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Feng Y, Gong C, Zhu J, Liu G, Tang Y, Li W. Unraveling the Ligand-Binding Sites of CYP3A4 by Molecular Dynamics Simulations with Solvent Probes. J Chem Inf Model 2024; 64:3451-3464. [PMID: 38593186 DOI: 10.1021/acs.jcim.4c00089] [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: 04/11/2024]
Abstract
Cytochrome P450 3A4 (CYP3A4) is one of the most important drug-metabolizing enzymes in the human body and is well known for its complicated, atypical kinetic characteristics. The existence of multiple ligand-binding sites in CYP3A4 has been widely recognized as being capable of interfering with the active pocket through allosteric effects. The identification of ligand-binding sites other than the canonical active site above the heme is especially important for understanding the atypical kinetic characteristics of CYP3A4 and the intriguing association between the ligand and the receptor. In this study, we first employed mixed-solvent molecular dynamics (MixMD) simulations coupled with the online computational predictive tools to explore potential ligand-binding sites in CYP3A4. The MixMD approach demonstrates better performance in dealing with the receptor flexibility compared with other computational tools. From the sites identified by MixMD, we then picked out multiple sites for further exploration using ensemble docking and conventional molecular dynamics (cMD) simulations. Our results indicate that three extra sites are suitable for ligand binding in CYP3A4, including one experimentally confirmed site and two novel sites.
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Affiliation(s)
- Yanjun Feng
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Changda Gong
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Jieyu Zhu
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Guixia Liu
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Yun Tang
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Weihua Li
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
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2
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Wang Y, Paidi VK, Wang W, Wang Y, Jia G, Yan T, Cui X, Cai S, Zhao J, Lee KS, Lee LYS, Wong KY. Spatial engineering of single-atom Fe adjacent to Cu-assisted nanozymes for biomimetic O 2 activation. Nat Commun 2024; 15:2239. [PMID: 38472201 DOI: 10.1038/s41467-024-46528-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 02/29/2024] [Indexed: 03/14/2024] Open
Abstract
The precise design of single-atom nanozymes (SAzymes) and understanding of their biocatalytic mechanisms hold great promise for developing ideal bio-enzyme substitutes. While considerable efforts have been directed towards mimicking partial bio-inspired structures, the integration of heterogeneous SAzymes configurations and homogeneous enzyme-like mechanism remains an enormous challenge. Here, we show a spatial engineering strategy to fabricate dual-sites SAzymes with atomic Fe active center and adjacent Cu sites. Compared to planar Fe-Cu dual-atomic sites, vertically stacked Fe-Cu geometry in FePc@2D-Cu-N-C possesses highly optimized scaffolds, favorable substrate affinity, and fast electron transfer. These characteristics of FePc@2D-Cu-N-C SAzyme induces biomimetic O2 activation through homogenous enzymatic pathway, resembling functional and mechanistic similarity to natural cytochrome c oxidase. Furthermore, it presents an appealing alternative of cytochrome P450 3A4 for drug metabolism and drug-drug interaction. These findings are expected to deepen the fundamental understanding of atomic-level design in next-generation bio-inspired nanozymes.
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Affiliation(s)
- Ying Wang
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
| | - Vinod K Paidi
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, Grenoble, 38043, Cedex 9, France
| | - Weizhen Wang
- Department of Applied Physics, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
| | - Yong Wang
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
| | - Guangri Jia
- State Key Laboratory of Automotive Simulation and Control, Department of Materials Science, Key Laboratory of Automobile Materials of MOE, Jilin University, Changchun, 130012, China
| | - Tingyu Yan
- Key Laboratory of Photonic and Electronic Bandgap Materials of MOE, College of Chemistry and Chemical Engineering, Harbin Normal University, Harbin, 150025, PR China
| | - Xiaoqiang Cui
- State Key Laboratory of Automotive Simulation and Control, Department of Materials Science, Key Laboratory of Automobile Materials of MOE, Jilin University, Changchun, 130012, China
| | - Songhua Cai
- Department of Applied Physics, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China.
| | - Jingxiang Zhao
- Key Laboratory of Photonic and Electronic Bandgap Materials of MOE, College of Chemistry and Chemical Engineering, Harbin Normal University, Harbin, 150025, PR China.
| | - Kug-Seung Lee
- Pohang Accelerator Laboratory (PAL), Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea.
| | - Lawrence Yoon Suk Lee
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China.
- Research Institute for Smart Energy, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China.
| | - Kwok-Yin Wong
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China.
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3
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Liu N, Gao P, Lu HY, Fang L, Nicolas J, Ha-Duong T, Shen JS. Polyfluoroalkyl Chain-Based Assemblies for Biomimetic Catalysis. Chemistry 2024; 30:e202302669. [PMID: 37823686 DOI: 10.1002/chem.202302669] [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: 08/15/2023] [Revised: 10/06/2023] [Accepted: 10/12/2023] [Indexed: 10/13/2023]
Abstract
Amphiphobic fluoroalkyl chains are exploited for creating robust and diverse self-assembled biomimetic catalysts. Long terminal perfluoroalkyl chains (Cn F2n+1 with n=6, 8, and 10) linked with a short perhydroalkyl chains (Cm H2m with m=2 and 3) were used to synthesize several 1,4,7-triazacyclononane (TACN) derivatives, Cn F2n+1 -Cm H2m -TACN. In the presence of an equimolar amount of Zn2+ ions that coordinate the TACN moiety and drive the self-assembly into micelle-like aggregates, the critical aggregation concentration of polyfluorinated Cn F2n+1 -Cm H2m -TACN⋅Zn2+ was lowered by ∼1 order of magnitude compared to the traditional perhyroalkyl counterpart with identical carbon number of alkyl chain. When 2'-hydroxypropyl-4-nitrophenyl phosphate was used as the model phosphate substrate, polyfluorinated Cn F2n+1 -Cm H2m -TACN⋅Zn2+ assemblies showed higher affinity and catalytic activity, compared to its perhyroalkyl chain-based counterpart. Coarse-grained molecular dynamic simulations have been introduced to explore the supramolecular assembly of polyfluoroalkyl chains in the presence of Zn2+ ions and to better understand their enhanced catalytic activity.
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Affiliation(s)
- Ning Liu
- College of Materials Science and Engineering, Huaqiao University, Xiamen, 361021, China
| | - Ping Gao
- Institut Galien Paris-Saclay, Université Paris-Saclay, CNRS, Orsay, 91400, France
- BioCIS, Université Paris-Saclay, CNRS, Orsay, 91400, France
| | - Hai-Yan Lu
- College of Materials Science and Engineering, Huaqiao University, Xiamen, 361021, China
| | - Lei Fang
- College of Materials Science and Engineering, Huaqiao University, Xiamen, 361021, China
| | - Julien Nicolas
- Institut Galien Paris-Saclay, Université Paris-Saclay, CNRS, Orsay, 91400, France
| | - Tâp Ha-Duong
- BioCIS, Université Paris-Saclay, CNRS, Orsay, 91400, France
| | - Jiang-Shan Shen
- College of Materials Science and Engineering, Huaqiao University, Xiamen, 361021, China
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4
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Mersal KI, Abdel-Maksoud MS, Ali EMH, Ammar UM, Zaraei SO, Haque MM, Das T, Hassan NF, Kim EE, Lee JS, Park H, Lee KH, El-Gamal MI, Kim HK, Ibrahim TM, Oh CH. Evaluation of novel pyrazol-4-yl pyridine derivatives possessing arylsulfonamide tethers as c-Jun N-terminal kinase (JNK) inhibitors in leukemia cells. Eur J Med Chem 2023; 261:115779. [PMID: 37776574 DOI: 10.1016/j.ejmech.2023.115779] [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: 05/18/2023] [Revised: 08/14/2023] [Accepted: 08/29/2023] [Indexed: 10/02/2023]
Abstract
A series of 36 pyrazol-4-yl pyridine derivatives (8a-i, 9a-i, 10a-i, and 11a-i) was designed, synthesized, and evaluated for its antiproliferative activity over NCI-60 cancer cell line panel and inhibitory effect against JNK isoforms (JNK1, JNK2, and JNK3). All the synthesized compounds were tested against the NCI-60 cancer cell line panel. Compounds 11b, 11c, 11g, and 11i were selected to determine their GI50s and exerted a superior potency over the reference standard SP600125 against the tested cell lines. 11c showed a GI50 of 1.28 μM against K562 leukemic cells. Vero cells were used to assess 11c cytotoxicity compared to the tested cancer cells. The target compounds were tested against hJNK isoforms in which compound 11e exhibited the highest potency against JNK isoforms with IC50 values of 1.81, 12.7, and 10.5 nM against JNK1, JNK2, and JNK3, respectively. Kinase profiling of 11e showed higher JNK selectivity in 50 kinase panels. Compounds 11c and 11e showed cell population arrest at the G2/M phase, induced early apoptosis, and slightly inhibited beclin-1 production at higher concentrations in K562 leukemia cells relative to SP600125. NanoBRET assay of 11e showed intracellular JNK1 inhibition with an IC50 of 2.81 μM. Also, it inhibited CYP2D6 and 3A4 with different extent and its hERG activity showed little cardiac toxicity with an IC50 of 4.82 μM. hJNK3 was used as a template to generate the hJNK1 crystal structure to explore the binding mode of 11e (PDB ID: 8ENJ) with a resolution of 2.8 °A and showed a typical type I kinase inhibition against hJNK1. Binding energy scores showed that selectivity of 11e towards JNK1 could be attributed to additional hydrophobic interactions relative to JNK3.
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Affiliation(s)
- Karim I Mersal
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Modern University for Technology and Information (MTI), Cairo, 12055, Egypt; University of Science & Technology (UST), Daejeon, Yuseong-gu, 34113, Republic of Korea; Center of Biomaterials, Korea Institute of Science & Technology (KIST School), Seoul, Seongbuk-gu, 02792, Republic of Korea
| | - Mohammed S Abdel-Maksoud
- Medicinal & Pharmaceutical Chemistry Department, Pharmaceutical and Drug Industries Research Institute, National Research Centre NRC (ID: 60014618), Dokki, Giza, 12622, Egypt
| | - Eslam M H Ali
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Modern University for Technology and Information (MTI), Cairo, 12055, Egypt; Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 575 West Stadium Avenue, West Lafayette, IN, 47907, USA
| | - Usama M Ammar
- School of Applied Sciences, Edinburgh Napier University, Sighthill Campus, 9 Sighthill Court, Edinburgh, EH11 4BN, United Kingdom
| | - Seyed-Omar Zaraei
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Md Mamunul Haque
- Department of Neural and Pain Sciences, School of Dentistry, University of Maryland, Baltimore, MD, 21201, USA
| | - Tanuza Das
- Department of Neurology, School of Medicine, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Noha F Hassan
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Modern University for Technology and Information (MTI), Cairo, 12055, Egypt
| | - Eunice EunKyeong Kim
- Biomedical Research Institute, Korea Institute of Science and Technology, Seoul, 02792, South Korea
| | - Jun-Seok Lee
- Department of Pharmacology, College of Medicine, Korea University, Seoul, 02841, South Korea
| | - HaJeung Park
- The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, USA
| | - Kwan Hyi Lee
- Center for Advanced Biomolecular Recognition, Korea Institute of Science & Technology (KIST School), Seoul, Seongbuk-gu, 02792, Republic of Korea; KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul, 02841, Republic of Korea
| | - Mohammed I El-Gamal
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, 27272, United Arab Emirates; Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah, 27272, United Arab Emirates; Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt
| | - Hee-Kwon Kim
- Department of Nuclear Medicine, Molecular Imaging & Therapeutic Medicine Research Center, Jeonbuk National University Medical School and Hospital, 20 Geonji-ro, Deokjin-gu, Jeonju, 54907, Republic of Korea; Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute of Jeonbuk National University Hospital, 20 Geonji-ro, Deokjin-gu, Jeonju, 54907, Republic of Korea.
| | - Tamer M Ibrahim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, P.O. Box 33516, Egypt
| | - Chang-Hyun Oh
- University of Science & Technology (UST), Daejeon, Yuseong-gu, 34113, Republic of Korea; Center of Biomaterials, Korea Institute of Science & Technology (KIST School), Seoul, Seongbuk-gu, 02792, Republic of Korea.
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5
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Gan Y, Xu Y, Zhang X, Hu H, Xiao W, Yu Z, Sun T, Zhang J, Wen C, Zheng S. Revisiting Supersaturation of a Biopharmaceutical Classification System IIB Drug: Evaluation via a Multi-Cup Dissolution Approach and Molecular Dynamic Simulation. Molecules 2023; 28:6962. [PMID: 37836805 PMCID: PMC10574532 DOI: 10.3390/molecules28196962] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/01/2023] [Accepted: 10/04/2023] [Indexed: 10/15/2023] Open
Abstract
As a subclass of the biopharmaceutical classification system (BCS) class II, basic drugs (BCS IIB) exhibit pH-dependent solubility and tend to generate supersaturation in the gastrointestinal tract, leading to less qualified in vitro-in vivo correlation (IVIVC). This study aims to develop a physiologically based multi-cup dissolution approach to improve the evaluation of the supersaturation for a higher quality of IVIVC and preliminarily explores the molecular mechanism of supersaturation and precipitation of ketoconazole affected by Polyvinylpyrrolidone-vinyl acetate copolymer (PVPVA) and hydroxypropyl methyl-cellulose (HPMC). The concentration of ketoconazole in each cup of the dynamic gastrointestinal model (DGIM) was measured using fiber optical probes. Molecular interactions between ketoconazole and PVPVA or HPMC were simulated by Materials Studio. The results demonstrated that PVPVA and HPMC improved and maintained the supersaturation of ketoconazole. PVPVA exhibited superior precipitation inhibitory effect on ketoconazole molecule aggregation due to slightly stronger van der Waals forces as well as unique electrostatic forces, thereby further enhancing in vitro drug absorption, which correlated well with in vivo drug absorption. Compared with a conventional dissolution apparatus paddle method, the DGIM improved the mean prediction error through the IVIVC from 19.30% to 9.96%, reaching the qualification criteria. In conclusion, the physiologically based multi-cup dissolution approach enables improved evaluation of supersaturation in gastrointestinal transportation of BCS IIB drug ketoconazole, enabling screening screen precipitation inhibitors and achieving qualified IVIVC for drug formulation studies.
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Affiliation(s)
- Yanxiong Gan
- School of Intelligent Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China; (Y.G.); (T.S.)
| | - Yaxin Xu
- School of Intelligent Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China; (Y.G.); (T.S.)
| | - Xue Zhang
- School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
- Jiangsu Hengrui Medicine Co., Ltd., Nanjing 210009, China
| | - Huiling Hu
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China (J.Z.)
| | - Wenke Xiao
- School of Intelligent Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China; (Y.G.); (T.S.)
| | - Zheng Yu
- School of Intelligent Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China; (Y.G.); (T.S.)
| | - Tao Sun
- School of Intelligent Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China; (Y.G.); (T.S.)
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China (J.Z.)
| | - Jinming Zhang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China (J.Z.)
| | - Chuanbiao Wen
- School of Intelligent Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China; (Y.G.); (T.S.)
| | - Shichao Zheng
- School of Intelligent Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China; (Y.G.); (T.S.)
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6
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Mishin V, Heck DE, Jan YH, Richardson JR, Laskin JD. Distinct effects of form selective cytochrome P450 inhibitors on cytochrome P450-mediated monooxygenase and hydrogen peroxide generating NADPH oxidase. Toxicol Appl Pharmacol 2022; 455:116258. [PMID: 36174671 DOI: 10.1016/j.taap.2022.116258] [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: 07/16/2022] [Revised: 09/14/2022] [Accepted: 09/22/2022] [Indexed: 11/16/2022]
Abstract
A characteristic of cytochrome P450 (CYP) enzymes is their ability to generate H2O2, either directly or indirectly via superoxide anion, a reaction referred to as "NADPH oxidase" activity. H2O2 production by CYPs can lead to the accumulation of cytotoxic reactive oxygen species which can compromise cellular functioning and contribute to tissue injury. Herein we determined if form selective CYP inhibitors could distinguish between the activities of the monooxygenase and NADPH oxidase activities of rat recombinant CYP1A2, CYP2E1, CYP3A1 and CYP3A2 and CYP1A1/2-enriched β-naphthoflavone-induced rat liver microsomes, CYP2E1-enriched isoniazide-induced rat liver microsomes and CYP3A subfamily-enriched dexamethasone-induced rat liver microsomes. In the presence of 7,8-benzoflavone (2.0 μM) for CYP1A2 and 4-methylpyrazole (32 μM) or DMSO (16 mM) for CYP2E1, monooxygenase activity was blocked without affecting NADPH oxidase activity for both the recombinant enzymes and microsomal preparations. Ketoconazole (1.0 μM), a form selective inhibitor for CYP3A subfamily enzymes, completely inhibited monooxygenase activity of rat recombinant CYP3A1/3A2 and CYP3A subfamily in rat liver microsomes; it also partially inhibited NADPH oxidase activity. 7,8-benzoflavone is a type I ligand, which competes with substrate binding, while 4-methylpyrazole and DMSO are type II heme binding ligands. Interactions of heme with these type II ligands was not sufficient to interfere with oxygen activation, which is required for NADPH oxidase activity. Ketoconazole, a type II ligand known to bind multiple sites on CYP3A subfamily enzymes in close proximity to heme, also interfered, at least in part, with oxygen activation. These data indicate that form specific inhibitors can be used to distinguish between monooxygenase reactions and H2O2 generating NADPH oxidase of CYP1A2 and CYP2E1. Mechanisms by which ketoconazole inhibits CYP3A NADPH oxidase remain to be determined.
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Affiliation(s)
- Vladimir Mishin
- Department of Pharmacology and Toxicology, Ernest Mario School of Pharmacy, Rutgers University, Piscataway, NJ 08854, USA
| | - Diane E Heck
- Department of Public Health, New York Medical College, Valhalla, NY 10595, USA
| | - Yi-Hua Jan
- Department of Environmental and Occupational Health and Justice, Rutgers University School of Public Health, Piscataway, NJ 08854, USA
| | - Jason R Richardson
- Department of Environmental Health Sciences, Robert Stempel College of Public Health and Social Work, Florida International University, Miami, FL 33199, USA
| | - Jeffrey D Laskin
- Department of Environmental and Occupational Health and Justice, Rutgers University School of Public Health, Piscataway, NJ 08854, USA.
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7
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Abu Rabah RR, Sebastian A, Vunnam S, Sultan S, Tarazi H, Anbar HS, Shehata MK, Zaraei SO, Elgendy SM, Al Shamma SA, Omar HA, Al-Tel TH, El-Gamal MI. Design, synthesis, and biological evaluation of a new series of pyrazole derivatives: Discovery of potent and selective JNK3 kinase inhibitors. Bioorg Med Chem 2022; 69:116894. [DOI: 10.1016/j.bmc.2022.116894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/16/2022] [Accepted: 06/16/2022] [Indexed: 11/02/2022]
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8
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Guttman Y, Kerem Z. Computer-Aided (In Silico) Modeling of Cytochrome P450-Mediated Food–Drug Interactions (FDI). Int J Mol Sci 2022; 23:ijms23158498. [PMID: 35955630 PMCID: PMC9369352 DOI: 10.3390/ijms23158498] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 07/26/2022] [Accepted: 07/28/2022] [Indexed: 02/01/2023] Open
Abstract
Modifications of the activity of Cytochrome 450 (CYP) enzymes by compounds in food might impair medical treatments. These CYP-mediated food–drug interactions (FDI) play a major role in drug clearance in the intestine and liver. Inter-individual variation in both CYP expression and structure is an important determinant of FDI. Traditional targeted approaches have highlighted a limited number of dietary inhibitors and single-nucleotide variations (SNVs), each determining personal CYP activity and inhibition. These approaches are costly in time, money and labor. Here, we review computational tools and databases that are already available and are relevant to predicting CYP-mediated FDIs. Computer-aided approaches such as protein–ligand interaction modeling and the virtual screening of big data narrow down hundreds of thousands of items in databanks to a few putative targets, to which the research resources could be further directed. Structure-based methods are used to explore the structural nature of the interaction between compounds and CYP enzymes. However, while collections of chemical, biochemical and genetic data are available today and call for the implementation of big-data approaches, ligand-based machine-learning approaches for virtual screening are still scarcely used for FDI studies. This review of CYP-mediated FDIs promises to attract scientists and the general public.
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9
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Koulgi S, Jani V, Phukan S, Sonavane U, Joshi R, Kamboj RK, Palle V. A Deep Dive into the Conformational Dynamics of CYP3A4 : Understanding the Binding of Homotropic and Non‐homotropic Ligands for Mitigating Drug‐Drug interaction (DDI). ChemistrySelect 2022. [DOI: 10.1002/slct.202200249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Shruti Koulgi
- High Performance Computing – Medical and Bioinformatics Applications Group Centre for Development of Advanced Computing C–DAC Innovation Park, Panchawati, Pashan Pune 411 008 India
| | - Vinod Jani
- High Performance Computing – Medical and Bioinformatics Applications Group Centre for Development of Advanced Computing C–DAC Innovation Park, Panchawati, Pashan Pune 411 008 India
| | - Samiron Phukan
- Lupin Limited (Research Park), Nande Village Pune 412115 India
| | - Uddhavesh Sonavane
- High Performance Computing – Medical and Bioinformatics Applications Group Centre for Development of Advanced Computing C–DAC Innovation Park, Panchawati, Pashan Pune 411 008 India
| | - Rajendra Joshi
- High Performance Computing – Medical and Bioinformatics Applications Group Centre for Development of Advanced Computing C–DAC Innovation Park, Panchawati, Pashan Pune 411 008 India
| | | | - Venkata Palle
- Lupin Limited (Research Park), Nande Village Pune 412115 India
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10
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Hsu MH, Johnson EF. Structural characterization of the homotropic cooperative binding of azamulin to human cytochrome P450 3A5. J Biol Chem 2022; 298:101909. [PMID: 35398097 PMCID: PMC9079302 DOI: 10.1016/j.jbc.2022.101909] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 04/01/2022] [Accepted: 04/03/2022] [Indexed: 01/02/2023] Open
Abstract
Cytochrome P450 3A4 and 3A5 catalyze the metabolic clearance of a large portion of therapeutic drugs. Azamulin is used as a selective inhibitor for 3A4 and 3A5 to define their roles in metabolism of new chemical entities during drug development. In contrast to 3A4, 3A5 exhibits homotropic cooperativity for the sequential binding of two azamulin molecules at concentrations used for inhibition. To define the underlying sites and mechanisms for cooperativity, an X-ray crystal structure of 3A5 was determined with two azamulin molecules in the active site that are stacked in an antiparallel orientation. One azamulin resides proximal to the heme in a pose similar to the 3A4-azamulin complex. Comparison to the 3A5 apo structure indicates that the distal azamulin in 3A5 ternary complex causes a significant induced fit that excludes water from the hydrophobic surfaces of binding cavity and the distal azamulin, which is augmented by the stacking interaction with the proximal azamulin. Homotropic cooperativity was not observed for the binding of related pleuromutilin antibiotics, tiamulin, retapamulin, and lefamulin, to 3A5, which are larger and unlikely to bind in the distal site in a stacked orientation. Formation of the 3A5 complex with two azamulin molecules may prevent time-dependent inhibition that is seen for 3A4 by restricting alternate product formation and/or access of reactive intermediates to vulnerable protein sites. These results also contribute to a better understanding of sites for cooperative binding and the differential structural plasticity of 3A5 and 3A4 that contribute to differential substrate and inhibitor binding.
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Affiliation(s)
- Mei-Hui Hsu
- Department of Molecular Medicine, Scripps Research, La Jolla, California, USA
| | - Eric F Johnson
- Department of Molecular Medicine, Scripps Research, La Jolla, California, USA.
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11
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Computational Insight into Biotransformation Profiles of Organophosphorus Flame Retardants to Their Diester Metabolites by Cytochrome P450. Molecules 2022; 27:molecules27092799. [PMID: 35566150 PMCID: PMC9102461 DOI: 10.3390/molecules27092799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 04/24/2022] [Accepted: 04/26/2022] [Indexed: 02/05/2023] Open
Abstract
Biotransformation of organophosphorus flame retardants (OPFRs) mediated by cytochrome P450 enzymes (CYPs) has a potential correlation with their toxicological effects on humans. In this work, we employed five typical OPFRs including tris(1,3-dichloro-2-propyl) phosphate (TDCIPP), tris(1-chloro-2-propyl) phosphate (TCIPP), tri(2-chloroethyl) phosphate (TCEP), triethyl phosphate (TEP), and 2-ethylhexyl diphenyl phosphate (EHDPHP), and performed density functional theory (DFT) calculations to clarify the CYP-catalyzed biotransformation of five OPFRs to their diester metabolites. The DFT results show that the reaction mechanism consists of Cα-hydroxylation and O-dealkylation steps, and the biotransformation activities of five OPFRs may follow the order of TCEP ≈ TEP ≈ EHDPHP > TCIPP > TDCIPP. We further performed molecular dynamics (MD) simulations to unravel the binding interactions of five OPFRs in the CYP3A4 isoform. Binding mode analyses demonstrate that CYP3A4-mediated metabolism of TDCIPP, TCIPP, TCEP, and TEP can produce the diester metabolites, while EHDPHP metabolism may generate para-hydroxyEHDPHP as the primary metabolite. Moreover, the EHDPHP and TDCIPP have higher binding potential to CYP3A4 than TCIPP, TCEP, and TEP. This work reports the biotransformation profiles and binding features of five OPFRs in CYP, which can provide meaningful clues for the further studies of the metabolic fates of OPFRs and toxicological effects associated with the relevant metabolites.
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12
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Discovery of first-in-class imidazothiazole-based potent and selective ErbB4 (HER4) kinase inhibitors. Eur J Med Chem 2021; 224:113674. [PMID: 34237622 DOI: 10.1016/j.ejmech.2021.113674] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 11/22/2022]
Abstract
This article reports on novel imidazothiazole derivatives as first-in-class potent and selective ErbB4 (HER4) inhibitors. There are no other reported selective inhibitors of this kinase in the literature, that's why they are considered as first-in-class. In addition, none of the reported non-selective ErbB4 inhibitors possesses imidazothiazole nucleus in its structure. Therefore, there is novelty in this work in both kinase selectivity and chemical structure. Compounds Ik and IIa are the most potent ErbB4 kinase inhibitor (IC50 = 15.24 and 17.70 nM, respectively). Compound Ik showed promising antiproliferative activity. It is selective towards cancer cell lines than normal cells. Its ability to penetrate T-47D cell membrane and inhibit ErbB4 kinase inside the cells has been confirmed. Moreover, both compound Ik and IIa have additional merits such as weak potency against hERG ion channels and against CYP 3A4 and 2D6. Molecular docking and dynamic simulation studies were carried out to explain binding interactions.
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13
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Molecular probes for human cytochrome P450 enzymes: Recent progress and future perspectives. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2020.213600] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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14
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Estrada DF, Kumar A, Campomizzi CS, Jay N. Crystal Structures of Drug-Metabolizing CYPs. Methods Mol Biol 2021; 2342:171-192. [PMID: 34272695 PMCID: PMC10813703 DOI: 10.1007/978-1-0716-1554-6_7] [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] [Indexed: 06/13/2023]
Abstract
The complex enzyme kinetics displayed by drug-metabolizing cytochrome P450 enzymes (CYPs) (see Chapter 9 ) can, in part, be explained by an examination of their crystallographic protein structures. Fortunately, despite low sequence similarity between different families of drug-metabolizing CYPs, there exists a high degree of structural homology within the superfamily. This similarity in the protein fold allows for a direct comparison of the structural features of CYPs that contribute toward differences in substrate binding, heterotropic and homotropic cooperativity, and genetic variability in drug metabolism. In this chapter, we first provide an overview of the nomenclature and the role of structural features that are common in all CYPs. We then apply these definitions to understand the different substrate specificities and functions in the CYP3A, CYP2C, and CYP2D families of enzymes.
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Affiliation(s)
| | - Amit Kumar
- Department of Biochemistry, University at Buffalo, Buffalo, NY, USA
| | | | - Natalie Jay
- Department of Biochemistry, University at Buffalo, Buffalo, NY, USA
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15
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Podlewska S, Latacz G, Łażewska D, Kieć-Kononowicz K, Handzlik J. In silico and in vitro studies on interaction of novel non-imidazole histamine H3R antagonists with CYP3A4. Bioorg Med Chem Lett 2020; 30:127147. [DOI: 10.1016/j.bmcl.2020.127147] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 03/25/2020] [Accepted: 03/26/2020] [Indexed: 12/29/2022]
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16
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Ma G, Yu H, Han C, Jia Y, Wei X, Wang Z. Binding and Metabolism of Brominated Flame Retardant β-1,2-Dibromo-4-(1,2-dibromoethyl)cyclohexane in Human Microsomal P450 Enzymes: Insights from Computational Studies. Chem Res Toxicol 2020; 33:1487-1496. [DOI: 10.1021/acs.chemrestox.0c00076] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Guangcai Ma
- College of Geography and Environmental Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Haiying Yu
- College of Geography and Environmental Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Cenyang Han
- College of Geography and Environmental Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Yue Jia
- College of Geography and Environmental Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Xiaoxuan Wei
- College of Geography and Environmental Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Zhiguo Wang
- Institute of Ageing Research, School of Medicine, Hangzhou Normal University, Hangzhou 311121, China
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Zia A, Imran M, Rashid S. In Silico Exploration of Conformational Dynamics and Novel Inhibitors for Targeting MEF2-Associated Transcriptional Activity. J Chem Inf Model 2020; 60:1892-1909. [PMID: 32031799 DOI: 10.1021/acs.jcim.0c00008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Myocyte enhancer factor 2 (MEF2; MEF2A-MEF2D) transcription factors regulate gene expression in a variety of developmental processes by binding to AT-rich DNA motifs via highly conserved N-terminal extensions known as MADS-box and MEF2 domains. Despite the fact that MEF2 proteins exhibit high similarity at their N-terminal regions and share a common consensus DNA binding motif, their functional preferences may vary significantly in the adjacent regions to the DNA binding core segment. The current study delineates the conformational paradigm, clustered recognition, and comparative DNA binding preferences for MEF2A and MEF2B-specific MADS-box/MEF2 domains at the YTA(A/T)4TAR consensus motif. In both MEF2A and MEF2B proteins, α1-helix plays a crucial role through acquiring more flexibility by attaining loop conformation. In comparison to apo-MEF2, an outward disposition of the distal portion of α1-helix and movement of its proximal part to β1 allows synergistic repositioning of the α1-α2 linker, C-terminal region, and MEF2 domain, resulting in the formation of a hydrophobic groove for DNA binding. In both instances, conformational switching of the helical content is the main contributing factor while preserving the overall β-topology to maintain the inside-out conformation of subdivided α1-helix flip. Multivariate statistical analysis reveals that MEF2B obscures less accessible conformational space for DNA binding as compared to the MEF2A-DNA complex. The presence of similar structural requirements and conserved residues including Arg10, Phe21, and Arg24 in accentuating the MEF2-specific DNA recognition mechanism led us to perform structure-based virtual screening for isolating novel inhibitors that are able to target MEF2-DNA binding regions. The top hits (acetamide, benzamide, carboxamide, and enamide) obtained through preliminary assay were scrutinized to binding potential analysis at the MEF2-DNA binding groove, energy values, absorption, distribution, toxicity, and Lipinski's rule of five assessments. Based on these findings, we propose valuable active drug-like molecules for selective applications against MEF2A and MEF2B. The current study may help in uncovering the atomistic-level mechanistic DNA binding patterns of MEF2 proteins, and data may be valuable in devising effective therapeutic strategies for MEF2-associated disorders.
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Affiliation(s)
- Ayisha Zia
- National Center for Bioinformatics, Quaid-i-Azam University, 45320 Islamabad, Pakistan
| | - Muhammad Imran
- National Center for Bioinformatics, Quaid-i-Azam University, 45320 Islamabad, Pakistan
| | - Sajid Rashid
- National Center for Bioinformatics, Quaid-i-Azam University, 45320 Islamabad, Pakistan
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18
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Ma G, Yu H, Xu X, Geng L, Wei X, Wen J, Wang Z. Molecular Basis for Metabolic Regioselectivity and Mechanism of Cytochrome P450s toward Carcinogenic 4-(Methylnitrosamino)-(3-pyridyl)-1-butanone. Chem Res Toxicol 2020; 33:436-447. [PMID: 31889441 DOI: 10.1021/acs.chemrestox.9b00353] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
As an abundantly present tobacco component, carcinogen 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) has also been detected in atmospheric particulate matter, suggesting the ineluctable exposure risk of this contaminant. NNK metabolic activation by cytochrome P450 enzymes (CYPs) is a prerequisite to exerting its genotoxicity, but the metabolic regioselectivity and mechanism are still unknown. Here the binding feature and regioselectivity of CYPs 1A1, 1A2, 2A6, 2A13, 2B6, and 3A4 toward NNK are unraveled through molecular docking and molecular dynamics (MD) simulations. Binding mode analyses reveal that 1A2 and 2B6 have definite preferences for NNK α-methyl hydroxylation, while the other four CYPs preferentially catalyze α-methylene hydroxylation. The binding affinities between NNK and CYPs evaluated by the binding free energies follow the order 2A13 > 2B6 > 1A2 > 2A6 > 1A1 > 3A4. Density functional theory (DFT) calculations are further performed to characterize the mechanism of NNK biotransformation. Results show that the α-hydroxyNNK generated from α-hydroxylation may undergo nonenzymatic decomposition to form genotoxic diazohydroxide and aldehyde, and further oxidation by P450 to yield nitrosamide, which mainly contributes to NNK toxification capacity. Meanwhile the pyridine N-oxidation and denitrosation of Cα-radical intermediate play an important role in detoxifying NNK. Overall, the present study provides the molecular basis for CYP-catalyzed regioselectivity and mechanism of NNK biotransformation, which can enable the identification of metabolites for assessing the health risk of individual NNK exposure.
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Affiliation(s)
- Guangcai Ma
- College of Geography and Environmental Sciences , Zhejiang Normal University , Jinhua 321004 , China
| | - Haiying Yu
- College of Geography and Environmental Sciences , Zhejiang Normal University , Jinhua 321004 , China
| | - Xiaoqin Xu
- College of Geography and Environmental Sciences , Zhejiang Normal University , Jinhua 321004 , China
| | - Liming Geng
- College of Geography and Environmental Sciences , Zhejiang Normal University , Jinhua 321004 , China
| | - Xiaoxuan Wei
- College of Geography and Environmental Sciences , Zhejiang Normal University , Jinhua 321004 , China
| | - Jiale Wen
- College of Geography and Environmental Sciences , Zhejiang Normal University , Jinhua 321004 , China
| | - Zhiguo Wang
- Institute of Ageing Research, School of Medicine , Hangzhou Normal University , Hangzhou 311121 , China
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Abstract
![]()
A correct estimate
of ligand binding modes and a ratio of their
occupancies is crucial for calculations of binding free energies.
The newly developed method BLUES combines molecular dynamics with
nonequilibrium candidate Monte Carlo. Nonequilibrium candidate Monte
Carlo generates a plethora of possible binding modes and molecular
dynamics enables the system to relax. We used BLUES to investigate
binding modes of caffeine in the active site of its metabolizing enzyme
Cytochrome P450 1A2 with the aim of elucidating metabolite-formation
profiles at different concentrations. Because the activation energies
of all sites of metabolism do not show a clear preference for one
metabolite over the others, the orientations in the active site must
play a key role. In simulations with caffeine located in a spacious
pocket above the I-helix, it points N3 and N1 to the heme iron, whereas
in simulations where caffeine is in close proximity to the heme N7
and C8 are preferably oriented toward the heme iron. We propose a
mechanism where at low caffeine concentrations caffeine binds to the
upper part of the active site, leading to formation of the main metabolite
paraxanthine. On the other hand, at high concentrations two molecules
are located in the active site, forcing one molecule into close proximity
to the heme and yielding metabolites theophylline and trimethyluretic
acid. Our results offer an explanation of previously published experimental
results.
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Affiliation(s)
- Zuzana Jandova
- Institute of Molecular Modeling and Simulation , University of Natural Resources and Life Sciences, Vienna , 1180 Vienna , Austria
| | | | | | | | - Chris Oostenbrink
- Institute of Molecular Modeling and Simulation , University of Natural Resources and Life Sciences, Vienna , 1180 Vienna , Austria
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20
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Dmitriev AV, Lagunin AA, Karasev DА, Rudik AV, Pogodin PV, Filimonov DA, Poroikov VV. Prediction of Drug-Drug Interactions Related to Inhibition or Induction of Drug-Metabolizing Enzymes. Curr Top Med Chem 2019; 19:319-336. [PMID: 30674264 DOI: 10.2174/1568026619666190123160406] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 01/02/2019] [Accepted: 01/07/2019] [Indexed: 02/07/2023]
Abstract
Drug-drug interaction (DDI) is the phenomenon of alteration of the pharmacological activity of a drug(s) when another drug(s) is co-administered in cases of so-called polypharmacy. There are three types of DDIs: pharmacokinetic (PK), pharmacodynamic, and pharmaceutical. PK is the most frequent type of DDI, which often appears as a result of the inhibition or induction of drug-metabolising enzymes (DME). In this review, we summarise in silico methods that may be applied for the prediction of the inhibition or induction of DMEs and describe appropriate computational methods for DDI prediction, showing the current situation and perspectives of these approaches in medicinal and pharmaceutical chemistry. We review sources of information on DDI, which can be used in pharmaceutical investigations and medicinal practice and/or for the creation of computational models. The problem of the inaccuracy and redundancy of these data are discussed. We provide information on the state-of-the-art physiologically- based pharmacokinetic modelling (PBPK) approaches and DME-based in silico methods. In the section on ligand-based methods, we describe pharmacophore models, molecular field analysis, quantitative structure-activity relationships (QSAR), and similarity analysis applied to the prediction of DDI related to the inhibition or induction of DME. In conclusion, we discuss the problems of DDI severity assessment, mention factors that influence severity, and highlight the issues, perspectives and practical using of in silico methods.
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Affiliation(s)
| | - Alexey A Lagunin
- Institute of Biomedical Chemistry, Moscow, Russian Federation.,Pirogov Russian National Research Medical University, Moscow, RussiaN Federation
| | | | | | - Pavel V Pogodin
- Institute of Biomedical Chemistry, Moscow, Russian Federation
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21
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Spinello A, Vecile E, Abbate A, Dobrina A, Magistrato A. How Can Interleukin-1 Receptor Antagonist Modulate Distinct Cell Death Pathways? J Chem Inf Model 2019; 59:351-359. [PMID: 30586302 DOI: 10.1021/acs.jcim.8b00565] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Multiple mechanisms of cell death exist (apoptosis, necroptosis, pyroptosis) and the subtle balance of several distinct proteins and inhibitors tightly regulates the cell fate toward one or the other pathway. Here, by combining coimmunoprecipitation, enzyme assays, and molecular simulations, we ascribe a new role, within this entangled regulatory network, to the interleukin-1 receptor antagonist (IL-1Ra). Our study enlightens that IL-1Ra, which usually inhibits the inflammatory effects of IL-1α/β by binding to IL-1 receptor, under advanced pathological states prevents apoptosis and/or necroptosis by noncompetitively inhibiting the activity of caspase-8 and -9. Consensus docking, followed by cumulative 10 μs of molecular dynamics simulations unprecedentedly reveal that IL-1Ra binds both caspases at their dimeric interface, preventing, in this manner, the formation of their catalytically/signaling active form. The resulting IL-1Ra/caspase-8(9) adducts are stabilized by hydrophobic and by few key hydrogen bonding interactions, formed by residues fully conserved across distinct caspases (-3, -6, -7, -8, and -9), and closely resemble the binding mode of the caspases inhibitors XIAP (X-linked inhibitor of apoptosis) and c-FLIP (cellular FLICE-like inhibitory protein). Tight regulation of the different forms of cell death has a major impact on distinct human illnesses (i.e., cancer, neurodegeneration, ischemic injury, atherosclerosis, viral/bacterial infections, and immune reaction). Hence, our study, pinpointing IL-1Ra as new actor of the intricate cell death regulatory network and gaining an atomic-scale understanding of its mechanism may open new avenues toward innovative therapeutic strategies to tackle major human diseases.
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Affiliation(s)
- Angelo Spinello
- CNR-IOM-Democritos c/o International School for Advanced Studies (SISSA) , via Bonomea 265 , 34136 , Trieste , Italy
| | - Elena Vecile
- Department of Life Sciences , University of Trieste , via Giorgieri 1 , I-34127 , Trieste , Italy
| | - Antonio Abbate
- Victoria Johnson Research Laboratory and VCU Pauley Heart Center , Virginia Commonwealth University , 1200 E Broad St , PO Box 980281, Richmond , Virginia United States of America
| | - Aldo Dobrina
- Department of Life Sciences , University of Trieste , via Giorgieri 1 , I-34127 , Trieste , Italy
| | - Alessandra Magistrato
- CNR-IOM-Democritos c/o International School for Advanced Studies (SISSA) , via Bonomea 265 , 34136 , Trieste , Italy
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Ghassabian S, Gillani TB, Rawling T, Crettol S, Nair PC, Murray M. Sorafenib N-Oxide Is an Inhibitor of Human Hepatic CYP3A4. AAPS JOURNAL 2019; 21:15. [DOI: 10.1208/s12248-018-0262-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 08/30/2018] [Indexed: 12/31/2022]
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23
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Interaction energy profile for diphenyl diselenide in complex with δ-aminolevulinic acid dehydratase enzyme using quantum calculations and a molecular fragmentation method. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.comtox.2018.05.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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24
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Gladovic M, Spaninger E, Bren U. Nucleic Bases Alkylation with Acrylonitrile and Cyanoethylene Oxide: A Computational Study. Chem Res Toxicol 2018; 31:97-104. [DOI: 10.1021/acs.chemrestox.7b00268] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Martin Gladovic
- Faculty
of Chemistry and Chemical Technology, University of Maribor, Smetanova
17, SI-2000 Maribor, Slovenia
- Faculty
of Chemistry and Chemical Technology, University of Ljubljana, Vecna pot
113, SI-1000 Ljubljana, Slovenia
| | - Eva Spaninger
- Faculty
of Chemistry and Chemical Technology, University of Maribor, Smetanova
17, SI-2000 Maribor, Slovenia
| | - Urban Bren
- Faculty
of Chemistry and Chemical Technology, University of Maribor, Smetanova
17, SI-2000 Maribor, Slovenia
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
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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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26
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Sun DR, Zheng QC, Zhang HX. Molecular dynamics investigation of stereoselective inhibition mechanism of HIF-2α/ARNT heterodimer. J Mol Recognit 2017; 31. [PMID: 28990233 DOI: 10.1002/jmr.2675] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 08/27/2017] [Accepted: 09/05/2017] [Indexed: 12/19/2022]
Abstract
Hypoxia-inducible factors (HIFs) are heterodimeric transcription factors related with the onset and progression of solid tumors. Studies demonstrated a class of tetrazole containing chiral inhibitors could stereoselectively disrupt the HIF-2 dimerization and reduce the target gene expression. However, the dynamical features and structural motifs of the HIF-2 heterodimer caused by the binding of enantiomers have not been rationalized at the atomistic level. In this work, molecular dynamics (MD) simulations combined with adaptive steered MD (ASMD) simulations were used to investigate stereoselective interrupting mechanism of HIF-2. Our results decipher that the binding of ligand A (S, R)-24 begets the significant conformation changes of β-sheets and interrupts the HIF-2α/ARNT heterodimerization, which may be attributed to the disruption of the hydrogen bond and salt bridge interactions formed by the 4 foremost residues (Asp240, Arg247, Glu362, and Arg366) and the destruction of hydrophobic interactions on the binding interface. By contrast, the binding of ligand B (R, S)-24 does not disrupt protein dimerization and causes the motion of Fα helix in HIF-2α PAS-B domain to further change the major tunnel for ligand ingress and engress. The present work provides important molecular-level insight into the effect of the binding enantiomers on HIF-2 heterodimerization and bridges the gap between theory and the experimental results, which may conduce to develop highly potent antagonists for intervening the HIF-2-driven tumors.
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Affiliation(s)
- Dong-Ru Sun
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Jilin University, Changchun, China
| | - Qing-Chuan Zheng
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, Jilin University, Changchun, China.,Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Jilin University, Changchun, China
| | - Hong-Xing Zhang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Jilin University, Changchun, China
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Rimac H, Dufour C, Debeljak Ž, Zorc B, Bojić M. Warfarin and Flavonoids Do Not Share the Same Binding Region in Binding to the IIA Subdomain of Human Serum Albumin. Molecules 2017; 22:molecules22071153. [PMID: 28696372 PMCID: PMC6152318 DOI: 10.3390/molecules22071153] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Accepted: 07/07/2017] [Indexed: 01/16/2023] Open
Abstract
Human serum albumin (HSA) binds a variety of xenobiotics, including flavonoids and warfarin. The binding of another ligand to the IIA binding site on HSA can cause warfarin displacement and potentially the elevation of its free concentration in blood. Studies dealing with flavonoid-induced warfarin displacement from HSA provided controversial results: estimated risk of displacement ranged from none to serious. To resolve these controversies, in vitro study of simultaneous binding of warfarin and eight different flavonoid aglycons and glycosides to HSA was carried out by fluorescence spectroscopy as well as molecular docking. Results show that warfarin and flavonoids do not share the same binding region in binding to HSA. Interactions were only observed at high warfarin concentrations not attainable under recommended dosing regimes. Docking experiments show that flavonoid aglycons and glycosides do not bind at warfarin high affinity sites, but rather to different regions within the IIA HSA subdomain. Thus, the risk of clinically significant warfarin-flavonoid interaction in binding to HSA should be regarded as negligible.
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Affiliation(s)
- Hrvoje Rimac
- Department of Medicinal Chemistry, University of Zagreb, Faculty of Pharmacy and Biochemistry, Ante Kovačića 1, 10000 Zagreb, Croatia.
| | - Claire Dufour
- UMR408 SQPOV, Safety and Quality of Plant Products, INRA, Avignon University, 228 Route de l'Aérodrome, 84000 Avignon, France.
| | - Željko Debeljak
- Institute of Clinical Laboratory Diagnostics, Osijek University Hospital Center, Josipa Huttlera 4, 31000 Osijek, Croatia.
- Department of Pharmacology, School of Medicine, University of Osijek, Cara Hadrijana 10/E, 31000 Osijek, Croatia.
| | - Branka Zorc
- Department of Medicinal Chemistry, University of Zagreb, Faculty of Pharmacy and Biochemistry, Ante Kovačića 1, 10000 Zagreb, Croatia.
| | - Mirza Bojić
- Department of Medicinal Chemistry, University of Zagreb, Faculty of Pharmacy and Biochemistry, Ante Kovačića 1, 10000 Zagreb, Croatia.
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Challenges in assignment of allosteric effects in cytochrome P450-catalyzed substrate oxidations to structural dynamics in the hemoprotein architecture. J Inorg Biochem 2017; 167:100-115. [DOI: 10.1016/j.jinorgbio.2016.11.025] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 10/17/2016] [Accepted: 11/22/2016] [Indexed: 12/19/2022]
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29
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Danielson ML, Hu B, Shen J, Desai PV. In Silico ADME Techniques Used in Early-Phase Drug Discovery. TRANSLATING MOLECULES INTO MEDICINES 2017. [DOI: 10.1007/978-3-319-50042-3_4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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30
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Exploring Molecular Mechanisms of Paradoxical Activation in the BRAF Kinase Dimers: Atomistic Simulations of Conformational Dynamics and Modeling of Allosteric Communication Networks and Signaling Pathways. PLoS One 2016; 11:e0166583. [PMID: 27861609 PMCID: PMC5115767 DOI: 10.1371/journal.pone.0166583] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 10/31/2016] [Indexed: 12/14/2022] Open
Abstract
The recent studies have revealed that most BRAF inhibitors can paradoxically induce kinase activation by promoting dimerization and enzyme transactivation. Despite rapidly growing number of structural and functional studies about the BRAF dimer complexes, the molecular basis of paradoxical activation phenomenon is poorly understood and remains largely hypothetical. In this work, we have explored the relationships between inhibitor binding, protein dynamics and allosteric signaling in the BRAF dimers using a network-centric approach. Using this theoretical framework, we have combined molecular dynamics simulations with coevolutionary analysis and modeling of the residue interaction networks to determine molecular determinants of paradoxical activation. We have investigated functional effects produced by paradox inducer inhibitors PLX4720, Dabrafenib, Vemurafenib and a paradox breaker inhibitor PLX7904. Functional dynamics and binding free energy analyses of the BRAF dimer complexes have suggested that negative cooperativity effect and dimer-promoting potential of the inhibitors could be important drivers of paradoxical activation. We have introduced a protein structure network model in which coevolutionary residue dependencies and dynamic maps of residue correlations are integrated in the construction and analysis of the residue interaction networks. The results have shown that coevolutionary residues in the BRAF structures could assemble into independent structural modules and form a global interaction network that may promote dimerization. We have also found that BRAF inhibitors could modulate centrality and communication propensities of global mediating centers in the residue interaction networks. By simulating allosteric communication pathways in the BRAF structures, we have determined that paradox inducer and breaker inhibitors may activate specific signaling routes that correlate with the extent of paradoxical activation. While paradox inducer inhibitors may facilitate a rapid and efficient communication via an optimal single pathway, the paradox breaker may induce a broader ensemble of suboptimal and less efficient communication routes. The central finding of our study is that paradox breaker PLX7904 could mimic structural, dynamic and network features of the inactive BRAF-WT monomer that may be required for evading paradoxical activation. The results of this study rationalize the existing structure-functional experiments by offering a network-centric rationale of the paradoxical activation phenomenon. We argue that BRAF inhibitors that amplify dynamic features of the inactive BRAF-WT monomer and intervene with the allosteric interaction networks may serve as effective paradox breakers in cellular environment.
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31
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Elucidating a chemical defense mechanism of Antarctic sponges: A computational study. J Mol Graph Model 2016; 71:104-115. [PMID: 27894019 DOI: 10.1016/j.jmgm.2016.11.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 10/21/2016] [Accepted: 11/06/2016] [Indexed: 11/22/2022]
Abstract
In 2000, a novel secondary metabolite (erebusinone, Ereb) was isolated from the Antarctic sea sponge, Isodictya erinacea. The bioactivity of Ereb was investigated, and it was found to inhibit molting when fed to the arthropod species Orchomene plebs. Xanthurenic acid (XA) is a known endogenous molt regulator present in arthropods. Experimental studies have confirmed that XA inhibits molting by binding to either (or both) of two P450 enzymes (CYP315a1 or CYP314a1) that are responsible for the final two hydroxylations in the production of the molt-inducing hormone, 20-hydroxyecdysone (20E). The lack of crystal structures and biochemical assays for CYP315a1 or CYP314a1, has prevented further experimental exploration of XA and Ereb's molt inhibition mechanisms. Herein, a wide array of computational techniques - homology modeling, molecular dynamics simulations, binding site bioinformatics, flexible receptor-flexible ligand docking, and molecular mechanics-generalized Born surface area calculations - have been employed to elucidate the structure-function relationships between the aforementioned P450s and the two described small molecule inhibitors (Ereb and XA). Results indicate that Ereb likely targets CYP315a1 by interacting with a network of aromatic residues in the binding site, while XA may inhibit both CYP315a1 and CYP314a1 because of its aromatic, as well as charged nature.
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32
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Ma X, Meng H, Lai L. Motions of Allosteric and Orthosteric Ligand-Binding Sites in Proteins are Highly Correlated. J Chem Inf Model 2016; 56:1725-33. [DOI: 10.1021/acs.jcim.6b00039] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Xiaomin Ma
- Center for Quantitative Biology, ‡BNLMS, State Key
Laboratory for Structural
Chemistry of Unstable and Stable Species, College of Chemistry and
Molecular Engineering, and §Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Hu Meng
- Center for Quantitative Biology, ‡BNLMS, State Key
Laboratory for Structural
Chemistry of Unstable and Stable Species, College of Chemistry and
Molecular Engineering, and §Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Luhua Lai
- Center for Quantitative Biology, ‡BNLMS, State Key
Laboratory for Structural
Chemistry of Unstable and Stable Species, College of Chemistry and
Molecular Engineering, and §Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
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33
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Stetz G, Verkhivker GM. Probing Allosteric Inhibition Mechanisms of the Hsp70 Chaperone Proteins Using Molecular Dynamics Simulations and Analysis of the Residue Interaction Networks. J Chem Inf Model 2016; 56:1490-517. [DOI: 10.1021/acs.jcim.5b00755] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Gabrielle Stetz
- Graduate
Program in Computational and Data Sciences, Department of Computational
Sciences, Schmid College of Science and Technology, Chapman University, One University Drive, Orange, California 92866, United States
| | - Gennady M. Verkhivker
- Graduate
Program in Computational and Data Sciences, Department of Computational
Sciences, Schmid College of Science and Technology, Chapman University, One University Drive, Orange, California 92866, United States
- Chapman University School of Pharmacy, Irvine, California 92618, United States
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34
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Brglez Mojzer E, Knez Hrnčič M, Škerget M, Knez Ž, Bren U. Polyphenols: Extraction Methods, Antioxidative Action, Bioavailability and Anticarcinogenic Effects. Molecules 2016; 21:molecules21070901. [PMID: 27409600 PMCID: PMC6273793 DOI: 10.3390/molecules21070901] [Citation(s) in RCA: 493] [Impact Index Per Article: 61.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 06/28/2016] [Accepted: 07/05/2016] [Indexed: 02/06/2023] Open
Abstract
Being secondary plant metabolites, polyphenols represent a large and diverse group of substances abundantly present in a majority of fruits, herbs and vegetables. The current contribution is focused on their bioavailability, antioxidative and anticarcinogenic properties. An overview of extraction methods is also given, with supercritical fluid extraction highlighted as a promising eco-friendly alternative providing exceptional separation and protection from degradation of unstable polyphenols. The protective role of polyphenols against reactive oxygen and nitrogen species, UV light, plant pathogens, parasites and predators results in several beneficial biological activities giving rise to prophylaxis or possibly even to a cure for several prevailing human diseases, especially various cancer types. Omnipresence, specificity of the response and the absence of or low toxicity are crucial advantages of polyphenols as anticancer agents. The main problem represents their low bioavailability and rapid metabolism. One of the promising solutions lies in nanoformulation of polyphenols that prevents their degradation and thus enables significantly higher concentrations to reach the target cells. Another, more practiced, solution is the use of mixtures of various polyphenols that bring synergistic effects, resulting in lowering of the required therapeutic dose and in multitargeted action. The combination of polyphenols with existing drugs and therapies also shows promising results and significantly reduces their toxicity.
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Affiliation(s)
- Eva Brglez Mojzer
- Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova ulica 17, SI-2000 Maribor, Slovenia.
| | - Maša Knez Hrnčič
- Laboratory of Separation Processes and Product Design, Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova ulica 17, SI-2000 Maribor, Slovenia.
| | - Mojca Škerget
- Laboratory of Separation Processes and Product Design, Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova ulica 17, SI-2000 Maribor, Slovenia.
| | - Željko Knez
- Laboratory of Separation Processes and Product Design, Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova ulica 17, SI-2000 Maribor, Slovenia.
| | - Urban Bren
- Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova ulica 17, SI-2000 Maribor, Slovenia.
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35
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Lonsdale R, Fort RM, Rydberg P, Harvey JN, Mulholland AJ. Quantum Mechanics/Molecular Mechanics Modeling of Drug Metabolism: Mexiletine N-Hydroxylation by Cytochrome P450 1A2. Chem Res Toxicol 2016; 29:963-71. [DOI: 10.1021/acs.chemrestox.5b00514] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Richard Lonsdale
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
| | - Rachel M. Fort
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
| | - Patrik Rydberg
- Department
of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Jeremy N. Harvey
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
| | - Adrian J. Mulholland
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
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36
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Nair PC, McKinnon RA, Miners JO. Cytochrome P450 structure–function: insights from molecular dynamics simulations. Drug Metab Rev 2016; 48:434-52. [DOI: 10.1080/03602532.2016.1178771] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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37
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Jeřábek P, Florián J, Martínek V. Membrane-Anchored Cytochrome P450 1A2–Cytochrome b5 Complex Features an X-Shaped Contact between Antiparallel Transmembrane Helices. Chem Res Toxicol 2016; 29:626-36. [DOI: 10.1021/acs.chemrestox.5b00349] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Petr Jeřábek
- Department
of Biochemistry, Faculty of Science, Charles University in Prague, Albertov 2030, 128 43 Prague 2, Czech Republic
| | - Jan Florián
- Department
of Chemistry and Biochemistry, Loyola University Chicago, 1032 West Sheridan
Road, Chicago, Illinois 60660, United States
| | - Václav Martínek
- Department
of Biochemistry, Faculty of Science, Charles University in Prague, Albertov 2030, 128 43 Prague 2, Czech Republic
- Department of Teaching and Didactics of Chemistry, Faculty of Science, Charles University in Prague, Albertov 3, 128 43 Prague 2, Czech Republic
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38
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Zhao Z, Martin C, Fan R, Bourne PE, Xie L. Drug repurposing to target Ebola virus replication and virulence using structural systems pharmacology. BMC Bioinformatics 2016; 17:90. [PMID: 26887654 PMCID: PMC4757998 DOI: 10.1186/s12859-016-0941-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2015] [Accepted: 02/10/2016] [Indexed: 01/09/2023] Open
Abstract
Background The recent outbreak of Ebola has been cited as the largest in history. Despite this global health crisis, few drugs are available to efficiently treat Ebola infections. Drug repurposing provides a potentially efficient solution to accelerating the development of therapeutic approaches in response to Ebola outbreak. To identify such candidates, we use an integrated structural systems pharmacology pipeline which combines proteome-scale ligand binding site comparison, protein-ligand docking, and Molecular Dynamics (MD) simulation. Results One thousand seven hundred and sixty-six FDA-approved drugs and 259 experimental drugs were screened to identify those with the potential to inhibit the replication and virulence of Ebola, and to determine the binding modes with their respective targets. Initial screening has identified a number of promising hits. Notably, Indinavir; an HIV protease inhibitor, may be effective in reducing the virulence of Ebola. Additionally, an antifungal (Sinefungin) and several anti-viral drugs (e.g. Maraviroc, Abacavir, Telbivudine, and Cidofovir) may inhibit Ebola RNA-directed RNA polymerase through targeting the MTase domain. Conclusions Identification of safe drug candidates is a crucial first step toward the determination of timely and effective therapeutic approaches to address and mitigate the impact of the Ebola global crisis and future outbreaks of pathogenic diseases. Further in vitro and in vivo testing to evaluate the anti-Ebola activity of these drugs is warranted. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-0941-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zheng Zhao
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei, P. R. China.,National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Che Martin
- The Graduate Center, The City University of New York, New York, USA
| | - Raymond Fan
- Department of Chemistry, Hunter College, The City University of New York, New York, USA
| | - Philip E Bourne
- Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Lei Xie
- The Graduate Center, The City University of New York, New York, USA. .,Department of Computer Science, Hunter College, The City University of New York, New York, USA.
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39
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Affiliation(s)
- A. Subha Mahadevi
- Centre for Molecular Modelling, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad, India 500607
| | - G. Narahari Sastry
- Centre for Molecular Modelling, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad, India 500607
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40
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Waldner BJ, Fuchs JE, Huber RG, von Grafenstein S, Schauperl M, Kramer C, Liedl KR. Quantitative Correlation of Conformational Binding Enthalpy with Substrate Specificity of Serine Proteases. J Phys Chem B 2016; 120:299-308. [PMID: 26709959 PMCID: PMC4724848 DOI: 10.1021/acs.jpcb.5b10637] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
![]()
Members of the same protease family
show different substrate specificity,
even if they share identical folds, depending on the physiological
processes they are part of. Here, we investigate the key factors for
subpocket and global specificity of factor Xa, elastase, and granzyme
B which despite all being serine proteases and sharing the chymotrypsin-fold
show distinct substrate specificity profiles. We determined subpocket
interaction potentials with GRID for static X-ray structures and an in silico generated ensemble of conformations. Subpocket
interaction potentials determined for static X-ray structures turned
out to be insufficient to explain serine protease specificity for
all subpockets. Therefore, we generated conformational ensembles using
molecular dynamics simulations. We identified representative binding
site conformations using distance-based hierarchical agglomerative
clustering and determined subpocket interaction potentials for each
representative conformation of the binding site. Considering the differences
in subpocket interaction potentials for these representative conformations
as well as their abundance allowed us to quantitatively explain subpocket
specificity for the nonprime side for all three example proteases
on a molecular level. The methods to identify key regions determining
subpocket specificity introduced in this study are directly applicable
to other serine proteases, and the results provide starting points
for new strategies in rational drug design.
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Affiliation(s)
- Birgit J Waldner
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck , Innrain 82, 6020 Innsbruck, Austria
| | - Julian E Fuchs
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck , Innrain 82, 6020 Innsbruck, Austria.,Centre for Molecular Informatics, Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Roland G Huber
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck , Innrain 82, 6020 Innsbruck, Austria.,Bioinformatics Institute (BII), Agency of Science, Technology and Research (A* STAR) , 30 Biopolis Street, Matrix#07-01, 138671 Singapore
| | - Susanne von Grafenstein
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck , Innrain 82, 6020 Innsbruck, Austria
| | - Michael Schauperl
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck , Innrain 82, 6020 Innsbruck, Austria
| | - Christian Kramer
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck , Innrain 82, 6020 Innsbruck, Austria
| | - Klaus R Liedl
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck , Innrain 82, 6020 Innsbruck, Austria
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41
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Barman A, Smitherman C, Souffrant M, Gadda G, Hamelberg D. Conserved Hydration Sites in Pin1 Reveal a Distinctive Water Recognition Motif in Proteins. J Chem Inf Model 2015; 56:139-47. [DOI: 10.1021/acs.jcim.5b00560] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Arghya Barman
- Departments
of Chemistry and ‡Biology and the §Centers for Diagnostics and Therapeutics and ∥Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Crystal Smitherman
- Departments
of Chemistry and ‡Biology and the §Centers for Diagnostics and Therapeutics and ∥Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Michael Souffrant
- Departments
of Chemistry and ‡Biology and the §Centers for Diagnostics and Therapeutics and ∥Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Giovanni Gadda
- Departments
of Chemistry and ‡Biology and the §Centers for Diagnostics and Therapeutics and ∥Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Donald Hamelberg
- Departments
of Chemistry and ‡Biology and the §Centers for Diagnostics and Therapeutics and ∥Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302-3965, United States
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42
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Rungnim C, Phunpee S, Kunaseth M, Namuangruk S, Rungsardthong K, Rungrotmongkol T, Ruktanonchai U. Co-solvation effect on the binding mode of the α-mangostin/β-cyclodextrin inclusion complex. Beilstein J Org Chem 2015; 11:2306-2317. [PMID: 26734079 PMCID: PMC4685766 DOI: 10.3762/bjoc.11.251] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 11/06/2015] [Indexed: 01/23/2023] Open
Abstract
Cyclodextrins (CDs) have been extensively utilized as host molecules to enhance the solubility, stability and bioavailability of hydrophobic drug molecules through the formation of inclusion complexes. It was previously reported that the use of co-solvents in such studies may result in ternary (host:guest:co-solvent) complex formation. The objective of this work was to investigate the effect of ethanol as a co-solvent on the inclusion complex formation between α-mangostin (α-MGS) and β-CD, using both experimental and theoretical studies. Experimental phase-solubility studies were carried out in order to assess complex formation, with the mechanism of association being probed using a mathematical model. It was found that α-MGS was poorly soluble at low ethanol concentrations (0–10% v/v), but higher concentrations (10–40% v/v) resulted in better α-MGS solubility at all β-CD concentrations studied (0–10 mM). From the equilibrium constant calculation, the inclusion complex is still a binary complex (1:1), even in the presence of ethanol. The results from our theoretical study confirm that the binding mode is binary complex and the presence of ethanol as co-solvent enhances the solubility of α-MGS with some effects on the binding affinity with β-CD, depending on the concentration employed.
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Affiliation(s)
- Chompoonut Rungnim
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani 12120, Thailand
| | - Sarunya Phunpee
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani 12120, Thailand
| | - Manaschai Kunaseth
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani 12120, Thailand
| | - Supawadee Namuangruk
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani 12120, Thailand
| | - Kanin Rungsardthong
- Faculty of Pharmacy Thammasat University, Rangsit Center, Pathumthani 12120 Thailand
| | - Thanyada Rungrotmongkol
- Structural and Computational Biology Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.,Ph.D. Program in Bioinformatics and Computational Biology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Uracha Ruktanonchai
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani 12120, Thailand
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Graf MMH, Sucharitakul J, Bren U, Chu DB, Koellensperger G, Hann S, Furtmüller PG, Obinger C, Peterbauer CK, Oostenbrink C, Chaiyen P, Haltrich D. Reaction of pyranose dehydrogenase from Agaricus meleagris with its carbohydrate substrates. FEBS J 2015; 282:4218-41. [PMID: 26284701 PMCID: PMC4950071 DOI: 10.1111/febs.13417] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 08/04/2015] [Accepted: 08/13/2015] [Indexed: 01/25/2023]
Abstract
Monomeric Agaricus meleagris pyranose dehydrogenase (AmPDH) belongs to the glucose-methanol-choline family of oxidoreductases. An FAD cofactor is covalently tethered to His103 of the enzyme. AmPDH can double oxidize various mono- and oligosaccharides at different positions (C1 to C4). To study the structure/function relationship of selected active-site residues of AmPDH pertaining to substrate (carbohydrate) turnover in more detail, several active-site variants were generated, heterologously expressed in Pichia pastoris, and characterized by biochemical, biophysical and computational means. The crystal structure of AmPDH shows two active-site histidines, both of which could take on the role as the catalytic base in the reductive half-reaction. Steady-state kinetics revealed that His512 is the only catalytic base because H512A showed a reduction in (kcat /KM )glucose by a factor of 10(5) , whereas this catalytic efficiency was reduced by two or three orders of magnitude for His556 variants (H556A, H556N). This was further corroborated by transient-state kinetics, where a comparable decrease in the reductive rate constant was observed for H556A, whereas the rate constant for the oxidative half-reaction (using benzoquinone as substrate) was increased for H556A compared to recombinant wild-type AmPDH. Steady-state kinetics furthermore indicated that Gln392, Tyr510, Val511 and His556 are important for the catalytic efficiency of PDH. Molecular dynamics (MD) simulations and free energy calculations were used to predict d-glucose oxidation sites, which were validated by GC-MS measurements. These simulations also suggest that van der Waals interactions are the main driving force for substrate recognition and binding.
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Affiliation(s)
- Michael M H Graf
- Food Biotechnology Laboratory, Department of Food Science and Technology, University of Natural Resources and Life Sciences Vienna (BOKU), Austria
| | - Jeerus Sucharitakul
- Department of Biochemistry, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand
| | - Urban Bren
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences Vienna (BOKU), Austria
- Laboratory for Physical Chemistry and Chemical Thermodynamics, Faculty of Chemistry and Chemical Technology, University of Maribor, Slovenia
| | - Dinh Binh Chu
- Division of Analytical Chemistry, Department of Chemistry, University of Natural Resources and Life Sciences Vienna (BOKU), Austria
- School of Chemical Engineering, Department of Analytical Chemistry, Hanoi University of Science and Technology, Hanoi, Vietnam
| | - Gunda Koellensperger
- Institute of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Austria
| | - Stephan Hann
- Division of Analytical Chemistry, Department of Chemistry, University of Natural Resources and Life Sciences Vienna (BOKU), Austria
| | - Paul G Furtmüller
- Division of Biochemistry, Department of Chemistry, University of Natural Resources and Life Sciences Vienna (BOKU), Austria
| | - Christian Obinger
- Division of Biochemistry, Department of Chemistry, University of Natural Resources and Life Sciences Vienna (BOKU), Austria
| | - Clemens K Peterbauer
- Food Biotechnology Laboratory, Department of Food Science and Technology, University of Natural Resources and Life Sciences Vienna (BOKU), Austria
| | - Chris Oostenbrink
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences Vienna (BOKU), Austria
| | - Pimchai Chaiyen
- Department of Biochemistry and Center of Excellence in Protein Structure and Function, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Dietmar Haltrich
- Food Biotechnology Laboratory, Department of Food Science and Technology, University of Natural Resources and Life Sciences Vienna (BOKU), Austria
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Kassem S, Ahmed M, El-Sheikh S, Barakat KH. Entropy in bimolecular simulations: A comprehensive review of atomic fluctuations-based methods. J Mol Graph Model 2015; 62:105-117. [PMID: 26407139 DOI: 10.1016/j.jmgm.2015.09.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 09/06/2015] [Accepted: 09/10/2015] [Indexed: 11/17/2022]
Abstract
Entropy of binding constitutes a major, and in many cases a detrimental, component of the binding affinity in biomolecular interactions. While the enthalpic part of the binding free energy is easier to calculate, estimating the entropy of binding is further more complicated. A precise evaluation of entropy requires a comprehensive exploration of the complete phase space of the interacting entities. As this task is extremely hard to accomplish in the context of conventional molecular simulations, calculating entropy has involved many approximations. Most of these golden standard methods focused on developing a reliable estimation of the conformational part of the entropy. Here, we review these methods with a particular emphasis on the different techniques that extract entropy from atomic fluctuations. The theoretical formalisms behind each method is explained highlighting its strengths as well as its limitations, followed by a description of a number of case studies for each method. We hope that this brief, yet comprehensive, review provides a useful tool to understand these methods and realize the practical issues that may arise in such calculations.
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Affiliation(s)
- Summer Kassem
- Department of Physics, American University in Cairo, Cairo, Egypt
| | - Marawan Ahmed
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada
| | - Salah El-Sheikh
- Department of Physics, American University in Cairo, Cairo, Egypt
| | - Khaled H Barakat
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada; Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada; Li Ka Shing Applied Virology Institute, University of Alberta, Edmonton, AB, Canada.
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45
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Identification of Protein–Protein Interactions by Detecting Correlated Mutation at the Interface. J Chem Inf Model 2015; 55:2042-9. [DOI: 10.1021/acs.jcim.5b00320] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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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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47
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Pi-pi Stacking Mediated Cooperative Mechanism for Human Cytochrome P450 3A4. Molecules 2015; 20:7558-73. [PMID: 25919277 PMCID: PMC6272561 DOI: 10.3390/molecules20057558] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 03/18/2015] [Accepted: 03/19/2015] [Indexed: 11/17/2022] Open
Abstract
Human Cytochrome P450 3A4 (CYP3A4) is an important member of the cytochrome P450 superfamily with responsibility for metabolizing ~50% of clinical drugs. Experimental evidence showed that CYP3A4 can adopt multiple substrates in its active site to form a cooperative binding model, accelerating substrate metabolism efficiency. In the current study, we constructed both normal and cooperative binding models of human CYP3A4 with antifungal drug ketoconazoles (KLN). Molecular dynamics simulation and free energy calculation were then carried out to study the cooperative binding mechanism. Our simulation showed that the second KLN in the cooperative binding model had a positive impact on the first one binding in the active site by two significant pi-pi stacking interactions. The first one was formed by Phe215, functioning to position the first KLN in a favorable orientation in the active site for further metabolism reactions. The second one was contributed by Phe304. This pi-pi stacking was enhanced in the cooperative binding model by the parallel conformation between the aromatic rings in Phe304 and the dioxolan moiety of the first KLN. These findings can provide an atomic insight into the cooperative binding in CYP3A4, revealing a novel pi-pi stacking mechanism for drug-drug interactions.
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Navrátilová V, Paloncýová M, Kajšová M, Berka K, Otyepka M. Effect of Cholesterol on the Structure of Membrane-Attached Cytochrome P450 3A4. J Chem Inf Model 2015; 55:628-35. [DOI: 10.1021/ci500645k] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Veronika Navrátilová
- Regional Centre of Advanced
Technologies and Materials, Department of Physical Chemistry, Faculty
of Science, Palacký University Olomouc, tř. 17. listopadu 12, 771 46, Olomouc, Czech Republic
| | - Markéta Paloncýová
- Regional Centre of Advanced
Technologies and Materials, Department of Physical Chemistry, Faculty
of Science, Palacký University Olomouc, tř. 17. listopadu 12, 771 46, Olomouc, Czech Republic
| | - Michaela Kajšová
- Regional Centre of Advanced
Technologies and Materials, Department of Physical Chemistry, Faculty
of Science, Palacký University Olomouc, tř. 17. listopadu 12, 771 46, Olomouc, Czech Republic
| | - Karel Berka
- Regional Centre of Advanced
Technologies and Materials, Department of Physical Chemistry, Faculty
of Science, Palacký University Olomouc, tř. 17. listopadu 12, 771 46, Olomouc, Czech Republic
| | - Michal Otyepka
- Regional Centre of Advanced
Technologies and Materials, Department of Physical Chemistry, Faculty
of Science, Palacký University Olomouc, tř. 17. listopadu 12, 771 46, Olomouc, Czech Republic
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Fashe MM, Juvonen RO, Petsalo A, Vepsäläinen J, Pasanen M, Rahnasto-Rilla M. In Silico Prediction of the Site of Oxidation by Cytochrome P450 3A4 That Leads to the Formation of the Toxic Metabolites of Pyrrolizidine Alkaloids. Chem Res Toxicol 2015; 28:702-10. [DOI: 10.1021/tx500478q] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Muluneh M. Fashe
- School of Pharmacy, Faculty
of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Risto O. Juvonen
- School of Pharmacy, Faculty
of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Aleksanteri Petsalo
- School of Pharmacy, Faculty
of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Jouko Vepsäläinen
- School of Pharmacy, Faculty
of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Markku Pasanen
- School of Pharmacy, Faculty
of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Minna Rahnasto-Rilla
- School of Pharmacy, Faculty
of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
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50
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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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