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Han Y, Cheng S, Guo F, Xiong J, Ji L. Mechanistic and predictive studies on the oxidation of furans by cytochrome P450: A DFT study. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 279:116460. [PMID: 38781888 DOI: 10.1016/j.ecoenv.2024.116460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 04/27/2024] [Accepted: 05/12/2024] [Indexed: 05/25/2024]
Abstract
Furan-containing compounds distribute widely in food, herbal medicines, industrial synthetic products, and environmental media. These compounds can undergo oxidative metabolism catalyzed by cytochrome P450 enzymes (CYP450) within organisms, which may produce reactive products, possibly reacting with biomolecules to induce toxic effects. In this work, we performed DFT calculations to investigate the CYP450-mediated metabolic mechanism of furan-ring oxidation using 2-methylfuran as a model substrate, meanwhile, we studied the regioselective competition of another hydroxylation reaction involving methyl group of 2-methylfuran. As a result, we found the toxicological-relevant cis-enedione product can be produced from O-addition directly via a concerted manner without formation of an epoxide intermediate as traditionally believed. Moreover, our calculations demonstrate the kinetic and thermodynamic feasibility of both furan-ring oxidation and methyl hydroxylation pathways, although the former pathway is a bit more favorable. We then constructed a linear model to predict the rate-limiting activation energies (ΔE*) of O-addition with 11 diverse furan substates based on their adiabatic ionization potentials (AIPs) and condensation Fukui functions (CFFs). The results show a good predictive ability (R2=0.94, Q2CV=0.87). Therefore, AIP and CFF with clear physichem meanings relevant to the mechanism, emerge as pivotal molecular descriptors to enable the fast prediction of furan-ring oxidation reactivities for quick insight into the toxicological risk of furans, using just ground-state calculations.
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Affiliation(s)
- Ye Han
- School of Environment Science and Spatial Informatics, China University of Mining and Technology, Xuzhou 221116, China
| | - Shiyang Cheng
- School of Environment Science and Spatial Informatics, China University of Mining and Technology, Xuzhou 221116, China.
| | - Fangjie Guo
- School of Management Engineering and Electronic Commerce, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Jibing Xiong
- School of Environment Science and Spatial Informatics, China University of Mining and Technology, Xuzhou 221116, China
| | - Li Ji
- School of Environment Science and Spatial Informatics, China University of Mining and Technology, Xuzhou 221116, China.
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2
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Kamel EM, Alwaili MA, Rudayni HA, Allam AA, Lamsabhi AM. Deciphering the Molecular Mechanisms of Reactive Metabolite Formation in the Mechanism-Based Inactivation of Cytochrome p450 1B1 by 8-Methoxypsoralen and Assessing the Driving Effect of phe268. Molecules 2024; 29:1433. [PMID: 38611713 PMCID: PMC11012842 DOI: 10.3390/molecules29071433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 03/19/2024] [Accepted: 03/21/2024] [Indexed: 04/14/2024] Open
Abstract
This study provides a comprehensive computational exploration of the inhibitory activity and metabolic pathways of 8-methoxypsoralen (8-MP), a furocoumarin derivative used for treating various skin disorders, on cytochrome P450 (P450). Employing quantum chemical DFT calculations, molecular docking, and molecular dynamics (MD) simulations analyses, the biotransformation mechanisms and the active site binding profile of 8-MP in CYP1B1 were investigated. Three plausible inactivation mechanisms were minutely scrutinized. Further analysis explored the formation of reactive metabolites in subsequent P450 metabolic processes, including covalent adduct formation through nucleophilic addition to the epoxide, 8-MP epoxide hydrolysis, and non-CYP-catalyzed epoxide ring opening. Special attention was paid to the catalytic effect of residue Phe268 on the mechanism-based inactivation (MBI) of P450 by 8-MP. Energetic profiles and facilitating conditions revealed a slight preference for the C4'=C5' epoxidation pathway, while recognizing a potential kinetic competition with the 8-OMe demethylation pathway due to comparable energy demands. The formation of covalent adducts via nucleophilic addition, particularly by phenylalanine, and the generation of potentially harmful reactive metabolites through autocatalyzed ring cleavage are likely to contribute significantly to P450 metabolism of 8-MP. Our findings highlight the key role of Phe268 in retaining 8-MP within the active site of CYP1B1, thereby facilitating initial oxygen addition transition states. This research offers crucial molecular-level insights that may guide the early stages of drug discovery and risk assessment related to the use of 8-MP.
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Affiliation(s)
- Emadeldin M. Kamel
- Chemistry Department, Faculty of Science, Beni-Suef University, Beni-Suef 62514, Egypt;
| | - Maha A. Alwaili
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Hassan A. Rudayni
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh 11623, Saudi Arabia; (H.A.R.); (A.A.A.)
| | - Ahmed A. Allam
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh 11623, Saudi Arabia; (H.A.R.); (A.A.A.)
- Department of Zoology, Faculty of Science, Beni-Suef University, Beni-Suef 65211, Egypt
| | - Al Mokhtar Lamsabhi
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC Cantoblanco, 28049 Madrid, Spain
- Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
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3
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Mokkawes T, De Visser T, Cao Y, De Visser SP. Melatonin Activation by Human Cytochrome P450 Enzymes: A Comparison between Different Isozymes. Molecules 2023; 28:6961. [PMID: 37836804 PMCID: PMC10574541 DOI: 10.3390/molecules28196961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 09/30/2023] [Accepted: 10/02/2023] [Indexed: 10/15/2023] Open
Abstract
Cytochrome P450 enzymes in the human body play a pivotal role in both the biosynthesis and the degradation of the hormone melatonin. Melatonin plays a key role in circadian rhythms in the body, but its concentration is also linked to mood fluctuations as well as emotional well-being. In the present study, we present a computational analysis of the binding and activation of melatonin by various P450 isozymes that are known to yield different products and product distributions. In particular, the P450 isozymes 1A1, 1A2, and 1B1 generally react with melatonin to provide dominant aromatic hydroxylation at the C6-position, whereas the P450 2C19 isozyme mostly provides O-demethylation products. To gain insight into the origin of these product distributions of the P450 isozymes, we performed a comprehensive computational study of P450 2C19 isozymes and compared our work with previous studies on alternative isozymes. The work covers molecular mechanics, molecular dynamics and quantum mechanics approaches. Our work highlights major differences in the size and shape of the substrate binding pocket amongst the different P450 isozymes. Consequently, substrate binding and positioning in the active site varies substantially within the P450 isozymes. Thus, in P450 2C19, the substrate is oriented with its methoxy group pointing towards the heme, and therefore reacts favorably through hydrogen atom abstraction, leading to the production of O-demethylation products. On the other hand, the substrate-binding pockets in P450 1A1, 1A2, and 1B1 are tighter, direct the methoxy group away from the heme, and consequently activate an alternative site and lead to aromatic hydroxylation instead.
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Affiliation(s)
| | | | | | - Sam P. De Visser
- Department of Chemical Engineering, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
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4
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Kamel EM, Tawfeek AM, El-Bassuony AA, Lamsabhi AM. Mechanistic aspects of reactive metabolite formation in clomethiazole catalyzed biotransformation by cytochrome P450 enzymes. Org Biomol Chem 2023; 21:7158-7172. [PMID: 37609887 DOI: 10.1039/d3ob01014g] [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: 08/24/2023]
Abstract
Clomethiazole (CLM), a sedative and anticonvulsant drug, is commonly employed for the treatment of alcohol withdrawal syndrome because it suppresses cytochrome P450 (P450) activity associated with the generation of free radicals and liver damage. The catalyzed biotransformation of thiazole-containing drugs by P450 is known to afford reactive metabolites. These metabolites can alter the biological functions of macromolecules and result in toxicity and adverse drug interactions. Multitargeted molecular modeling and quantum chemical DFT calculations were performed to explore the binding modes and molecular mechanisms underlying the mechanism-based inactivation (MBI) of P450 by CLM. The mechanistic details associated with reactive metabolite formation from further metabolic processes were extensively assessed. Seven possible routes were proposed for CLM-P450 biotransformation including CLM hydroxylation, sulfoxidation, N-oxidation, CN epoxidation (oxaziridine formation), and CC epoxidation. The results revealed a degree of preference for the C-N epoxidation pathway because of the low energy requirements of its rate-determining step (8.74 and 10.07 kcal mol-1 for LS and HS states, respectively). A kinetic competition for the CLM-methyl hydroxylation pathway was detected because the H-abstraction energy barrier was relatively comparable to the thermodynamically prevailing oxaziridine formation rate-determining step (12.58 and 14.52 kcal mol-1 for quartet and doublet states, respectively). Our studies assessed the mechanisms of covalent nucleophilic epoxide adduct formation through nucleophilic addition, hydrolysis of epoxidation products, and nonenzymatic degradation. CLM was shown to display P450-inhibitory activity by forming covalent adducts rather than further metabolization to reactive metabolites. The outcomes of molecular docking allowed assessing the binding profile of CLM with three human P450 isozymes, namely, CYP2E1, CYP3A4, and CYP2D6.
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Affiliation(s)
- Emadeldin M Kamel
- Chemistry Department, Faculty of Science, Beni-Suef University, Beni-Suef 62514, Egypt.
| | - Ahmed M Tawfeek
- Chemistry Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Ashraf A El-Bassuony
- Chemistry Department, Faculty of Science, Beni-Suef University, Beni-Suef 62514, Egypt.
| | - Al Mokhtar Lamsabhi
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC Cantoblanco, Madrid 28049, Spain
- Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, Madrid 28049, Spain
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5
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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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6
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Zhao J, He J, Xu J. Mechanism-Based Inactivation of Cytochrome P450 3A by Evodol. Xenobiotica 2023:1-11. [PMID: 37092795 DOI: 10.1080/00498254.2023.2207200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
1. Evodol is one of the furanoids isolated from the fruits of Evodia rutaecarpa that has been widely prescribed for the treatment of gastrointestinal diseases in China. The aim of this study was to investigate the inhibitory effect of evodol on CYP3A.2. A 30-min preincubation of evodol with human liver microsomes raised an obvious left IC50 shift, 3.9-fold for midazolam 1'-hydroxylation and 3.2-fold for testosterone 6β-hydroxylation. Evodol inactivated CYP3A in a time-, concentration- and NADPH-dependent manner, with KI and kinact of 5.1 μM and 0.028 min-1 for midazolam 1'-hydroxylation and 3.0 μM and 0.022 min-1 for testosterone 6β-hydroxylation.3. Co-incubation of ketoconazole attenuated the inactivation while inclusion of glutathione (GSH) and catalase/superoxide dismutase displayed no such protection.4. cis-Butene-1, 4-dial (BDA) intermediate derived from evodol were trapped by glutathione and N-acetyl-lysine in microsomes and characterized by HR-MS spectra. The BDA intermediate was believed to play a key role in CYP3A inactivation. CYP3A4 and 2C9 were the primary enzymes contributing to the bioactivation of evodol.5. To sum up, for the first time evodol was characterized as a mechanism-based inactivator of CYP3A.
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Affiliation(s)
- Jie Zhao
- Pharmaceutical Animal Experimental Center, China Pharmaceutical University, Nanjing 210009, China
| | - Jingyu He
- R&D Institute, Chia Tai Tianqing Pharmaceutical Group Co., LTD, Nanjing 211122, China
| | - Jie Xu
- Department of Phase I Clinical Trial Research, Nanjing Gaoxin Hospital, Nanjing 210031, China
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7
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Batool Z, Chen JH, Liu B, Chen F, Wang M. Review on Furan as a Food Processing Contaminant: Identifying Research Progress and Technical Challenges for Future Research. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:5093-5106. [PMID: 36951248 DOI: 10.1021/acs.jafc.3c01352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
A wide range of food processing contaminants (FPCs) are usually formed while thermal processing of food products. Furan is a highly volatile compound among FPCs and could be formed in a variety of thermally processed foods. Therefore, identification of possible reasons of furan occurrence in different thermally processed foods, identification of the most consequential sources of furan exposure, factors impacting its formation, and its detection by specific analytical approaches are necessary to indicate gaps and challenges for future research findings. Furthermore, controlling furan formation in processed foods on a factory scale is also challenging, and research advancements are still ongoing in this context. Meanwhile, understanding adverse effects of furan on human health on a molecular level is necessary to gain insights into human risk assessment.
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Affiliation(s)
- Zahra Batool
- College of Civil and Transportation Engineering, Shenzhen University, Shenzhen, Guangdong 518060, People's Republic of China
- Institute for Innovative Development of Food Industry, Shenzhen University, Shenzhen, Guangdong 518060, People's Republic of China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong 518060, People's Republic of China
| | - Jie-Hua Chen
- Institute for Innovative Development of Food Industry, Shenzhen University, Shenzhen, Guangdong 518060, People's Republic of China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong 518060, People's Republic of China
| | - Bin Liu
- Institute for Innovative Development of Food Industry, Shenzhen University, Shenzhen, Guangdong 518060, People's Republic of China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong 518060, People's Republic of China
| | - Feng Chen
- Institute for Innovative Development of Food Industry, Shenzhen University, Shenzhen, Guangdong 518060, People's Republic of China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong 518060, People's Republic of China
| | - Mingfu Wang
- Institute for Innovative Development of Food Industry, Shenzhen University, Shenzhen, Guangdong 518060, People's Republic of China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong 518060, People's Republic of China
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8
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Liu S, Hirao H. Energy Decomposition Analysis of the Nature of Coordination Bonding at the Heme Iron Center in Cytochrome P450 Inhibition. Chem Asian J 2022; 17:e202200360. [PMID: 35514038 DOI: 10.1002/asia.202200360] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 04/26/2022] [Indexed: 11/11/2022]
Abstract
Drug compounds or their metabolic intermediates (MIs) sometimes inhibit the function of cytochrome P450 enzymes (P450s) by forming a coordination bond with the Fe(III) heme or Fe(II) heme of P450s. Such inhibition is one of the major causes of drug-drug interactions (DDIs), a subject of longstanding academic and practical interest. However, such coordination bonding is not fully understood at the quantum mechanical level, thus hampering rational improvement of the accuracy of DDI-related predictions. In this work, we employed density functional theory (DFT) and the generalized Kohn-Sham energy decomposition analysis (GKS-EDA) scheme to investigate the nature of the coordination bonding formed in the reversible and quasi-irreversible inhibition of P450s. The GKS-EDA results highlighted a previously unrecognized role of the electron correlation effect in P450 inhibition. The correlation effect tends to be larger in Fe(II) complexes of MI-type inhibitors and is particularly prominent for the nitrosoalkane ligand. An additional natural bond orbital (NBO) analysis provided insight into the relative significance of the σ donation and π backdonation effects in various heme-inhibitor complexes.
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Affiliation(s)
- Shuyang Liu
- The Chinese University of Hong Kong - Shenzhen, School of Life and Health Sciences, CHINA
| | - Hajime Hirao
- The Chinese University of Hong Kong - Shenzhen, School of Life and Health Sciences, …, Shenzhen, CHINA
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9
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Tang LWT, Teng JW, Koh SK, Zhou L, Go ML, Chan ECY. Mechanism-Based Inactivation of Cytochrome P450 3A4 and 3A5 by the Fibroblast Growth Factor Receptor Inhibitor Erdafitinib. Chem Res Toxicol 2021; 34:1800-1813. [PMID: 34189909 DOI: 10.1021/acs.chemrestox.1c00178] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Erdafitinib (ERD) is a first-in-class pan inhibitor of fibroblast growth factor receptor 1-4 that has garnered global regulatory approval for the treatment of advanced or metastatic urothelial carcinoma. Although it has been previously reported that ERD elicits time-dependent inhibition (TDI) of cytochrome P450 (P450) 3A4 (CYP3A4), the exact biochemical nature underpinning this observation remains obfuscated. Moreover, it is also uninterrogated if CYP3A5-its highly homologous counterpart-could be susceptible to such interactions. Mechanism-based inactivation (MBI) of P450 is a unique subset of TDI that hinges on prior bioactivation of the drug to a reactive intermediate and possesses profound clinical and toxicological implications due to its irreversible nature. Here, we investigated and confirmed that ERD inactivated both CYP3A isoforms in a time-, concentration-, and NADPH-dependent manner with KI, kinact, and partition ratio of 4.01 and 10.04 μM, 0.120 and 0.045 min-1, and 32 and 55 for both CYP3A4 and CYP3A5, respectively, when rivaroxaban was employed as the probe substrate. Co-incubation with an alternative substrate or direct inhibitor of CYP3A attenuated the rate of inactivation, whereas the addition of glutathione or catalase did not induce such protection. The lack of enzyme activity recovery following dialysis for 4 h and oxidation with potassium ferricyanide combined with the lack of a Soret peak in spectral scans collectively substantiated that ERD is an irreversible covalent MBI of CYP3A. Finally, glutathione trapping and high-resolution mass spectrometry experiments illuminated a plausible bioactivation mechanism of ERD by CYP3A arising from metabolic epoxidation of its quinoxaline ring.
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Affiliation(s)
- Lloyd Wei Tat Tang
- Department of Pharmacy, Faculty of Science, National University of Singapore, 169856 Singapore
| | - Jian Wei Teng
- Department of Pharmacy, Faculty of Science, National University of Singapore, 169856 Singapore
| | | | - Lei Zhou
- Singapore Eye Research Institute (SERI), Singapore.,Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, 117597 Singapore.,Ophthalmology and Visual Sciences Academia Clinical Program, Duke-National University of Singapore Medical School, 169857 Singapore
| | - Mei Lin Go
- Department of Pharmacy, Faculty of Science, National University of Singapore, 169856 Singapore
| | - Eric Chun Yong Chan
- Department of Pharmacy, Faculty of Science, National University of Singapore, 169856 Singapore
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10
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Jaladanki CK, Khatun S, Gohlke H, Bharatam PV. Reactive Metabolites from Thiazole-Containing Drugs: Quantum Chemical Insights into Biotransformation and Toxicity. Chem Res Toxicol 2021; 34:1503-1517. [PMID: 33900062 DOI: 10.1021/acs.chemrestox.0c00450] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Drugs containing thiazole and aminothiazole groups are known to generate reactive metabolites (RMs) catalyzed by cytochrome P450s (CYPs). These RMs can covalently modify essential cellular macromolecules and lead to toxicity and induce idiosyncratic adverse drug reactions. Molecular docking and quantum chemical hybrid DFT study were carried out to explore the molecular mechanisms involved in the biotransformation of thiazole (TZ) and aminothiazole (ATZ) groups leading to RM epoxide, S-oxide, N-oxide, and oxaziridine. The energy barrier required for the epoxidation is 13.63 kcal/mol, that is lower than that of S-oxidation, N-oxidation, and oxaziridine formation (14.56, 17.90, and 20.20, kcal/mol respectively). The presence of the amino group in ATZ further facilitates all the metabolic pathways, for example, the barrier for the epoxidation reaction is reduced by ∼2.5 kcal/mol. Some of the RMs/their isomers are highly electrophilic and tend to form covalent bonds with nucleophilic amino acids, finally leading to the formation of metabolic intermediate complexes (MICs). The energy profiles of these competitive pathways have also been explored.
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Affiliation(s)
- Chaitanya K Jaladanki
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Sector -67, S. A. S. Nagar (Mohali), 160 062 Punjab, India
| | - Samima Khatun
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Sector -67, S. A. S. Nagar (Mohali), 160 062 Punjab, India
| | - Holger Gohlke
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany.,Forschungszentrum Jülich GmbH, John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), and Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Wilhelm-Johnen-Straße, 52425 Jülich, Germany
| | - Prasad V Bharatam
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Sector -67, S. A. S. Nagar (Mohali), 160 062 Punjab, India
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11
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Mirzaei MS, Ivanov MV, Taherpour AA, Mirzaei S. Mechanism-Based Inactivation of Cytochrome P450 Enzymes: Computational Insights. Chem Res Toxicol 2021; 34:959-987. [PMID: 33769041 DOI: 10.1021/acs.chemrestox.0c00483] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mechanism-based inactivation (MBI) refers to the metabolic bioactivation of a xenobiotic by cytochrome P450s to a highly reactive intermediate which subsequently binds to the enzyme and leads to the quasi-irreversible or irreversible inhibition. Xenobiotics, mainly drugs with specific functional units, are the major sources of MBI. Two possible consequences of MBI by medicinal compounds are drug-drug interaction and severe toxicity that are observed and highlighted by clinical experiments. Today almost all of these latent functional groups (e.g., thiophene, furan, alkylamines, etc.) are known, and their features and mechanisms of action, owing to the vast experimental and theoretical studies, are determined. In the past decade, molecular modeling techniques, mostly density functional theory, have revealed the most feasible mechanism that a drug undergoes by P450 enzymes to generate a highly reactive intermediate. In this review, we provide a comprehensive and detailed picture of computational advances toward the elucidation of the activation mechanisms of various known groups with MBI activity. To this aim, we briefly describe the computational concepts to carry out and analyze the mechanistic investigations, and then, we summarize the studies on compounds with known inhibition activity including thiophene, furan, alkylamines, terminal acetylene, etc. This study can be reference literature for both theoretical and experimental (bio)chemists in several different fields including rational drug design, the process of toxicity prevention, and the discovery of novel inhibitors and catalysts.
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Affiliation(s)
- M Saeed Mirzaei
- Department of Organic Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Iran 67149-67346
| | - Maxim V Ivanov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Avat Arman Taherpour
- Department of Organic Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Iran 67149-67346.,Medical Biology Research Centre, University of Medical Sciences, Kermanshah, Iran 67149-67346
| | - Saber Mirzaei
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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12
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Jaladanki CK, Gahlawat A, Rathod G, Sandhu H, Jahan K, Bharatam PV. Mechanistic studies on the drug metabolism and toxicity originating from cytochromes P450. Drug Metab Rev 2020; 52:366-394. [DOI: 10.1080/03602532.2020.1765792] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Chaitanya K. Jaladanki
- Department of Medicinal Chemistry and Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), SAS Nagar, Punjab, India
| | - Anuj Gahlawat
- Department of Medicinal Chemistry and Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), SAS Nagar, Punjab, India
| | - Gajanan Rathod
- Department of Medicinal Chemistry and Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), SAS Nagar, Punjab, India
| | - Hardeep Sandhu
- Department of Medicinal Chemistry and Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), SAS Nagar, Punjab, India
| | - Kousar Jahan
- Department of Medicinal Chemistry and Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), SAS Nagar, Punjab, India
| | - Prasad V. Bharatam
- Department of Medicinal Chemistry and Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), SAS Nagar, Punjab, India
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Thiel D, Blume F, Jäger C, Deska J. Chloroperoxidase-Catalyzed Achmatowicz Rearrangements. European J Org Chem 2018. [DOI: 10.1002/ejoc.201800333] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Daniel Thiel
- Department of Chemistry and Materials Science; Aalto-yliopisto; Kemistintie 1 02150 Espoo Finland
| | - Fabian Blume
- Department of Chemistry and Materials Science; Aalto-yliopisto; Kemistintie 1 02150 Espoo Finland
| | - Christina Jäger
- Department of Chemistry and Materials Science; Aalto-yliopisto; Kemistintie 1 02150 Espoo Finland
| | - Jan Deska
- Department of Chemistry and Materials Science; Aalto-yliopisto; Kemistintie 1 02150 Espoo Finland
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14
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Jaladanki CK, Shaikh A, Bharatam PV. Biotransformation of Isoniazid by Cytochromes P450: Analyzing the Molecular Mechanism using Density Functional Theory. Chem Res Toxicol 2017; 30:2060-2073. [DOI: 10.1021/acs.chemrestox.7b00129] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Chaitanya K. Jaladanki
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Sector -67, S. A. S. Nagar, Mohali, 160 062 Punjab, India
| | - Akbar Shaikh
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Sector -67, S. A. S. Nagar, Mohali, 160 062 Punjab, India
| | - Prasad V. Bharatam
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Sector -67, S. A. S. Nagar, Mohali, 160 062 Punjab, India
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15
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Knutsen HK, Alexander J, Barregård L, Bignami M, Brüschweiler B, Ceccatelli S, Cottrill B, Dinovi M, Edler L, Grasl-Kraupp B, Hogstrand C, Hoogenboom LR, Nebbia CS, Oswald IP, Petersen A, Rose M, Roudot AC, Schwerdtle T, Vleminckx C, Vollmer G, Chipman K, De Meulenaer B, Dinovi M, Mennes W, Schlatter J, Schrenk D, Baert K, Dujardin B, Wallace H. Risks for public health related to the presence of furan and methylfurans in food. EFSA J 2017; 15:e05005. [PMID: 32625300 PMCID: PMC7009982 DOI: 10.2903/j.efsa.2017.5005] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The European Commission asked EFSA for a scientific evaluation on the risk to human health of the presence of furan and methylfurans (2-methylfuran, 3-methylfuran and 2,5-dimethylfuran) in food. They are formed in foods during thermal processing and can co-occur. Furans are produced from several precursors such as ascorbic acid, amino acids, carbohydrates, unsaturated fatty acids and carotenoids, and are found in a variety of foods including coffee and canned and jarred foods. Regarding furan occurrence, 17,056 analytical results were used in the evaluation. No occurrence data were received on methylfurans. The highest exposures to furan were estimated for infants, mainly from ready-to-eat meals. Grains and grain-based products contribute most for toddlers, other children and adolescents. In adults, elderly and very elderly, coffee is the main contributor to dietary exposure. Furan is absorbed from the gastrointestinal tract and is found in highest amounts in the liver. It has a short half-life and is metabolised by cytochrome P450 2E1 (CYP2E1) to the reactive metabolite, cis-but-2-ene-1,4-dialdehyde (BDA). BDA can bind covalently to amino acids, proteins and DNA. Furan is hepatotoxic in rats and mice with cholangiofibrosis in rats and hepatocellular adenomas/carcinomas in mice being the most prominent effects. There is limited evidence of chromosomal damage in vivo and a lack of understanding of the underlying mechanism. Clear evidence for indirect mechanisms involved in carcinogenesis include oxidative stress, gene expression alterations, epigenetic changes, inflammation and increased cell proliferation. The CONTAM Panel used a margin of exposure (MOE) approach for the risk characterisation using as a reference point a benchmark dose lower confidence limit for a benchmark response of 10% of 0.064 mg/kg body weight (bw) per day for the incidence of cholangiofibrosis in the rat. The calculated MOEs indicate a health concern. This conclusion was supported by the calculated MOEs for the neoplastic effects.
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Ghosh AK, Brindisi M. Achmatowicz Reaction and its Application in the Syntheses of Bioactive Molecules. RSC Adv 2016; 6:111564-111598. [PMID: 28944049 PMCID: PMC5603243 DOI: 10.1039/c6ra22611f] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Substituted pyranones and tetrahydropyrans are structural subunits of many bioactive natural products. Considerable efforts are devoted toward the chemical synthesis of these natural products due to their therapeutic potential as well as low natural abundance. These embedded pyranones and tetrahydropyran structural motifs have been the subject of synthetic interest over the years. While there are methods available for the syntheses of these subunits, there are issues related to regio and stereochemical outcomes, as well as versatility and compatibility of reaction conditions and functional group tolerance. The Achmatowicz reaction, an oxidative ring enlargement of furyl alcohol, was developed in the 1970s. The reaction provides a unique entry to a variety of pyranone derivatives from functionalized furanyl alcohols. These pyranones provide convenient access to substituted tetrahydropyran derivatives. This review outlines general approaches to the synthesis of tetrahydropyrans, covering general mechanistic aspects of the Achmatowicz reaction or rearrangement with an overview of the reagents utilized for the Achmatowicz reaction. The review then focuses on the synthesis of functionalized tetrahydropyrans and pyranones and their applications in the synthesis of natural products and medicinal agents.
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Affiliation(s)
- Arun K. Ghosh
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Margherita Brindisi
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA
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17
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Jaladanki CK, Taxak N, Varikoti RA, Bharatam PV. Toxicity Originating from Thiophene Containing Drugs: Exploring the Mechanism using Quantum Chemical Methods. Chem Res Toxicol 2015; 28:2364-76. [PMID: 26574776 DOI: 10.1021/acs.chemrestox.5b00364] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Drug metabolism of thiophene containing substrates by cytochrome P450s (CYP450) leads to toxic side effects, for example, nephrotoxicity (suprofen, ticlopidine), hepatotoxicity (tienilic acid), thrombotic thrombocytopenic purpura (clopidogrel), and aplastic anemia (ticlopidine). The origin of toxicity in these cases has been attributed to two different CYP450 mediated metabolic reactions: S-oxidation and epoxidation. In this work, the molecular level details of the bioinorganic chemistry associated with the generation of these competitive reactions are reported. Density functional theory was utilized (i) to explore the molecular mechanism for S-oxidation and epoxidation using the radical cationic center Cpd I [(iron(IV)-oxo-heme porphine system with SH(-) as the axial ligand, to mimic CYP450s] as the model oxidant, (ii) to establish the 3D structures of the reactants, transition states, and products on both the metabolic pathways, and (iii) to examine the potential energy (PE) profile for both the pathways to determine the energetically preferred toxic metabolite formation. The energy barrier required for S-oxidation was observed to be 14.75 kcal/mol as compared to that of the epoxidation reaction (13.23 kcal/mol) on the doublet PE surface of Cpd I. The formation of the epoxide metabolite was found to be highly exothermic (-23.24 kcal/mol), as compared to S-oxidation (-8.08 kcal/mol). Hence, on a relative scale the epoxidation process was observed to be thermodynamically and kinetically more favorable. The energy profiles associated with the reactions of the S-oxide and epoxide toxic metabolites were also explored. This study helps in understanding the CYP450-catalyzed toxic reactions of drugs containing the thiophene ring at the atomic level.
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Affiliation(s)
- Chaitanya K Jaladanki
- Department of Medicinal Chemistry and ‡Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER) , Sector-67, S. A. S. Nagar (Mohali), 160 062 Punjab, India
| | - Nikhil Taxak
- Department of Medicinal Chemistry and ‡Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER) , Sector-67, S. A. S. Nagar (Mohali), 160 062 Punjab, India
| | - Rohith A Varikoti
- Department of Medicinal Chemistry and ‡Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER) , Sector-67, S. A. S. Nagar (Mohali), 160 062 Punjab, India
| | - Prasad V Bharatam
- Department of Medicinal Chemistry and ‡Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER) , Sector-67, S. A. S. Nagar (Mohali), 160 062 Punjab, India
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18
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Liu J, Pham PT, Skripnikova EV, Zheng S, Lovings LJ, Wang Y, Goyal N, Bellow SM, Mensah LM, Chatters AJ, Bratton MR, Wiese TE, Zhao M, Wang G, Foroozesh M. A Ligand-Based Drug Design. Discovery of 4-Trifluoromethyl-7,8-pyranocoumarin as a Selective Inhibitor of Human Cytochrome P450 1A2. J Med Chem 2015. [PMID: 26222195 DOI: 10.1021/acs.jmedchem.5b00494] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
In humans, cytochrome P450 1A2 is the major enzyme metabolizing environmental arylamines or heterocyclic amines into carcinogens. Since evidence shows that planar triangle-shaped molecules are capable of selectively inhibiting P450 1A2, 16 triangular flavone, and coumarin derivatives were designed and synthesized for these studies. Among these compounds, 7,8-furanoflavone time-dependently inhibits P450 1A2 with a K(I) value of 0.44 μM. With a 5 min preincubation in the presence of NADPH, 0.01 μM 7,8-furanoflavone completely inactivates P450 1A2 but does not influence the activities of P450s 1A1 and 1B1. Another target compound, 7,8-pyrano-4-trifluoromethylcoumarin, is found to be a competitive inhibitor, showing high selectivity for the inhibition of P450 1A2 with a K(i) of 0.39 μM, 155- and 52-fold lower than its K(i) values against P450s 1A1 and 1B1, respectively. In yeast AhR activation assays, 7,8-pyrano-4-trifluoromethylcoumarin does not activate aryl hydrocarbon receptor when the concentration is lower than 1 μM, suggesting that this compound would not up-regulate AhR-caused P450 enzyme expression. In-cell P450 1A2 inhibition assays show that 7,8-pyrano-4-trifluoromethylcoumarin decreases the MROD activity in HepG2 cells at concentrations higher than 1 μM. Thus, using 7,8-pyrano-4-trifluoromethylcoumarin, a selective and specific P450 1A2 action suppression could be achieved, indicating the potential for the development of P450 1A2-targeting cancer preventive agents.
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Affiliation(s)
- Jiawang Liu
- Department of Chemistry, Xavier University of Louisiana , 1 Drexel Drive, New Orleans, Louisiana 70125, United States
| | - Peter T Pham
- Department of Chemistry, Xavier University of Louisiana , 1 Drexel Drive, New Orleans, Louisiana 70125, United States
| | - Elena V Skripnikova
- Cell and Molecular Biology Core, College of Pharmacy, Xavier University of Louisiana , New Orleans, Louisiana 70125, United States
| | - Shilong Zheng
- Department of Chemistry, Xavier University of Louisiana , 1 Drexel Drive, New Orleans, Louisiana 70125, United States.,RCMI Cancer Research Center, Xavier University of Louisiana , 1 Drexel Drive, New Orleans, Louisiana 70125, United States
| | - La'nese J Lovings
- Department of Chemistry, Xavier University of Louisiana , 1 Drexel Drive, New Orleans, Louisiana 70125, United States
| | - Yuji Wang
- College of Pharmaceutical Sciences, Capital Medical University , Beijing 100069, P. R. China
| | - Navneet Goyal
- Department of Chemistry, Xavier University of Louisiana , 1 Drexel Drive, New Orleans, Louisiana 70125, United States
| | - Sydni M Bellow
- Department of Chemistry, Xavier University of Louisiana , 1 Drexel Drive, New Orleans, Louisiana 70125, United States
| | - Lydia M Mensah
- Department of Chemistry, Xavier University of Louisiana , 1 Drexel Drive, New Orleans, Louisiana 70125, United States
| | - Amari J Chatters
- Department of Chemistry, Xavier University of Louisiana , 1 Drexel Drive, New Orleans, Louisiana 70125, United States
| | - Melyssa R Bratton
- Cell and Molecular Biology Core, College of Pharmacy, Xavier University of Louisiana , New Orleans, Louisiana 70125, United States
| | - Thomas E Wiese
- Cell and Molecular Biology Core, College of Pharmacy, Xavier University of Louisiana , New Orleans, Louisiana 70125, United States
| | - Ming Zhao
- College of Pharmaceutical Sciences, Capital Medical University , Beijing 100069, P. R. China.,Faculty of Biomedical Science and Environmental Biology, Kaohsiung Medical University , Kaohsiung 807, Taiwan
| | - Guangdi Wang
- Department of Chemistry, Xavier University of Louisiana , 1 Drexel Drive, New Orleans, Louisiana 70125, United States.,RCMI Cancer Research Center, Xavier University of Louisiana , 1 Drexel Drive, New Orleans, Louisiana 70125, United States
| | - Maryam Foroozesh
- Department of Chemistry, Xavier University of Louisiana , 1 Drexel Drive, New Orleans, Louisiana 70125, United States
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19
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Chuanprasit P, Goh SH, Hirao H. Benzyne Formation in the Mechanism-Based Inactivation of Cytochrome P450 by 1-Aminobenzotriazole and N-Benzyl-1-Aminobenzotriazole: Computational Insights. ACS Catal 2015. [DOI: 10.1021/acscatal.5b00423] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Pratanphorn Chuanprasit
- Division of Chemistry and
Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
| | - Shu Hui Goh
- Division of Chemistry and
Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
| | - Hajime Hirao
- Division of Chemistry and
Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
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20
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DFT study on the oxygen transfer mechanism in nitroethenediamine based H2-receptor antagonists using the bis-dithiolene complex as the model catalyst for N-oxide reductase enzyme. J Inorg Biochem 2014; 142:84-91. [PMID: 25450022 DOI: 10.1016/j.jinorgbio.2014.09.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 09/17/2014] [Accepted: 09/18/2014] [Indexed: 12/24/2022]
Abstract
Nitroethenediamine is an important functional unit, which is present in H2-receptor antagonists. These drugs show low bioavailability due to the bacterial degradation caused by the N-oxide reductase type of enzymes present in the human colon. Quantum chemical studies have been carried out to elucidate the mechanism of metabolic degradation of nitroethenediamine in the active site of N-oxide reductase. Three different pathways have been explored for the N-oxide bond cleavage by the model system, Mo(IV) bis-dithiolene complex [Mo(OMe)(mdt)2](-), (where mdt=1,2-dimethyl-ethene-1,2-dithiolate) using B3LYP/6-311+G(d,p) and M06/6-311+G(d,p) Density Functional Theory methods. The oxygen atom transfer from the nitrogen atom of nitroethenediamine to the Mo(IV) complex, involves simultaneous weakening of the N-oxide bond and the formation of Mo-O bond through a least motion path. During this transfer, Mo center is converted from a square pyramidal geometry to a distorted octahedral geometry, to facilitate the process of oxygen atom transfer. The energy barrier for the oxygen atom transfer from the imine tautomer has been estimated to be 25.9kcal/mol however, the overall reaction has been found to be endothermic. On the other hand, oxygen transfer reaction from the nitronic acid tautomer requires 30.5kcal/mol energy leading to a highly exothermic metabolite (M-1) directly hence, this path can be considered thermodynamically favorable for this metabolite. The alternative path involving the oxygen atom transfer from the enamine tautomer requires comparatively a higher energy barrier (32.6kcal/mol) and leads to a slightly endothermic metabolite. This study established the structural and energetic details associated with the Mo(IV) bis-dithiolene complex that catalyzes the degradation of nitroethenediamine based drug molecules.
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Arfeen M, Patel DS, Abbat S, Taxak N, Bharatam PV. Importance of cytochromes in cyclization reactions: Quantum chemical study on a model reaction of proguanil to cycloguanil. J Comput Chem 2014; 35:2047-55. [DOI: 10.1002/jcc.23719] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2014] [Revised: 08/04/2014] [Accepted: 08/06/2014] [Indexed: 12/23/2022]
Affiliation(s)
- Minhajul Arfeen
- Department of Medicinal Chemistry; National Institute of Pharmaceutical Education and Research (NIPER); S. A. S. Nagar (Mohali) 160 062 Punjab India
| | - Dhilon S. Patel
- Department of Medicinal Chemistry; National Institute of Pharmaceutical Education and Research (NIPER); S. A. S. Nagar (Mohali) 160 062 Punjab India
| | - Sheenu Abbat
- Department of Pharmacoinformatics; National Institute of Pharmaceutical Education and Research (NIPER); S. A. S. Nagar (Mohali) 160 062 Punjab India
| | - Nikhil Taxak
- Department of Medicinal Chemistry; National Institute of Pharmaceutical Education and Research (NIPER); S. A. S. Nagar (Mohali) 160 062 Punjab India
| | - Prasad V. Bharatam
- Department of Medicinal Chemistry; National Institute of Pharmaceutical Education and Research (NIPER); S. A. S. Nagar (Mohali) 160 062 Punjab India
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22
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Hirao H, Thellamurege N, Zhang X. Applications of density functional theory to iron-containing molecules of bioinorganic interest. Front Chem 2014; 2:14. [PMID: 24809043 PMCID: PMC4010748 DOI: 10.3389/fchem.2014.00014] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 03/10/2014] [Indexed: 12/29/2022] Open
Abstract
The past decades have seen an explosive growth in the application of density functional theory (DFT) methods to molecular systems that are of interest in a variety of scientific fields. Owing to its balanced accuracy and efficiency, DFT plays particularly useful roles in the theoretical investigation of large molecules. Even for biological molecules such as proteins, DFT finds application in the form of, e.g., hybrid quantum mechanics and molecular mechanics (QM/MM), in which DFT may be used as a QM method to describe a higher prioritized region in the system, while a MM force field may be used to describe remaining atoms. Iron-containing molecules are particularly important targets of DFT calculations. From the viewpoint of chemistry, this is mainly because iron is abundant on earth, iron plays powerful (and often enigmatic) roles in enzyme catalysis, and iron thus has the great potential for biomimetic catalysis of chemically difficult transformations. In this paper, we present a brief overview of several recent applications of DFT to iron-containing non-heme synthetic complexes, heme-type cytochrome P450 enzymes, and non-heme iron enzymes, all of which are of particular interest in the field of bioinorganic chemistry. Emphasis will be placed on our own work.
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Affiliation(s)
- Hajime Hirao
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological UniversitySingapore, Singapore
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