method to maintain potent anti-Hh activity while also reducing the molecular weight for the ITZ scaffold and achieving improved pharmacokinetic properties.
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Affiliation(s)
- Jiachen Wen
- Department of Pharmaceutical Sciences, University of Connecticut, 69 North Eagleville Road, Unit 3092, Storrs, Connecticut 06029-3092, United States
| | - Divya Chennamadhavuni
- Department of Pharmaceutical Sciences, University of Connecticut, 69 North Eagleville Road, Unit 3092, Storrs, Connecticut 06029-3092, United States
| | - Shana R. Morel
- Department of Pharmaceutical Sciences, University of Connecticut, 69 North Eagleville Road, Unit 3092, Storrs, Connecticut 06029-3092, United States
| | - M. Kyle Hadden
- Department of Pharmaceutical Sciences, University of Connecticut, 69 North Eagleville Road, Unit 3092, Storrs, Connecticut 06029-3092, United States
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24
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Affiliation(s)
- Christine Beedham
- Honorary Senior Lecturer, Faculty of Life Sciences, School of Pharmacy and Medical Sciences, University of Bradford, Bradford, UK
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25
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Bao L, Liu W, Li Y, Wang X, Xu F, Yang Z, Yue Y, Zuo C, Zhang Q, Wang W. Carcinogenic Metabolic Activation Process of Naphthalene by the Cytochrome P450 Enzyme 1B1: A Computational Study. Chem Res Toxicol 2019; 32:603-612. [PMID: 30794404 DOI: 10.1021/acs.chemrestox.8b00297] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The metabolic activation and transformation of naphthalene by the cytochrome P450 enzyme (CYP 1B1) plays an important role in its potential carcinogenicity. The process has been explored by a quantum mechanics/molecular mechanics (QM/MM) computational method. Molecular dynamic simulations were performed to explore the interaction between naphthalene and CYP 1B1. Naphthalene involves α- and β-carbon, the electrophilic addition of which would result in different reaction pathways. Our computational results show that both additions on α- and β-carbon can generate naphthalene 1,2-oxide. The activation barrier for the addition on β-carbon is higher than that for the α-carbon by 2.6 kcal·mol-1, which is possibly caused by the proximity between β-carbon and the iron-oxo group of Cpd I in the system. We also found that naphthalene 1,2-oxide is unstable and the O-C bond cleavage easily occurs via cellular hydronium ion, hydroxyl radical/anion; then it will convert to the potential ultimate carcinogen 1,2-naphthoquinone. The results demonstrate and inform a detailed process of generating naphthalene 1,2-oxide and new predictions for its conversion.
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Affiliation(s)
- Lei Bao
- Environment Research Institute , Shandong University , Qingdao 266237 , People's Republic of China
| | - Wen Liu
- Environment Research Institute , Shandong University , Qingdao 266237 , People's Republic of China
| | - Yanwei Li
- Environment Research Institute , Shandong University , Qingdao 266237 , People's Republic of China
| | - Xueyu Wang
- Environment Research Institute , Shandong University , Qingdao 266237 , People's Republic of China
| | - Fei Xu
- Shenzhen Research Institute of Shandong University , Shenzhen 518057 , People's Republic of China
| | - Zhongyue Yang
- Department of Chemical Engineering , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Yue Yue
- Environment Research Institute , Shandong University , Qingdao 266237 , People's Republic of China
| | - Chenpeng Zuo
- Environment Research Institute , Shandong University , Qingdao 266237 , People's Republic of China
| | - Qingzhu Zhang
- Environment Research Institute , Shandong University , Qingdao 266237 , People's Republic of China
| | - Wenxing Wang
- Environment Research Institute , Shandong University , Qingdao 266237 , People's Republic of China
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26
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Leth R, Ercig B, Olsen L, Jørgensen FS. Both Reactivity and Accessibility Are Important in Cytochrome P450 Metabolism: A Combined DFT and MD Study of Fenamic Acids in BM3 Mutants. J Chem Inf Model 2019; 59:743-753. [DOI: 10.1021/acs.jcim.8b00750] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Rasmus Leth
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Bogac Ercig
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Lars Olsen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Flemming Steen Jørgensen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
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27
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Ma G, Yu H, Xu T, Wei X, Chen J, Lin H, Schüürmann G. Computational Insight into the Activation Mechanism of Carcinogenic N'-Nitrosonornicotine (NNN) Catalyzed by Cytochrome P450. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:11838-11847. [PMID: 30209943 DOI: 10.1021/acs.est.8b02795] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Tobacco-specific N'-nitrosonornicotine (NNN), a genotoxic nitrosamine classified as Group 1 carcinogen, is also present in atmospheric particulate matter and has even been detected as a new disinfection byproduct in wastewaters. NNN generally requires metabolic activation by cytochrome P450 enzymes to exert its genotoxicity, but the respective biotransformation pathways have not been described in detail. In this work, we performed density functional theory (DFT) calculations to unravel possible NNN activation pathways including α-hydroxylation, β-hydroxylation, pyridine N-oxidation, and norcotinine formation. The results reveal an initial rate-determining Hα-atom abstraction step for α-hydroxylation, followed by an unexpected kinetic competition between denitrosation and OH rebound, leading to ( iso-)myosmine as a detoxified product and α-hydroxyNNNs as the precursor of carcinogenic diazohydroxides, respectively. Further detoxification routes are given by β-hydroxylation with relative high reaction barrier and N-oxidation with comparable barrier to the toxifying α-hydroxylation. Moreover, we show for the first time how norcotinine can be generated as a minor NNN metabolite that is formed from iso-myosmine through a unique porphyrin-assisted H atom 1,2-transfer mechanism. These results demonstrate that the carcinogenic potential of NNN is subject to a kinetic competition between activating and deactivating metabolic routes, and identify respective biomarkers to inform about the individual risk associated with NNN exposure.
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Affiliation(s)
- Guangcai Ma
- College of Geography and Environmental Sciences , Zhejiang Normal University , Yingbin Avenue 688 , 321004 , Jinhua , China
| | - Haiying Yu
- College of Geography and Environmental Sciences , Zhejiang Normal University , Yingbin Avenue 688 , 321004 , Jinhua , China
| | - Ting Xu
- College of Geography and Environmental Sciences , Zhejiang Normal University , Yingbin Avenue 688 , 321004 , Jinhua , China
| | - Xiaoxuan Wei
- College of Geography and Environmental Sciences , Zhejiang Normal University , Yingbin Avenue 688 , 321004 , Jinhua , China
| | - Jianrong Chen
- College of Geography and Environmental Sciences , Zhejiang Normal University , Yingbin Avenue 688 , 321004 , Jinhua , China
| | - Hongjun Lin
- College of Geography and Environmental Sciences , Zhejiang Normal University , Yingbin Avenue 688 , 321004 , Jinhua , China
| | - Gerrit Schüürmann
- UFZ Department of Ecological Chemistry , Helmholtz Centre for Environmental Research , Permoserstrasse 15 , 04318 , Leipzig , Germany
- Institute of Organic Chemistry , Technical University Bergakademie Freiberg , Leipzig Strasse 29 , 09596 Freiberg , Germany
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28
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Luirink RA, Dekker SJ, Capoferri L, Janssen LF, Kuiper CL, Ari ME, Vermeulen NP, Vos JC, Commandeur JN, Geerke DP. A combined computational and experimental study on selective flucloxacillin hydroxylation by cytochrome P450 BM3 variants. J Inorg Biochem 2018; 184:115-122. [DOI: 10.1016/j.jinorgbio.2018.04.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Revised: 03/23/2018] [Accepted: 04/18/2018] [Indexed: 12/20/2022]
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29
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Huang X, Groves JT. Oxygen Activation and Radical Transformations in Heme Proteins and Metalloporphyrins. Chem Rev 2018; 118:2491-2553. [PMID: 29286645 PMCID: PMC5855008 DOI: 10.1021/acs.chemrev.7b00373] [Citation(s) in RCA: 591] [Impact Index Per Article: 98.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Indexed: 12/20/2022]
Abstract
As a result of the adaptation of life to an aerobic environment, nature has evolved a panoply of metalloproteins for oxidative metabolism and protection against reactive oxygen species. Despite the diverse structures and functions of these proteins, they share common mechanistic grounds. An open-shell transition metal like iron or copper is employed to interact with O2 and its derived intermediates such as hydrogen peroxide to afford a variety of metal-oxygen intermediates. These reactive intermediates, including metal-superoxo, -(hydro)peroxo, and high-valent metal-oxo species, are the basis for the various biological functions of O2-utilizing metalloproteins. Collectively, these processes are called oxygen activation. Much of our understanding of the reactivity of these reactive intermediates has come from the study of heme-containing proteins and related metalloporphyrin compounds. These studies not only have deepened our understanding of various functions of heme proteins, such as O2 storage and transport, degradation of reactive oxygen species, redox signaling, and biological oxygenation, etc., but also have driven the development of bioinorganic chemistry and biomimetic catalysis. In this review, we survey the range of O2 activation processes mediated by heme proteins and model compounds with a focus on recent progress in the characterization and reactivity of important iron-oxygen intermediates. Representative reactions initiated by these reactive intermediates as well as some context from prior decades will also be presented. We will discuss the fundamental mechanistic features of these transformations and delineate the underlying structural and electronic factors that contribute to the spectrum of reactivities that has been observed in nature as well as those that have been invented using these paradigms. Given the recent developments in biocatalysis for non-natural chemistries and the renaissance of radical chemistry in organic synthesis, we envision that new enzymatic and synthetic transformations will emerge based on the radical processes mediated by metalloproteins and their synthetic analogs.
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Affiliation(s)
- Xiongyi Huang
- Department
of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
- Department
of Chemistry, California Institute of Technology, Pasadena, California 91125, United States
| | - John T. Groves
- Department
of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
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30
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de Ruiter G, Carsch KM, Takase MK, Agapie T. Selectivity of C-H versus C-F Bond Oxygenation by Homo- and Heterometallic Fe 4 , Fe 3 Mn, and Mn 4 Clusters. Chemistry 2017; 23:10744-10748. [PMID: 28658508 PMCID: PMC5659184 DOI: 10.1002/chem.201702302] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Indexed: 02/03/2023]
Abstract
A series of tetranuclear [LM3 (HFArPz)3 OM'][OTf]2 (M, M'=Fe or Mn) clusters that displays 3-(2-fluorophenyl)pyrazolate (HFArPz) as bridging ligand is reported. With these complexes, manganese was demonstrated to facilitate C(sp2 )-F bond oxygenation via a putative terminal metal-oxo species. Moreover, the presence of both ortho C(sp2 )-H and C(sp2 )-F bonds in proximity of the apical metal center provided an opportunity to investigate the selectivity of intramolecular C(sp2 )-X bond oxygenation (X=H or F) in these isostructural compounds. With iron as the apical metal center, (M'=Fe) C(sp2 )-F bond oxygenation occur almost exclusively, whereas with manganese (M'=Mn), the opposite reactivity is preferred.
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Affiliation(s)
- Graham de Ruiter
- Department of Chemistry and Chemical Engineering, California Institute of Technology; MC 127-72, Pasadena, California, 91125, USA
| | - Kurtis M Carsch
- Department of Chemistry and Chemical Engineering, California Institute of Technology; MC 127-72, Pasadena, California, 91125, USA
| | - Michael K Takase
- Department of Chemistry and Chemical Engineering, California Institute of Technology; MC 127-72, Pasadena, California, 91125, USA
| | - Theodor Agapie
- Department of Chemistry and Chemical Engineering, California Institute of Technology; MC 127-72, Pasadena, California, 91125, USA
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31
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Ai CZ, Liu Y, Li W, Chen DM, Zhu XX, Yan YW, Chen DC, Jiang YZ. Computational explanation for bioactivation mechanism of targeted anticancer agents mediated by cytochrome P450s: A case of Erlotinib. PLoS One 2017. [PMID: 28628631 PMCID: PMC5476264 DOI: 10.1371/journal.pone.0179333] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
EGFR inhibitors, even with therapeutics superiorities in anticancer, can cause idiosyncratic pulmonary and hepatic toxicities that are associated with the reactive electrophile bioactivated by Cytochrome P450s (P450s). Until now, neither has the electrophilic intermediate been caught experimentally, nor has the subtle mechanism been declared. Herein, the underlying mechanism of bioactivation mediated by P450s was explored by DFT calculations for a case of EGFR inhibitor, Erlotinib. Based on the calculation and analysis, we suggest that with other metabolites, reactive electrophiles of Erlotinib: epoxide and quinine-imine, can be generated by several steps along the oxidative reaction pathway. The generation of epoxide needs two steps: (1) the addition of Erlotinib to Compound I (Cpd I) and (2) the rearrangement of protons. Whereas, quinine-imine needs a further oxidation step (3) via which quinone is generated and ultimately turns into quinine-imine. Although both reactive electrophiles can be produced for either face-on or side-on pose of Erlotinib, the analysis of energy barriers indicates that the side-on path is preferred in solvent environment. In the rate-determining step, e.g. the addition of Erlotinib to the porphyrin, the reaction barrier for side-on conformation is decreased in aqueous and protein environment compared with gas phase, whereas, the barrier for face-on pose is increased in solvent environment. The simulated mechanism is in good agreement with the speculation in previous experiment. The understanding of the subtle mechanism of bioactivation of Erlotinib will provide theoretical support for toxicological mechanism of EGFR inhibitors.
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Affiliation(s)
- Chun-Zhi Ai
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong, China
| | - Yong Liu
- School of Life Science and Medicine, Dalian University of Technology, Panjin, Liaoning, China
| | - Wei Li
- College of Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - De-Meng Chen
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
- School of Dentistry, University of California, Los Angeles, California, United States of America
| | - Xin-Xing Zhu
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong, China
| | - Ya-Wei Yan
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong, China
| | - Du-Chu Chen
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong, China
| | - Yi-Zhou Jiang
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
- * E-mail:
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32
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Rühlmann A, Antovic D, Müller TJJ, Urlacher VB. Regioselective Hydroxylation of Stilbenes by Engineered Cytochrome P450 fromThermobifida fuscaYX. Adv Synth Catal 2017. [DOI: 10.1002/adsc.201601168] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Ansgar Rühlmann
- Institute of Biochemistry; Heinrich-Heine University Düsseldorf; Universitätsstr.1 40225 Düsseldorf Germany
| | - Dragutin Antovic
- Institute of Macromolecular and Organic Chemistry, Chair of Organic Chemistry; Heinrich-Heine University Düsseldorf; Universitätsstr. 1 40225 Düsseldorf Germany
| | - Thomas J. J. Müller
- Institute of Macromolecular and Organic Chemistry, Chair of Organic Chemistry; Heinrich-Heine University Düsseldorf; Universitätsstr. 1 40225 Düsseldorf Germany
| | - Vlada B. Urlacher
- Institute of Biochemistry; Heinrich-Heine University Düsseldorf; Universitätsstr.1 40225 Düsseldorf Germany
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33
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Gul T, Bischoff R, Permentier HP. Mechanism of aromatic hydroxylation of lidocaine at a Pt electrode under acidic conditions. Electrochim Acta 2017. [DOI: 10.1016/j.electacta.2016.12.089] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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34
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Lábas A, Krámos B, Oláh J. Combined Docking and Quantum Chemical Study on CYP-Mediated Metabolism of Estrogens in Man. Chem Res Toxicol 2016; 30:583-594. [PMID: 27966929 DOI: 10.1021/acs.chemrestox.6b00330] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Long-term exposure to estrogens seriously increases the incidence of various diseases including breast cancer. Experimental studies indicate that cytochrome P450 (CYP) enzymes catalyze the bioactivation of estrogens to catechols, which can exert their harmful effects via various routes. It has been shown that the 4-hydroxylation pathway of estrogens is the most malign, while 2-hydroxylation is considered a benign pathway. It is also known experimentally that with increasing unsaturation of ring B of estrogens the prevalence of the 4-hydroxylation pathway significantly increases. In this study, we used a combination of structural analysis, docking, and quantum chemical calculations at the B3LYP/6-311+G* level to investigate the factors that influence the regioselectivity of estrogen metabolism in man. We studied the structure of human estrogen metabolizing enzymes (CYP1A1, CYP1A2, CYP1B1, and CYP3A4) in complex with estrone using docking and investigated the susceptibility of estrone, equilin, and equilenin (which only differ in the unsaturation of ring B) to undergo 2- and 4-hydroxylation using several models of CYP enzymes (Compound I, methoxy, and phenoxy radical). We found that even the simplest models could account for the experimental difference between the 2- and 4- hydroxylation pathways and thus might be used for fast screening purposes. We also show that reactivity indices, specifically in this case the radical and nucleophilic condensed Fukui functions, also correctly predict the likeliness of estrogen derivatives to undergo 2- or 4-hydroxylation.
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Affiliation(s)
- Anikó Lábas
- Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics , Szent Gellért tér 4, H-1111 Budapest, Hungary
| | - Balázs Krámos
- Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics , Szent Gellért tér 4, H-1111 Budapest, Hungary.,Institute of Organic Chemistry Research Centre for Natural Sciences, Hungarian Academy of Sciences , Magyar Tudósok körútja 2, Budapest, P.O. Box 286, 1519 Hungary
| | - Julianna Oláh
- Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics , Szent Gellért tér 4, H-1111 Budapest, Hungary
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35
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Silva PJ. Will 1,2-dihydro-1,2-azaborine-based drugs resist metabolism by cytochrome P450 compound I? PeerJ 2016; 4:e2299. [PMID: 27547588 PMCID: PMC4974919 DOI: 10.7717/peerj.2299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 07/06/2016] [Indexed: 11/20/2022] Open
Abstract
1,2-dihydro-1,2-azaborine is a structural and electronic analogue of benzene which is able to occupy benzene-binding pockets in T4 lysozyme and has been proposed as suitable arene-mimicking group for biological and pharmaceutical applications. Its applicability in a biological context requires it to be able to resist modification by xenobiotic-degrading enzymes like the P450 cytochromes. Quantum chemical computations described in this work show that 1,2-dihydro-1,2-azaborine is much more prone to modification by these enzymes than benzene, unless steric crowding of the ring prevents it from reaching the active site, or otherwise only allows reaction at the less reactive C4-position. This novel heterocyclic compound is therefore expected to be of limited usefulness as an aryl bioisostere.
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Affiliation(s)
- Pedro J Silva
- FP-ENAS, Faculdade de Ciências da Saúde, Universidade Fernando Pessoa , Porto , Portugal
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36
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Pesci L, Kara S, Liese A. Evaluation of the Substrate Scope of Benzoic Acid (De)carboxylases According to Chemical and Biochemical Parameters. Chembiochem 2016; 17:1845-1850. [PMID: 27505856 DOI: 10.1002/cbic.201600333] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Indexed: 11/06/2022]
Abstract
The enzymatic carboxylation of phenolic compounds has been attracting increasing interest in recent years, owing to its regioselectivity and technical potential as a biocatalytic equivalent for the Kolbe-Schmitt reaction. Mechanistically the reaction was demonstrated to occur through electrophilic aromatic substitution/water elimination with bicarbonate as a cosubstrate. The effects of the substituents on the phenolic ring have not yet been elucidated in detail, but this would give detailed insight into the substrate-activity relationship and would provide predictability for the acceptance of future substrates. In this report we show how the kinetic and (apparent) thermodynamic behavior can be explained through the evaluation of linear free energy relationships based on electronic, steric, and geometric parameters and through the consideration of enzyme-ligand interactions. Moreover, the similarity between the benzoic acid decarboxylases and the amidohydrolases superfamily is investigated, and promiscuous hydrolytic activity of the decarboxylase in the context of the hydrolysis of an activated ester bond has been established.
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Affiliation(s)
- Lorenzo Pesci
- Institute of Technical Biocatalysis, Hamburg University of Technology, Denickestrasse 15, 21073, Hamburg, Germany
| | - Selin Kara
- Institute of Technical Biocatalysis, Hamburg University of Technology, Denickestrasse 15, 21073, Hamburg, Germany
| | - Andreas Liese
- Institute of Technical Biocatalysis, Hamburg University of Technology, Denickestrasse 15, 21073, Hamburg, Germany.
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37
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Grandner JM, Cacho RA, Tang Y, Houk KN. Mechanism of the P450-Catalyzed Oxidative Cyclization in the Biosynthesis of Griseofulvin. ACS Catal 2016; 6:4506-4511. [PMID: 28503354 DOI: 10.1021/acscatal.6b01068] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Griseofulvin is an anti-fungal agent which has recently been determined to have potential anti-viral and anti-cancer applications. The role of specific enzymes involved in the biosynthesis of this natural product has previously been determined, but the mechanism by which a p450, GsfF, catalyzes the key oxidative cyclization of griseophenone B remains unknown. Using density functional theory (DFT), we have determined the mechanism of this oxidation that forms the oxa-spiro core of griseofulvin. Computations show GsfF preferentially performs two sequential phenolic O-H abstractions rather than epoxidation to form an arene oxide intermediate. This conclusion is supported by experimental kinetic isotope effects.
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Affiliation(s)
- Jessica M. Grandner
- Department
of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Ralph A. Cacho
- Department
of Chemical and Biomolecular Engineering, University of California, Los
Angeles, California 90095, United States
| | - Yi Tang
- Department
of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
- Department
of Chemical and Biomolecular Engineering, University of California, Los
Angeles, California 90095, United States
| | - K. N. Houk
- Department
of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
- Department
of Chemical and Biomolecular Engineering, University of California, Los
Angeles, California 90095, United States
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38
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Stok JE, Chow S, Krenske EH, Farfan Soto C, Matyas C, Poirier RA, Williams CM, De Voss JJ. Direct Observation of an Oxepin from a Bacterial Cytochrome P450‐Catalyzed Oxidation. Chemistry 2016; 22:4408-12. [DOI: 10.1002/chem.201600246] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Jeanette E. Stok
- School of Chemistry and Molecular Biosciences The University of Queensland Brisbane Qld 4072 Australia
| | - Sharon Chow
- School of Chemistry and Molecular Biosciences The University of Queensland Brisbane Qld 4072 Australia
| | - Elizabeth H. Krenske
- School of Chemistry and Molecular Biosciences The University of Queensland Brisbane Qld 4072 Australia
| | - Clementina Farfan Soto
- School of Chemistry and Molecular Biosciences The University of Queensland Brisbane Qld 4072 Australia
| | - Csongor Matyas
- Department of Chemistry Memorial University of Newfoundland St. John's NL A1B 3X7 Canada
| | - Raymond A. Poirier
- Department of Chemistry Memorial University of Newfoundland St. John's NL A1B 3X7 Canada
| | - Craig M. Williams
- School of Chemistry and Molecular Biosciences The University of Queensland Brisbane Qld 4072 Australia
| | - James J. De Voss
- School of Chemistry and Molecular Biosciences The University of Queensland Brisbane Qld 4072 Australia
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Capoferri L, Leth R, ter Haar E, Mohanty AK, Grootenhuis PDJ, Vottero E, Commandeur JNM, Vermeulen NPE, Jørgensen FS, Olsen L, Geerke DP. Insights into regioselective metabolism of mefenamic acid by cytochrome P450 BM3 mutants through crystallography, docking, molecular dynamics, and free energy calculations. Proteins 2016; 84:383-96. [PMID: 26757175 DOI: 10.1002/prot.24985] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 12/21/2015] [Accepted: 01/05/2016] [Indexed: 12/21/2022]
Abstract
Cytochrome P450 BM3 (CYP102A1) mutant M11 is able to metabolize a wide range of drugs and drug-like compounds. Among these, M11 was recently found to be able to catalyze formation of human metabolites of mefenamic acid and other nonsteroidal anti-inflammatory drugs (NSAIDs). Interestingly, single active-site mutations such as V87I were reported to invert regioselectivity in NSAID hydroxylation. In this work, we combine crystallography and molecular simulation to study the effect of single mutations on binding and regioselective metabolism of mefenamic acid by M11 mutants. The heme domain of the protein mutant M11 was expressed, purified, and crystallized, and its X-ray structure was used as template for modeling. A multistep approach was used that combines molecular docking, molecular dynamics (MD) simulation, and binding free-energy calculations to address protein flexibility. In this way, preferred binding modes that are consistent with oxidation at the experimentally observed sites of metabolism (SOMs) were identified. Whereas docking could not be used to retrospectively predict experimental trends in regioselectivity, we were able to rank binding modes in line with the preferred SOMs of mefenamic acid by M11 and its mutants by including protein flexibility and dynamics in free-energy computation. In addition, we could obtain structural insights into the change in regioselectivity of mefenamic acid hydroxylation due to single active-site mutations. Our findings confirm that use of MD and binding free-energy calculation is useful for studying biocatalysis in those cases in which enzyme binding is a critical event in determining the selective metabolism of a substrate.
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Affiliation(s)
- Luigi Capoferri
- AIMMS Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, VU University, De Boelelaan 1083, 1081 HV Amsterdam, the Netherlands
| | - Rasmus Leth
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Ernst ter Haar
- Vertex Pharmaceuticals Incorporated, 50 Northern Avenue, Boston, MA, 02210
| | - Arun K Mohanty
- Vertex Pharmaceuticals Incorporated, 50 Northern Avenue, Boston, MA, 02210
| | | | - Eduardo Vottero
- AIMMS Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, VU University, De Boelelaan 1083, 1081 HV Amsterdam, the Netherlands
| | - Jan N M Commandeur
- AIMMS Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, VU University, De Boelelaan 1083, 1081 HV Amsterdam, the Netherlands
| | - Nico P E Vermeulen
- AIMMS Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, VU University, De Boelelaan 1083, 1081 HV Amsterdam, the Netherlands
| | - Flemming Steen Jørgensen
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Lars Olsen
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Daan P Geerke
- AIMMS Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, VU University, De Boelelaan 1083, 1081 HV Amsterdam, the Netherlands
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40
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Mirzaei S, Taherpour AA, Mohamadi S. Mechanistic study of allopurinol oxidation using aldehyde oxidase, xanthine oxidase and cytochrome P450 enzymes. RSC Adv 2016. [DOI: 10.1039/c6ra19197e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The oxidation reaction of allopurinol to its active metabolite (oxypurinol) is investigated using the AO and P450 enzymes. To the contrary of AO (and XO), the P450 enzyme can metabolize the allopurinol with a not self-inhibitory mechanism.
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Affiliation(s)
- Saber Mirzaei
- Department of Organic Chemistry
- Faculty of Chemistry
- Razi University
- Kermanshah
- Iran
| | - Avat Arman Taherpour
- Department of Organic Chemistry
- Faculty of Chemistry
- Razi University
- Kermanshah
- Iran
| | - Shahryar Mohamadi
- Department of Organic Chemistry
- Faculty of Chemistry
- Razi University
- Kermanshah
- Iran
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41
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Li XX, Wang Y, Zheng QC, Zhang HX. Detoxification of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) by cytochrome P450 enzymes: A theoretical investigation. J Inorg Biochem 2015; 154:21-8. [PMID: 26544505 DOI: 10.1016/j.jinorgbio.2015.10.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 10/12/2015] [Accepted: 10/19/2015] [Indexed: 11/24/2022]
Abstract
Two types of detoxification routes, N-demethylation to form 4-phenyl-1,2,3,6-tetrahydropyridine (PTP) and aromatic hydroxylation to generate 4-(4'-hydroxyphenyl)-1-methyl-1,2,3,6-tetrahydropyridine (MPTP-OH), for 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) mediated by Compound I (Cpd I) of cytochrome P450 are investigated theoretically using hybrid density functional calculations. Quantum chemical results reveal that for the N-demethylation, the initial C-H bond activation is achieved via a hydrogen atom transfer (HAT) mechanism. This is followed by a subsequent O-rebound to yield the carbinolamine intermediate. Due to the nature of pericyclic reaction, the generated carbinolamine decomposes in a non-enzymatic aqueous environment with the assistance of water molecules, forming amine and hydrated formaldehyde. For the aromatic hydroxylation, an initial addition of Cpd I to the substrate occurs mainly through a side-on approach with a subsequent proton shuttle to form the phenol product. A comparison of the energy barriers for both routes indicates that the N-demethylation (7.5/5.7kcal/mol for the quartet/doublet state in solvent) is thermodynamically more favorable than the aromatic hydroxylation process (14.9/14.8kcal/mol for the quartet/doublet state in solvent). This trend is in good agreement with the experimental product distribution, viz., the N-demethylation product PTP is more than the aromatic hydroxylation product MPTP-OH. Taken together, these observations not only enrich our knowledge on the mechanistic details of the N-dealkylation and the aromatic hydroxylation by P450s, but also provide certain insights into the metabolism of other analogous toxins.
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Affiliation(s)
- Xiao-Xi Li
- State Key Laboratory for Oxo Synthesis and Selective Oxidation, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou 730000, People's Republic of China; State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, People's Republic of China
| | - Yong Wang
- State Key Laboratory for Oxo Synthesis and Selective Oxidation, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou 730000, People's Republic of China
| | - Qing-Chuan Zheng
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, Jilin University, Changchun 130023, People's Republic of China; State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, People's Republic of China.
| | - Hong-Xing Zhang
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, People's Republic of China
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42
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Olsen L, Oostenbrink C, Jørgensen FS. Prediction of cytochrome P450 mediated metabolism. Adv Drug Deliv Rev 2015; 86:61-71. [PMID: 25958010 DOI: 10.1016/j.addr.2015.04.020] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 03/30/2015] [Accepted: 04/27/2015] [Indexed: 10/23/2022]
Abstract
Cytochrome P450 enzymes (CYPs) form one of the most important enzyme families involved in the metabolism of xenobiotics. CYPs comprise many isoforms, which catalyze a wide variety of reactions, and potentially, a large number of different metabolites can be formed. However, it is often hard to rationalize what metabolites these enzymes generate. In recent years, many different in silico approaches have been developed to predict binding or regioselective product formation for the different CYP isoforms. These comprise ligand-based methods that are trained on experimental CYP data and structure-based methods that consider how the substrate is oriented in the active site or/and how reactive the part of the substrate that is accessible to the heme group is. We will review key aspects for various approaches that are available to predict binding and site of metabolism (SOM), what outcome can be expected from the predictions, and how they could potentially be improved.
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43
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Leth R, Rydberg P, Jørgensen FS, Olsen L. Density Functional Theory Study on the Formation of Reactive Benzoquinone Imines by Hydrogen Abstraction. J Chem Inf Model 2015; 55:660-6. [DOI: 10.1021/ci500653b] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rasmus Leth
- Department of Drug Design
and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Patrik Rydberg
- Department of Drug Design
and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Flemming Steen Jørgensen
- Department of Drug Design
and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Lars Olsen
- Department of Drug Design
and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
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44
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Wang X, Chen J, Wang Y, Xie H, Fu Z. Transformation pathways of MeO-PBDEs catalyzed by active center of P450 enzymes: a DFT investigation employing 6-MeO-BDE-47 as a case. CHEMOSPHERE 2015; 120:631-636. [PMID: 25462307 DOI: 10.1016/j.chemosphere.2014.09.105] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Revised: 09/27/2014] [Accepted: 09/29/2014] [Indexed: 06/04/2023]
Abstract
Recent in vivo and in vitro experiments indicated that methoxylated polybrominated diphenyl ethers (MeO-PBDEs) can be biotransformed into hydroxylated PBDEs (HO-PBDEs) that are more toxic than PBDEs and MeO-PBDEs. Nevertheless, the enzymatic transformation mechanism is not clear. We hypothesized that cytochrome P450 enzymes (CYPs) play a key role in the transformation and employed the density functional theory calculations to unveil the mechanism. The transformation of a model compound, 6-MeO-BDE-47, catalyzed by the active center of CYPs (Compound I), was computed. For the first time, our results show that the energy barriers for the addition of Compound I to the C atoms on the phenyl of 6-MeO-BDE-47 are much higher than that for hydroxylation of the methoxyl, indicating that O-demethylation is a dominating metabolic pathway. This is in line with experimental observations performed by others. The pathways for the transformation of 6-MeO-BDE-47 catalyzed by Compound I were clarified. A C-H bond of the methoxyl is activated by Compound I, followed by radical rebound to form carbinol intermediates, then the carbinols decompose to form 6-HO-BDE-47 with the assistance of water molecules. The computational method can be potentially employed to develop models that predict biotransformation of xenobiotics catalyzed by CYPs.
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Affiliation(s)
- Xingbao Wang
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China; State Key Laboratory of Fine Chemicals, School of Pharmaceutical Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Jingwen Chen
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China.
| | - Yong Wang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Hongbin Xie
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Zhiqiang Fu
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
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45
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Ansari A, Jayapal P, Rajaraman G. CH Bond Activation by Metal-Superoxo Species: Magnetic Coupling Correlated to High Reactivity in Metal-Superoxo species. Angew Chem Int Ed Engl 2014; 54:564-8. [DOI: 10.1002/anie.201409844] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Indexed: 11/12/2022]
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46
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Ansari A, Jayapal P, Rajaraman G. CH Bond Activation by Metal-Superoxo Species: What Drives High Reactivity? Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201409844] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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47
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Zhang T, Wei D. Recent progress on structural bioinformatics research of cytochrome P450 and its impact on drug discovery. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 827:327-39. [PMID: 25387973 DOI: 10.1007/978-94-017-9245-5_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
Cytochrome P450 is predominantly responsible for human drug metabolism, which is of critical importance for drug discovery and development. Structural bioinformatics focuses on analysis and prediction of three-dimentional structure of biological macromolecules and elucidation of structure-function relationship as well as identification of important binding interactions. Rapid advancement of structural bioinformatics has been made over the last decade. With more information available for CYP structures, the methods of structural bioinformatics may be used in the CYP field. In this review, we demonstrate three previous studies on CYP using the methods of structural bioinformatics, including the investigation of reasons for decrease of enzymatic activity of CYP1A2 caused by a peripheral mutation, the construction of a pharmacophore model specific to active site of CYP1A2 and the prediction of the functional consequences of single residue mutation in CYP. By illustrating these studies we attempt to show the potential role of structural bioinformatics in CYP research and help better understanding the importance of structural bioinformatics in drug designing.
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Affiliation(s)
- Tao Zhang
- State Key Laboratory of Microbial Metabolism, College of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China,
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48
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Bussy U, Boujtita M. Advances in the Electrochemical Simulation of Oxidation Reactions Mediated by Cytochrome P450. Chem Res Toxicol 2014; 27:1652-68. [DOI: 10.1021/tx5001943] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Ugo Bussy
- Department
of Fisheries and Wildlife, Michigan State University, Room 13 Natural
Resources Building, 480 Wilson Road, East Lansing, Michigan 48824, United States
| | - Mohammed Boujtita
- LUNAM Université de Nantes, CNRS, Chimie et Interdisciplinarité: Synthèse, Analyse et Modélisation (CEISAM), UMR 6230, 2 rue de la Houssinière, BP 92208, F-44322 Nantes cedex 3, France
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49
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Rydberg P. Reactivity‐Based Approaches and Machine Learning Methods for Predicting the Sites of Cytochrome P450‐Mediated Metabolism. ACTA ACUST UNITED AC 2014. [DOI: 10.1002/9783527673261.ch11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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50
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Usharani D, Lai W, Li C, Chen H, Danovich D, Shaik S. A tutorial for understanding chemical reactivity through the valence bond approach. Chem Soc Rev 2014; 43:4968-88. [PMID: 24710199 DOI: 10.1039/c4cs00043a] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This is a tutorial on the usage of valence bond (VB) diagrams for understanding chemical reactivity in general, and hydrogen atom transfer (HAT) reactivity in particular. The tutorial instructs the reader how to construct the VB diagrams and how to estimate HAT barriers from raw data, starting with the simplest reaction H + H2 and going all the way to HAT in the enzyme cytochrome P450. Other reactions are treated as well, and some unifying principles are outlined. The tutorial projects the unity of reactivity treatments, following Coulson's dictum "give me insight, not numbers", albeit with its modern twist: giving numbers and insight.
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Affiliation(s)
- Dandamudi Usharani
- Institute of Chemistry and The Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel.
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