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N MP, C GPD, R M. Exploring natural products library to identify potential inhibitors targeting isoniazid-resistant tuberculosis. J Biomol Struct Dyn 2023:1-15. [PMID: 37993985 DOI: 10.1080/07391102.2023.2283159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 11/06/2023] [Indexed: 11/24/2023]
Abstract
Mycobacterium tuberculosis (MTB) causing tuberculosis (TB) infection is a leading source of illness and death in developing nations, and the emergence of drug-resistant TB remains a significant global threat and a challenge in treating the disease. Mutations in the inhA and katG genes are connected to the principal molecular mechanism of isoniazid (INH) resistance, and continuous treatment of INH for more than a decade led to the evolution of INH resistant-TB (inhR-TB). Structure-based drug discovery approaches on traditional natural compounds are the contemporary source to identify significant lead molecules. This work focuses on discovering effective small compounds from natural compound libraries and applying pharmacophore-based virtual screening to filter out the molecules. The best-identified hit complexes were used for molecular dynamics simulations (MDS) to observe their stability and compactness. A three-dimensional e-pharmacophore hypothesis and screening generated 62 hits based on phase fitness scores from the pharmacophore-based virtual screening. Molecular docking experiments in Maestro's GLIDE module indicated that ZINC000002383126 and ASN22022 may be potential inhibitors of inhA and katG (native, inhA mutants S94A, Y158A, Y158F and Y158S and D137S, Y229F, S315T, W321F, and R418L mutants of katG). In addition, MDS analysis indicated that the native and mutant docked complexes of inhA and katG had good stability and remained compact in the binding pocket of the targets. In vitro studies can further validate the compounds that can act as INH competitive inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Madhana Priya N
- Department of Biotechnology, Faculty of Biomedical Sciences & Technology, Sri Ramachandra Institute of Higher Education and Research (DU), Chennai, India
| | - George Priya Doss C
- Laboratory of Integrative Genomics, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Magesh R
- Department of Biotechnology, Faculty of Biomedical Sciences & Technology, Sri Ramachandra Institute of Higher Education and Research (DU), Chennai, India
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Role of Mitochondrial Cytochrome P450 2E1 in Healthy and Diseased Liver. Cells 2022; 11:cells11020288. [PMID: 35053404 PMCID: PMC8774478 DOI: 10.3390/cells11020288] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/05/2022] [Accepted: 01/11/2022] [Indexed: 12/14/2022] Open
Abstract
Cytochrome P450 2E1 (CYP2E1) is pivotal in hepatotoxicity induced by alcohol abuse and different xenobiotics. In this setting, CYP2E1 generates reactive metabolites inducing oxidative stress, mitochondrial dysfunction and cell death. In addition, this enzyme appears to play a role in the progression of obesity-related fatty liver to nonalcoholic steatohepatitis. Indeed, increased CYP2E1 activity in nonalcoholic fatty liver disease (NAFLD) is deemed to induce reactive oxygen species overproduction, which in turn triggers oxidative stress, necroinflammation and fibrosis. In 1997, Avadhani’s group reported for the first time the presence of CYP2E1 in rat liver mitochondria, and subsequent investigations by other groups confirmed that mitochondrial CYP2E1 (mtCYP2E1) could be found in different experimental models. In this review, we first recall the main features of CYP2E1 including its role in the biotransformation of endogenous and exogenous molecules, the regulation of its expression and activity and its involvement in different liver diseases. Then, we present the current knowledge on the physiological role of mtCYP2E1, its contribution to xenobiotic biotransformation as well as the mechanism and regulation of CYP2E1 targeting to mitochondria. Finally, we discuss experimental investigations suggesting that mtCYP2E1 could have a role in alcohol-associated liver disease, xenobiotic-induced hepatotoxicity and NAFLD.
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Bello M. Prediction of potential inhibitors of the dimeric SARS-CoV2 main proteinase through the MM/GBSA approach. J Mol Graph Model 2020; 101:107762. [PMID: 33022569 PMCID: PMC7511853 DOI: 10.1016/j.jmgm.2020.107762] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 09/15/2020] [Accepted: 09/21/2020] [Indexed: 01/27/2023]
Abstract
Since the emergence of SARS-CoV2, to date, no effective antiviral drug has been approved to treat the disease, and no vaccine against SARS-CoV2 is available. Under this scenario, the combination of two HIV-1 protease inhibitors, lopinavir and ritonavir, has attracted attention since they have been previously employed against the SARS-CoV main proteinase (Mpro) and exhibited some signs of effectiveness. Recently, the 3D structure of SARS-CoV2 Mpro was constructed based on the monomeric SARS-CoV Mpro and employed to identify potential approved small inhibitors against SARS-CoV2 Mpro, allowing the selection of 15 drugs among 1903 approved drugs to be employed. In this study, we performed docking of these 15 approved drugs against the recently solved X-ray crystallography structure of SARS-CoV2 Mpro in the monomeric and dimeric states; the latter is the functional state that was determined in a biological context, and these were submitted to molecular dynamics (MD) simulations coupled with the molecular mechanics generalized Born surface area (MM/GBSA) approach to obtain insight into the inhibitory activity of these compounds. Similar studies were performed with lopinavir and ritonavir coupled to monomeric and dimeric SARS-CoV Mpro and SARS-CoV2 Mpro to compare the inhibitory differences. Our study provides the structural and energetic basis of the inhibitory properties of lopinavir and ritonavir on SARS-CoV Mpro and SARS-CoV2 Mpro, allowing us to identify two FDA-approved drugs that can be used against SARS-CoV2 Mpro. This study also demonstrated that drug discovery requires the dimeric state to obtain good results.
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Affiliation(s)
- Martiniano Bello
- Laboratorio de Modelado Molecular, Bioinformática y Diseño de Fármacos de La Escuela Superior de Medicina, Instituto Politécnico Nacional, México. Plan de San Luis Y Diaz Mirón S/N, Col. Casco de Santo Tomas, México City, CP, 11340, Mexico.
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Bello M, Martínez-Muñoz A, Balbuena-Rebolledo I. Identification of saquinavir as a potent inhibitor of dimeric SARS-CoV2 main protease through MM/GBSA. J Mol Model 2020; 26:340. [PMID: 33184722 PMCID: PMC7661016 DOI: 10.1007/s00894-020-04600-4] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 11/05/2020] [Indexed: 12/23/2022]
Abstract
Among targets selected for studies aimed at identifying potential inhibitors against COVID-19, SARS-CoV2 main proteinase (Mpro) is highlighted. Mpro is indispensable for virus replication and is a promising target of potential inhibitors of COVID-19. Recently, monomeric SARS-CoV2 Mpro, drug repurposing, and docking methods have facilitated the identification of several potential inhibitors. Results were refined through the assessment of dimeric SARS-CoV2 Mpro, which represents the functional state of enzyme. Docking and molecular dynamics (MD) simulations combined with molecular mechanics/generalized Born surface area (MM/GBSA) studies indicated that dimeric Mpro most significantly impacts binding affinity tendency compared with the monomeric state, which suggests that dimeric state is most useful when performing studies aimed at identifying drugs targeting Mpro. In this study, we extend previous research by performing docking and MD simulation studies coupled with an MM/GBSA approach to assess binding of dimeric SARS-CoV2 Mpro to 12 FDA-approved drugs (darunavir, indinavir, saquinavir, tipranavir, diosmin, hesperidin, rutin, raltegravir, velpatasvir, ledipasvir, rosuvastatin, and bortezomib), which were identified as the best candidates for the treatment of COVID-19 in some previous dockings studies involving monomeric SARS-CoV2 Mpro. This analysis identified saquinavir as a potent inhibitor of dimeric SARS-CoV2 Mpro; therefore, the compound may have clinical utility against COVID-19. Graphical abstract ![]()
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Affiliation(s)
- Martiniano Bello
- Laboratorio de Modelado Molecular, Bioinformática y Diseño de Fármacos de la Escuela Superior de Medicina, Instituto Politécnico Nacional, México, Plan de San Luis Y Diaz Mirón S/N, Col. Casco de Santo Tomas, 11340, México City, Mexico.
| | - Alberto Martínez-Muñoz
- Laboratorio de Modelado Molecular, Bioinformática y Diseño de Fármacos de la Escuela Superior de Medicina, Instituto Politécnico Nacional, México, Plan de San Luis Y Diaz Mirón S/N, Col. Casco de Santo Tomas, 11340, México City, Mexico
| | - Irving Balbuena-Rebolledo
- Laboratorio de Modelado Molecular, Bioinformática y Diseño de Fármacos de la Escuela Superior de Medicina, Instituto Politécnico Nacional, México, Plan de San Luis Y Diaz Mirón S/N, Col. Casco de Santo Tomas, 11340, México City, Mexico
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Mendieta-Wejebe JE, Silva-Trujillo A, Bello M, Mendoza-Figueroa HL, Galindo-Alvarez NL, Albores A, Tamay-Cach F, Rosales-Hernández MC, Romero-Castro A, Correa-Basurto J. Exploring the biotransformation of N-(2-hydroxyphenyl)-2-propylpentanamide (an aryl valproic acid derivative) by CYP2C11, using in silico predictions and in vitro studies. J Pharm Pharmacol 2020; 72:938-955. [PMID: 32307724 DOI: 10.1111/jphp.13270] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 03/21/2020] [Indexed: 01/22/2023]
Abstract
OBJECTIVES N-(2-hydroxyphenyl)-2-propylpentanamide (HO-AAVPA), a derivative of valproic acid (VPA), has been proposed as a potential anticancer agent due to its improved antiproliferative effects in some cancer cell lines. Although there is evidence that VPA is metabolized by cytochrome P450 2C11 rat isoform, HO-AAVPA CYP-mediated metabolism has not yet been fully explored. Therefore, in this work, the biotransformation of HO-AAVPA by CYP2C11 was investigated. METHODS Kinetic parameters and spectral interaction between HO-AAVPA and CYP were evaluated using rat liver microsomes. The participation of CYP2C11 in metabolism of HO-AAVPA was confirmed by cimetidine (CIM) inhibition assay. Docking and molecular dynamics simulations coupled to MMGBSA methods were used in theoretical study. KEY FINDINGS HO-AAVPA is metabolized by CYP enzymes (KM = 38.94 µm), yielding a hydroxylated metabolite according to its HPLC retention time (5.4 min) and MS analysis (252.2 m/z). In addition, CIM inhibition in rat liver microsomes (Ki = 59.23 µm) confirmed that CYP2C11 is mainly involved in HO-AAVPA metabolism. Furthermore, HO-AAVPA interacts with CYP2C11 as a type I ligand. HO-AAVPA is stabilized at the CYP2C11 ligand recognition site through a map of interactions similar to other typical CYP2C11 substrates. CONCLUSION Therefore, rat liver CYP2C11 isoform is able to metabolize HO-AAVPA.
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Affiliation(s)
- Jessica Elena Mendieta-Wejebe
- Laboratorio de Biofísica y Biocatálisis, Escuela Superior de Medicina, Instituto Politécnico Nacional, Ciudad de México, México
| | - Arianna Silva-Trujillo
- Laboratorio de Biofísica y Biocatálisis, Escuela Superior de Medicina, Instituto Politécnico Nacional, Ciudad de México, México
| | - Martiniano Bello
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica (Laboratory for the Design and Development of New Drugs and Biotechnological Innovation), Escuela Superior de Medicina, Instituto Politécnico Nacional, Ciudad de México, México
| | - Humberto L Mendoza-Figueroa
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica (Laboratory for the Design and Development of New Drugs and Biotechnological Innovation), Escuela Superior de Medicina, Instituto Politécnico Nacional, Ciudad de México, México
| | - Norma Lizeth Galindo-Alvarez
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica (Laboratory for the Design and Development of New Drugs and Biotechnological Innovation), Escuela Superior de Medicina, Instituto Politécnico Nacional, Ciudad de México, México
| | - Arnulfo Albores
- Sección de Toxicología, Centro de Investigación y de Estudios Avanzados, Instituto Politécnico Nacional, Ciudad de México, México
| | - Feliciano Tamay-Cach
- Laboratorio de Investigación Bioquímica, Escuela Superior de Medicina, Instituto Politécnico Nacional, Ciudad de México, México
| | | | | | - José Correa-Basurto
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica (Laboratory for the Design and Development of New Drugs and Biotechnological Innovation), Escuela Superior de Medicina, Instituto Politécnico Nacional, Ciudad de México, México
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Exploring the inhibitory activity of valproic acid against the HDAC family using an MMGBSA approach. J Comput Aided Mol Des 2020; 34:857-878. [PMID: 32180123 DOI: 10.1007/s10822-020-00304-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Accepted: 03/07/2020] [Indexed: 12/30/2022]
Abstract
Valproic acid (VPA) is a compound currently used in clinical practice for the treatment of epilepsy as well as bipolar and mood disorders. VPA targets histone deacetylases (HDACs), which participate in the removal of acetyl groups from lysine in several proteins, regulating a wide variety of functions within the organism. An imbalance or malfunction of these enzymes is associated with the development and progression of several diseases, such as cancer and neurodegenerative diseases. HDACs are divided into four classes, but VPA only targets Class I (HDAC1-3 and 8) and Class IIa (HDAC4-5, 7 and 9) HDACs; however, structural and energetic information regarding the manner by which VPA inhibits these HDACs is lacking. Here, the structural and energetic features that determine this recognition were studied using molecular docking and molecular dynamics (MD) simulation. It was found that VPA reaches the catalytic site in HDAC1-3 and 7, whereas in HDAC6, VPA only reaches the catalytic tunnel. In HDAC4, VPA was bound adjacent to L1 and L2, a zone that participates in corepressor binding, and in HDAC8, VPA was bound to the hydrophobic active site channel (HASC), in line with previous reports.
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Rudik A, Bezhentsev V, Dmitriev A, Lagunin A, Filimonov D, Poroikov V. Metatox - Web application for generation of metabolic pathways and toxicity estimation. J Bioinform Comput Biol 2020; 17:1940001. [PMID: 30866738 DOI: 10.1142/s0219720019400018] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Xenobiotics biotransformation in humans is a process of the chemical modifications, which may lead to the formation of toxic metabolites. The prediction of such metabolites is very important for drug development and ecotoxicology studies. We created the web-application MetaTox ( http://way2drug.com/mg ) for the generation of xenobiotics metabolic pathways in the human organism. For each generated metabolite, the estimations of the acute toxicity (based on GUSAR software prediction), organ-specific carcinogenicity and adverse effects (based on PASS software prediction) are performed. Generation of metabolites by MetaTox is based on the fragments datasets, which describe transformations of substrates structures to a metabolites structure. We added three new classes of biotransformation reactions: Dehydrogenation, Glutathionation, and Hydrolysis, and now metabolite generation for 15 most frequent classes of xenobiotic's biotransformation reactions are available. MetaTox calculates the probability of formation of generated metabolite - it is the integrated assessment of the biotransformation reactions probabilities and their sites using the algorithm of PASS ( http://way2drug.com/passonline ). The prediction accuracy estimated by the leave-one-out cross-validation (LOO-CV) procedure calculated separately for the probabilities of biotransformation reactions and their sites is about 0.9 on the average for all reactions.
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Affiliation(s)
- Anastasiya Rudik
- * Department of Bioinformatics, Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, Moscow 119121, Russia
| | - Vladislav Bezhentsev
- * Department of Bioinformatics, Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, Moscow 119121, Russia
| | - Alexander Dmitriev
- * Department of Bioinformatics, Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, Moscow 119121, Russia
| | - Alexey Lagunin
- * Department of Bioinformatics, Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, Moscow 119121, Russia.,† Medico-Biological Faculty, Pirogov Russian National Research Medical University, 1 Ostrovitianov Street, Moscow 117997, Russia
| | - Dmitry Filimonov
- * Department of Bioinformatics, Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, Moscow 119121, Russia
| | - Vladimir Poroikov
- * Department of Bioinformatics, Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, Moscow 119121, Russia
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Kiani YS, Ranaghan KE, Jabeen I, Mulholland AJ. Molecular Dynamics Simulation Framework to Probe the Binding Hypothesis of CYP3A4 Inhibitors. Int J Mol Sci 2019; 20:E4468. [PMID: 31510073 PMCID: PMC6769491 DOI: 10.3390/ijms20184468] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 08/22/2019] [Accepted: 09/01/2019] [Indexed: 12/20/2022] Open
Abstract
The Cytochrome P450 family of heme-containing proteins plays a major role in catalyzing phase I metabolic reactions, and the CYP3A4 subtype is responsible for the metabolism of many currently marketed drugs. Additionally, CYP3A4 has an inherent affinity for a broad spectrum of structurally diverse chemical entities, often leading to drug-drug interactions mediated by the inhibition or induction of the metabolic enzyme. The current study explores the binding of selected highly efficient CYP3A4 inhibitors by docking and molecular dynamics (MD) simulation protocols and their binding free energy calculated using the WaterSwap method. The results indicate the importance of binding pocket residues including Phe57, Arg105, Arg106, Ser119, Arg212, Phe213, Thr309, Ser312, Ala370, Arg372, Glu374, Gly481 and Leu483 for interaction with CYP3A4 inhibitors. The residue-wise decomposition of the binding free energy from the WaterSwap method revealed the importance of binding site residues Arg106 and Arg372 in the stabilization of all the selected CYP3A4-inhibitor complexes. The WaterSwap binding energies were further complemented with the MM(GB/PB)SA results and it was observed that the binding energies calculated by both methods do not differ significantly. Overall, our results could guide towards the use of multiple computational approaches to achieve a better understanding of CYP3A4 inhibition, subsequently leading to the design of highly specific and efficient new chemical entities with suitable ADMETox properties and reduced side effects.
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Affiliation(s)
- Yusra Sajid Kiani
- Research Center for Modeling and Simulation (RCMS), National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan.
| | - Kara E Ranaghan
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK.
| | - Ishrat Jabeen
- Research Center for Modeling and Simulation (RCMS), National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan.
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK.
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Bello M. Impact of tetramerization on the ligand recognition of N1 influenza neuraminidase via MMGBSA approach. Biopolymers 2018; 110:e23251. [PMID: 30589081 DOI: 10.1002/bip.23251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 12/03/2018] [Accepted: 12/07/2018] [Indexed: 11/09/2022]
Abstract
Influenza virus neuraminidase (NA) is a homotetrameric surface protein that, in contrast to other non-influenza NAs, requires a quaternary assembly to exhibit enzymatic activity, suggesting that the oligomeric state significantly impacts the active site of influenza NA. Nevertheless, most structure-based drug design studies have been reported by employing the monomeric state in the closed or open-loop due to the computational cost of employing the tetrameric NA. In this work, we present MD simulations coupled to the MMGBSA approach of avian N1 type NA in its monomeric and tetrameric closed and open-loop state both with and without the inhibitor oseltamivir and its natural substrate, sialic acid. Structural and energetic analyses revealed that the tetrameric state impacts flexibility as well as the map of interactions participating in stabilizing the protein-ligand complexes with respect to the monomeric state. It was observed that the tetrameric state exerts dissimilar effects in binding affinity, characteristic of positive and negative cooperativity for oseltamivir and sialic acid, respectively. Based on our results, to perform a confident structure-based drug design, as well as to evaluate the impact of key mutations through MD simulations, it is important to consider the tetrameric state closed-loop state.
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Affiliation(s)
- Martiniano Bello
- Laboratorio de Modelado Molecular, Bioinformática y Diseño de Fármacos de la Escuela Superior de Medicina, Instituto Politécnico Nacional, México City, Mexico
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Bello M, Morales-González JA. Molecular recognition between potential natural inhibitors of the Keap1-Nrf2 complex. Int J Biol Macromol 2017; 105:981-992. [PMID: 28746889 DOI: 10.1016/j.ijbiomac.2017.07.117] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 07/13/2017] [Accepted: 07/18/2017] [Indexed: 02/07/2023]
Abstract
Disrupting the Keap1-Nrf2 pathway enhances Nrf2 activity, which has been identified as an important approach for the prevention of different chronic diseases in which oxidative stress and inflammation are present, such as cancer, diabetes, Alzheimer's and Parkinson's. Based on the high potential to modulate antioxidant, anti-inflammatory and anticancer properties that the discovery of Keap1-Nrf2 protein-protein interaction inhibitors would represent, the utilization of some natural compounds has emerged as a promising strategy to identify new drugs. To gain insight into the structural and energetic basis of the molecular recognition between some natural inhibitors that could work as inhibitors of the Keap1-Nrf2 complex, we evaluated the binding properties between four natural compounds present in the extract of Geranium schiedeanum (Gs): 3-O-a-L arabinofuranoside-7-O-a-l-rhamnopyranoside of kaempferol (KAM), gallic acid (GAL), ellagic acid (ELL) and geranium acetonitrile (ACE), which based on experimental findings have been proposed as possible Keap1-Nrf2 PPI inhibitors. Computational studies combining docking and MD simulations accompanied by the MMGBSA approach revealed that KAM and ACE directly interact with residues in the Kelch domain that participate in the molecular recognition of Nrf2, indicating that both natural compounds could act as activators of Nrf2, whereas GAL and ELL are possible free radical scavengers.
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Affiliation(s)
- Martiniano Bello
- Laboratorio de Modelado Molecular, Bioinformática y Diseño de Fármacos de la Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón, Col. Casco de Santo Tomás, Del. Miguel Hidalgo, México D.F. 11340, Mexico.
| | - José Antonio Morales-González
- Laboratorio Medicina de Conservación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón, Col. Casco de Santo Tomás, Del. Miguel Hidalgo, México D.F. 11340, Mexico
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Abstract
Abstract
Cytochrome P450s belong to a superfamily of enzymes that catalyse a wide variety of oxidative transformations. Hydroxylation is one the most thoroughly investigated of all identified P450-catalysed reactions whilst dehydrogenation has been relatively much less explored to date. P450-catalysed dehydrogenation is often found to occur with hydroxylation and thus, it was initially suspected to be a stepwise process consisting of hydroxylation and subsequent dehydration to yield the final olefin product. This theory has been proven to be invalid and the olefin was shown to be the direct product of a P450-catalysed reaction. This interesting reaction plays a vital role in the metabolism of xenobiotics and the biosynthesis of endogenous compounds, including a number of steroids. A number of well-known examples of P450 mediated dehydrogenation, including those in the metabolism of valproic acid, capsaicin and 3-methylindole and those in the biosynthesis of plant and fungal sterols are discussed in this review.
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Kumar V, Sobhia ME. Molecular Dynamics Assisted Mechanistic Study of Isoniazid-Resistance against Mycobacterium tuberculosis InhA. PLoS One 2015; 10:e0144635. [PMID: 26658674 PMCID: PMC4682841 DOI: 10.1371/journal.pone.0144635] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 11/21/2015] [Indexed: 12/20/2022] Open
Abstract
Examination of InhA mutants I16T, I21V, I47T, S94A, and I95P showed that direct and water mediated H-bond interactions between NADH and binding site residues reduced drastically. It allowed conformational flexibility to NADH, particularly at the pyrophosphate region, leading to weakening of its binding at dinucleotide binding site. The highly scattered distribution of pyrophosphate dihedral angles and chi1 side chain dihedral angles of corresponding active site residues therein confirmed weak bonding between InhA and NADH. The average direct and water mediated bridged H-bond interactions between NADH and mutants were observed weaker as compared to wild type. Further, estimated NADH binding free energy in mutants supported the observed weakening of InhA-NADH interactions. Similarly, per residue contribution to NADH binding was also found little less as compared to corresponding residues in wild type. This investigation clearly depicted and supported the effect of mutations on NADH binding and can be accounted for isoniazid resistance as suggested by previous biochemical and mutagenic studies. Further, structural analysis of InhA provided the crucial points to enhance the NADH binding affinity towards InhA mutants in the presence of direct InhA inhibitors to combat isoniazid drug resistance. This combination could be a potential alternative for treatment of drug resistant tuberculosis.
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Affiliation(s)
- Vivek Kumar
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S. Nagar- 160 062, Punjab, India
| | - M. Elizabeth Sobhia
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S. Nagar- 160 062, Punjab, India
- * E-mail:
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Liu H, An X, Li S, Wang Y, Li J, Liu H. Interaction mechanism exploration of R-bicalutamide/S-1 with WT/W741L AR using molecular dynamics simulations. MOLECULAR BIOSYSTEMS 2015; 11:3347-54. [PMID: 26442831 DOI: 10.1039/c5mb00499c] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
R-Bicalutamide is a first generation antiandrogen used to treat prostate cancer, which inhibits androgen action by competitively binding to the androgen receptor (AR). However, R-bicalutamide was discovered to exhibit some agonistic properties in clinical application. According to reports, the W741L AR mutation may lead to resistance towards R-bicalutamide. But the mechanism of the R-bicalutamide switch from an antagonist to an agonist due to the mutation of AR W741L is still not so clear. Another molecule, S-1, owing to a very similar structure to R-bicalutamide, is always agonistic to both the wild type and W741L AR. The main difference between these two chemicals is that S-1 has an ether linkage while R-bicalutamide has a sulfonyl group. To study the drug-resistant mechanism caused by W741L mutation and the opposite effects arising from subtle structure differences, molecular dynamics (MD) simulations and molecular mechanics generalized Born surface area (MM-GBSA) calculations were employed to explore the interaction mechanisms between R-bicalutamide/S-1 and WT/W741L AR. The calculated binding free energies are in accordance with the reported experimental values. The obtained results indicate that M895 and W741 are vital amino acids in the antagonism of R-bicalutamide. The bulkier substitution of sulfonyl and tryptophan push aside M895, together with helix 12 (H12), to expose the ligand-binding domain resulting in the antagonistic conformation of the AR. If W741 is mutated to L741, the B-ring of these two chemicals would shift toward L741. At the same time, M895 dragging helix H12, would also move closer to L741. So H12 tends to cover the AR ligand-binding domain to a certain degree, changing the androgen receptor from an antagonistic to an agonistic conformation, which may explain the agonism of R-bicalutamide to the mutant W741L AR.
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Affiliation(s)
- Hongli Liu
- School of Pharmacy, Lanzhou University, 199 West Donggang Rd, 730000 Lanzhou, China.
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A Combined Molecular Docking/Dynamics Approach to Probe the Binding Mode of Cancer Drugs with Cytochrome P450 3A4. Molecules 2015; 20:14915-35. [PMID: 26287147 PMCID: PMC6332164 DOI: 10.3390/molecules200814915] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 08/11/2015] [Accepted: 08/12/2015] [Indexed: 12/23/2022] Open
Abstract
Cytarabine, daunorubicin, doxorubicin and vincristine are clinically used for combinatorial therapies of cancers in different combinations. However, the knowledge about the interaction of these drugs with the metabolizing enzyme cytochrome P450 is limited. Therefore, we utilized computational methods to predict and assess the drug-binding modes. In this study, we performed docking, MD simulations and free energy landscape analysis to understand the drug-enzyme interactions, protein domain motions and the most populated free energy minimum conformations of the docked protein-drug complexes, respectively. The outcome of docking and MD simulations predicted the productive, as well as the non-productive binding modes of the selected drugs. Based on these interaction studies, we observed that S119, R212 and R372 are the major drug-binding residues in CYP3A4. The molecular mechanics Poisson–Boltzmann surface area analysis revealed the dominance of hydrophobic forces in the CYP3A4-drug association. Further analyses predicted the residues that may contain favorable drug-specific interactions. The probable binding modes of the cancer drugs from this study may extend the knowledge of the protein-drug interaction and pave the way to design analogs with reduced toxicity. In addition, they also provide valuable insights into the metabolism of the cancer drugs.
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