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Soliman SSM, Hamoda AM, Nayak Y, Mostafa A, Hamdy R. Novel compounds with dual inhibition activity against SARS-CoV-2 critical enzymes RdRp and human TMPRSS2. Eur J Med Chem 2024; 276:116671. [PMID: 39004019 DOI: 10.1016/j.ejmech.2024.116671] [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: 02/11/2024] [Revised: 07/05/2024] [Accepted: 07/09/2024] [Indexed: 07/16/2024]
Abstract
COVID-19 caused major worldwide problems. The spread of variants and limited treatment encouraged the design of novel anti-SARS-CoV-2 compounds. A series of compounds RH1-23 were designed to dually target RNA-dependent RNA polymerase (RdRp) and transmembrane serine protease 2 (TMPRSS2). Compared to remdesivir, in vitro screening indicated the highest selectivity and potent activity of RH11-13 with half maximum inhibitory concentration (IC50) 3.9, 5.7, and 19.72 nM, respectively. RH11-12 showed superior inhibition activity against TMPRSS2 and RdRP with IC50 (1.7 and 4.2), and (6.1 and 4.42) nM, respectively. WaterMap analysis and molecular dynamics studies demonstrated the superior enzyme binding activity of RH11 and RH12. On Vero-E6 cells, RH11 and RH12 significantly inhibited the viral replication with 66 % and 63.2 %, and viral adsorption with 44 % and 65 %, alongside virucidal effect with 51.40 % and 90.5 %, respectively. Furthermore, the potent activity of RH12 was tested on TMPRSS2-expressing cells (Calu-3) compared to camostat. RH12 exhibited selectivity index (26.05) similar to camostat (28.01) and comparable to its SI on Vero-E6 cells (22.6). RH12 demonstrated also a significant inhibition of the viral adsorption on Calu-3 cells with 60 % inhibition at 30 nM. The designed compounds exhibited good physiochemical properties. These findings indicate a broad-spectrum antiviral efficacy of the designed compounds, particularly RH12, with a promise for further development.
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Affiliation(s)
- Sameh S M Soliman
- Research Institute for Medical and Health Sciences, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates; College of Pharmacy, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates.
| | - Alshaimaa M Hamoda
- Research Institute for Medical and Health Sciences, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates; College of Medicine, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates; Department of Pharmacognosy, Faculty of Pharmacy, Assiut University, Assiut, 71526, Egypt
| | - Yogendra Nayak
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Ahmed Mostafa
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza, 12622, Egypt; Disease Intervention & Prevention and Host Pathogen Interactions Programs, Texas Biomedical Research Institute, San Antonio, TX, 78227, United States
| | - Rania Hamdy
- Research Institute for Medical and Health Sciences, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates; Faculty of Pharmacy, Zagazig University, Zagazig, 44519, Egypt
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Bhat S, Rather M, Gani S, Nabi A, Ganai SA, Shah MD, Sofi P, Jeelani F, Hussain A, Ashraf S, Anwar A, Iqbal I, Nisa TU, Summuna B, Banday S. Identification of plant based potential antifungal compounds against BMK-1 protein of Bipolaris oryzae using molecular docking approach. Sci Rep 2024; 14:15665. [PMID: 38977720 PMCID: PMC11231321 DOI: 10.1038/s41598-024-61431-6] [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: 11/26/2023] [Accepted: 05/06/2024] [Indexed: 07/10/2024] Open
Abstract
Rice brown spot is an important disease of rice worldwide that inflicts substantial yield losses. The antimicrobial potential of methanol, acetone and dimethyl sulfoxide (DMSO) extracts of different medicinal plants, viz., Syzygium aromaticum, Saussurea costus, Acorus calamus, Bergenia ciliate, Geranium pratense, Mentha longifolia, Inula racemosa, Podophyllum hexandrum, Heracleum candicans and Picrorhiza kurroa, against the brown spot pathogen Bipolaris oryzae in vitro was evaluated via mycelial growth inhibition and spore germination inhibition assays. Among the plant extracts tested, 100% mycelial inhibition was observed for the methanol extract of Syzygium aromaticum at all three concentrations (2000 ppm, 3000 ppm and 4000 ppm), followed by the methanol extract of Inula racemosa (90.33%) at 4000 ppm. A maximum conidial germination inhibition of 83.54% was exhibited by the Heracleum candicans leaf extract. Phytochemical profiling of Syzygium aromaticum and Inula racemosa through liquid chromatography and mass spectrometry (HR-LCMS) revealed the presence of several compounds, such as eugenol, ursolic acid, quercetin, chlorogenic acid, and noscapine. A molecular docking approach was used to identify key inhibitory molecules against B. oryzae. Among the compounds detected in S. aromaticum and Inula racemosa, ursolic acid and noscapine were found to have the greatest binding affinity for the Big Mitogen Activated Protein Kinase (BMK-1) enzyme present in B. oryzae. In conclusion, S. aromaticum and Inula racemosa are potent compounds that could serve as lead compounds for drug discovery in the future.
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Affiliation(s)
- Sheeba Bhat
- Division of Plant Pathology, Faculty of Agriculture, Sher-e-Kashmir University of Agricultural Sciences and Technology-Kashmir, Wadura, Sopore, Jammu and Kashmir, 193201, India
| | - Mariya Rather
- Division of Plant Pathology, Faculty of Horticulture, Sher-e-Kashmir University of Agricultural Sciences and Technology-Kashmir, Shalimar, Srinagar, Jammu and Kashmir, 190025, India
| | - Saima Gani
- Division of Plant Pathology, Faculty of Agriculture, Sher-e-Kashmir University of Agricultural Sciences and Technology-Kashmir, Wadura, Sopore, Jammu and Kashmir, 193201, India
| | - Asha Nabi
- Division of Plant Pathology, Faculty of Agriculture, Sher-e-Kashmir University of Agricultural Sciences and Technology-Kashmir, Wadura, Sopore, Jammu and Kashmir, 193201, India.
| | - Shabir Ahmad Ganai
- Research Centre for Residue and Quality Analysis, Faculty of Horticulture, Sher-e-Kashmir University of Agricultural Sciences and Technology, Shalimar, Srinagar, Jammu and Kashmir, 190025, India
| | - Mehraj D Shah
- Division of Plant Pathology, Faculty of Horticulture, Sher-e-Kashmir University of Agricultural Sciences and Technology-Kashmir, Shalimar, Srinagar, Jammu and Kashmir, 190025, India
| | - Parvaze Sofi
- Division of Genetics and Plant Breeding, Faculty of Agriculture, Sher-e-Kashmir University of Agricultural Sciences and Technology-Kashmir, Wadura, Sopore, Jammu and Kashmir, 193201, India
| | - Fehim Jeelani
- Division of Agri-Economics and Statistics, Faculty of Agriculture, Sher-e-Kashmir University of Agricultural Sciences and Technology-Kashmir, Wadura, Sopore, Jammu and Kashmir, 193201, India
| | - Arif Hussain
- Division of Horticulture, Faculty of Agriculture, Sher-e-Kashmir University of Agricultural Sciences and Technology-Kashmir, Wadura, Sopore, Jammu and Kashmir, 193201, India
| | - Sabiha Ashraf
- College of Temperate Sericulture, Sher-e-Kashmir University of Agricultural Sciences and Technology-Kashmir, Mirgund, Jammu and Kashmir, 193121, India
| | - Ali Anwar
- Division of Plant Pathology, Faculty of Agriculture, Sher-e-Kashmir University of Agricultural Sciences and Technology-Kashmir, Wadura, Sopore, Jammu and Kashmir, 193201, India
| | - Iram Iqbal
- Division of Plant Pathology, Faculty of Agriculture, Sher-e-Kashmir University of Agricultural Sciences and Technology-Kashmir, Wadura, Sopore, Jammu and Kashmir, 193201, India
| | - Tawkeer Un Nisa
- Division of Plant Pathology, Faculty of Agriculture, Sher-e-Kashmir University of Agricultural Sciences and Technology-Kashmir, Wadura, Sopore, Jammu and Kashmir, 193201, India
| | - Baby Summuna
- Directorate of Research, Faculty of Horticulture, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Srinagar, Jammu and Kashmir, 190025, India
| | - Saba Banday
- Division of Plant Pathology, Faculty of Horticulture, Sher-e-Kashmir University of Agricultural Sciences and Technology-Kashmir, Shalimar, Srinagar, Jammu and Kashmir, 190025, India
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3
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Qubais Saeed B, Hamdy R, Akbar N, Sajeevan SE, Khan NA, Soliman SSM. Azole-based compounds as potential anti- Acanthamoeba agents. RSC Med Chem 2024; 15:1578-1588. [PMID: 38784450 PMCID: PMC11110792 DOI: 10.1039/d4md00029c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 02/22/2024] [Indexed: 05/25/2024] Open
Abstract
Acanthamoeba castellanii is an opportunistic pathogen with public health implications, largely due to its invasive nature and non-specific symptoms. Our study focuses on the potential of azole compounds, particularly those with triazole scaffolds, as anti-amoebic agents. Out of 10 compounds, compounds T1 and T8 exhibited effective anti-Acanthamoeba activity with MIC50 values of 125.37 and 143.92 μg mL-1, respectively. Interestingly, compounds T1, T4, T5 and T8 revealed profound anti-excystation activity with MIC50 at 32.01, 85.53, 19.54 and 80.57 μg mL-1, respectively, alongside limited cytotoxicity to human cells. The study underscores the potential of T1, T4, T5, and T8, thiazole-based compounds, as anti-Acanthamoeba agents by both eliminating amoeba viability and preventing excystation, via preserving the amoeba in its latent cyst form, exposing them to elimination by the immune system. Notably, compounds T1, T4, T5, and T8 showed optimal molecular properties, moderate oral bioavailability, and stable complex formation with Acanthamoeba CYP51. They also display superior binding interactions. Further research is needed to understand their mechanisms and optimize their efficacy against Acanthamoeba infections.
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Affiliation(s)
- Balsam Qubais Saeed
- Research Institute of Medical and Health Sciences, University of Sharjah Sharjah 27272 United Arab Emirates
- Department of Clinical Sciences, College of Medicine, University of Sharjah Sharjah 27272 United Arab Emirates
| | - Rania Hamdy
- Research Institute of Medical and Health Sciences, University of Sharjah Sharjah 27272 United Arab Emirates
- Research Institute for Science and Engineering (RISE), University of Sharjah Sharjah 27272 United Arab Emirates
- Faculty of Pharmacy, Zagazig University Zagazig 44519 Egypt
| | - Noor Akbar
- Research Institute of Medical and Health Sciences, University of Sharjah Sharjah 27272 United Arab Emirates
- Department of Clinical Sciences, College of Medicine, University of Sharjah Sharjah 27272 United Arab Emirates
| | | | - Naveed Ahmed Khan
- Microbiota Research Centre, Istinye University Istanbul 34010 Turkey
| | - Sameh S M Soliman
- Research Institute of Medical and Health Sciences, University of Sharjah Sharjah 27272 United Arab Emirates
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah Sharjah P.O. Box 27272 United Arab Emirates +97165057472
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Curcio A, Rocca R, Alcaro S, Artese A. The Histone Deacetylase Family: Structural Features and Application of Combined Computational Methods. Pharmaceuticals (Basel) 2024; 17:620. [PMID: 38794190 PMCID: PMC11124352 DOI: 10.3390/ph17050620] [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: 04/18/2024] [Revised: 05/03/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Histone deacetylases (HDACs) are crucial in gene transcription, removing acetyl groups from histones. They also influence the deacetylation of non-histone proteins, contributing to the regulation of various biological processes. Thus, HDACs play pivotal roles in various diseases, including cancer, neurodegenerative disorders, and inflammatory conditions, highlighting their potential as therapeutic targets. This paper reviews the structure and function of the four classes of human HDACs. While four HDAC inhibitors are currently available for treating hematological malignancies, numerous others are undergoing clinical trials. However, their non-selective toxicity necessitates ongoing research into safer and more efficient class-selective or isoform-selective inhibitors. Computational methods have aided the discovery of HDAC inhibitors with the desired potency and/or selectivity. These methods include ligand-based approaches, such as scaffold hopping, pharmacophore modeling, three-dimensional quantitative structure-activity relationships, and structure-based virtual screening (molecular docking). Moreover, recent developments in the field of molecular dynamics simulations, combined with Poisson-Boltzmann/molecular mechanics generalized Born surface area techniques, have improved the prediction of ligand binding affinity. In this review, we delve into the ways in which these methods have contributed to designing and identifying HDAC inhibitors.
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Affiliation(s)
- Antonio Curcio
- Dipartimento di Scienze della Salute, Campus “S. Venuta”, Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy; (A.C.); (S.A.); (A.A.)
| | - Roberta Rocca
- Dipartimento di Scienze della Salute, Campus “S. Venuta”, Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy; (A.C.); (S.A.); (A.A.)
- Net4Science S.r.l., Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Stefano Alcaro
- Dipartimento di Scienze della Salute, Campus “S. Venuta”, Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy; (A.C.); (S.A.); (A.A.)
- Net4Science S.r.l., Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Anna Artese
- Dipartimento di Scienze della Salute, Campus “S. Venuta”, Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy; (A.C.); (S.A.); (A.A.)
- Net4Science S.r.l., Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy
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Esther Rubavathy SM, Rajapandian V, Prakash M. Exploration of novel hydroxamate zinc binding group inhibitors against HDAC-1-3 enzymes by AI-based virtual screening: atomistic insights from steered molecular dynamics. J Biomol Struct Dyn 2024:1-12. [PMID: 38456827 DOI: 10.1080/07391102.2024.2325104] [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: 11/09/2023] [Accepted: 02/24/2024] [Indexed: 03/09/2024]
Abstract
Overexpression of histone deacetylase (HDAC) enzymes is linked to a wide variety of illnesses, including malignancies and neurological disorders, which makes HDAC inhibitors potentially therapeutic. However, most HDAC inhibitors lack subclass or isoform selectivity, which can be dangerous. Featuring both enhanced selectivity and toxicity profiles, slow-binding HDAC inhibitors offer promising treatment options for a variety of disorders. Diseases like cardiac, neurodegenerative disorders and diabetes are mainly associated with the HDAC1, HDAC2 and HDAC3 enzymes. The AI-based virtual screening tool PyRMD is implemented to identify the potential inhibitors from ∼2 million compounds. Based on the IC50 values, the top 10 compounds were selected for molecular docking. From the docking and ADMET study, the top-ranked three compounds were selected for molecular dynamics (MD) simulations. Further, to get more insights into the binding/unbinding mechanism of the ligand, we have employed the steered molecular dynamics (SMD) simulations. This study assists in developing Amber force field parameters for the HDAC1, HDAC2 and HDAC3 proteins and sheds light on the discovery of a potent drug. Our study suggests that hydroxamic acid derivative (i.e. referred to as Comp-1, CHEMBL600072) is the potential inhibitor for the series of HDAC-related diseases.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- S M Esther Rubavathy
- Department of Chemistry, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, India
| | - V Rajapandian
- Department of Chemistry, Sri Ramakrishna Mission Vidyalaya College of Arts and Science, Coimbatore, Tamil Nadu, India
| | - M Prakash
- Department of Chemistry, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, India
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Uba AI, Zengin G. In the quest for histone deacetylase inhibitors: current trends in the application of multilayered computational methods. Amino Acids 2023; 55:1709-1726. [PMID: 37367966 DOI: 10.1007/s00726-023-03297-y] [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: 04/15/2023] [Accepted: 06/20/2023] [Indexed: 06/28/2023]
Abstract
Histone deacetylase (HDAC) inhibitors have gained attention over the past three decades because of their potential in the treatment of different diseases including various forms of cancers, neurodegenerative disorders, autoimmune, inflammatory diseases, and other metabolic disorders. To date, 5 HDAC inhibitor drugs are marketed for the treatment of hematological malignancies and several drug-candidate HDAC inhibitors are at different stages of clinical trials. However, due to the toxic side effects of these drugs resulting from the lack of target selectivity, active studies are ongoing to design and develop either class-selective or isoform-selective inhibitors. Computational methods have aided the discovery of HDAC inhibitors with the desired potency and/or selectivity. These methods include ligand-based approaches such as scaffold hopping, pharmacophore modeling, three-dimensional quantitative structure-activity relationships (3D-QSAR); and structure-based virtual screening (molecular docking). The current trends involve the application of the combination of these methods and incorporating molecular dynamics simulations coupled with Poisson-Boltzmann/molecular mechanics generalized Born surface area (MM-PBSA/MM-GBSA) to improve the prediction of ligand binding affinity. This review aimed at understanding the current trends in applying these multilayered strategies and their contribution to the design/identification of HDAC inhibitors.
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Affiliation(s)
- Abdullahi Ibrahim Uba
- Department of Molecular Biology and Genetics, Istanbul AREL University, Istanbul, 34537, Turkey.
| | - Gokhan Zengin
- Department of Biology, Science Faculty, Selcuk University, Konya, 42130, Turkey.
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Castillo Ordoñez WO, Aristizabal-Pachon AF, Alves LB, Giuliatti S. Epigenetic regulation exerted by Caliphruria subedentata and galantamine: an in vitro and in silico approach for mimic Alzheimer's disease. J Biomol Struct Dyn 2023:1-16. [PMID: 37814967 DOI: 10.1080/07391102.2023.2261034] [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: 04/18/2023] [Accepted: 09/13/2023] [Indexed: 10/11/2023]
Abstract
At the interface between genes and environment, epigenetic mechanisms, including DNA methylation and histone modification, regulate neurogenic processes such as differentiation, proliferation, and maturation of neural stem cells. However, these mechanisms are altered in Alzheimer's disease (AD), a neurodegenerative condition that mainly affects older adults. Since epigenetic mechanisms are known to be reversible, a number of molecules from natural sources are being studied as epigenetic regulators in AD. Recently, in vitro and in silico studies have shown that C. subedentata and its alkaloids modulated neurotoxicity. However, studies exploring the epigenetic activity of these alkaloids are limited. We conducted a set of bioassays to evaluate neuronal differentiation and the sensitivity of undifferentiated SH-SY5 cells against a neurotoxic stimulus. In addition, we analyzed the methylation profiles in genes such as APP, PSI, and BACE1 due to their role in amyloid processing. Docking and molecular dynamic analysis were used to explore the effect exerted by C. subedentata alkaloids on the regulation of histone deacetylases (HDAC2, HDAC3 and HDAC7). The results demonstrated that C. subedentata and galantamine induce neuronal differentiation and protect the undifferentiated SH-SY5Y cells against Aβ(1-42)-induced neurotoxicity. The methylation profiles of the studied genes show no statistically significant differences between C. subedentata, galantamine. However, these findings should be interpreted with caution, since small changes in methylation promoters in the brain could not be easily detected. Results from in silico approaches describe for the first time the potential promissing epigenetic effects of galantamine by regulating HDAC3 and HDAC7 modification.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Willian Orlando Castillo Ordoñez
- Facultad de Ciencias Naturales-Exactas y de la Educación, Departamento de Biología, Universidad del Cauca, Popayán-Cauca, Colombia
- Departamento de Estudios Psicológicos, Universidad Icesi, Cali, Colombia
| | - Andrés F Aristizabal-Pachon
- Departamento de Nutrición y Bioquímica, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Levy Bueno Alves
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo-USP, Brazil
| | - Silvana Giuliatti
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo-USP, Brazil
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Ganai SA, Rajamanikandan S, Shah BA, Lone A, Arwa F, Malik FA. Comparative structural study of selective and non-selective NSAIDs against the enzyme cyclooxygenase-2 through real-time molecular dynamics linked to post-dynamics MM-GBSA and e-pharmacophores mapping. J Mol Model 2023; 29:192. [PMID: 37256432 DOI: 10.1007/s00894-023-05603-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 05/23/2023] [Indexed: 06/01/2023]
Abstract
BACKGROUND Inflammation-provoked disorders including cancer are arbitrated by cyclooxygenase-2 (COX-2). Celecoxib and niflumic acid are among the potent and selective inhibitors of this enzyme while aspirin (acetylsalicylic acid) and sodium salicylate are its non-selective and lesser potent inhibitors. Despite these proven studies, the comparative structural study of these selective and non-selective molecules at atomistic scale in complex state with COX-2 that may answer this differential inhibitory behavior has not been accomplished spotlighting the imperative need of additional research in this area. Thus, this study was framed to provide a strong explanation for the enigma of higher inhibitory activity of celecoxib-niflumic acid duo in comparison to aspirin and sodium salicylate towards COX-2. METHODS A contemporary approach including advanced molecular docking against COX2, molecular dynamics of receptor-ligand complexes, simulation-trajectory-backed MMGBSA for different time points, radius of gyration (Rg) calculations, and e-pharmacophores approach was employed to attain a rational conclusion. RESULTS Our findings demonstrated the higher binding affinity of celecoxib and niflumic acid over aspirin and sodium salicylate against COX-2. Although both selective and non-selective COX-2 inhibitors manifested nearly the same stability in the active site of this enzyme but the e-pharmocophoric features found in the case of selective inhibitors scored over non-selective ones. Thus, our findings excluded the differential stability to be the cause of stronger potency of selective inhibitors but attributed their potency to greater number of complementary features present in these inhibitors against the active site of inflammation engendering COX-2.
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Affiliation(s)
- Shabir Ahmad Ganai
- Research Centre for Residue and Quality Analysis, FoH, SKUAST-Kashmir, Shalimar, Srinagar, 190025, Jammu & Kashmir, India.
| | - Sundararaj Rajamanikandan
- Department of Biochemistry, Karpagam Academy of Higher Education, Coimbatore, 641021, Tamil Nadu, India
- Centre for Drug Discovery, Karpagam Academy of Higher Education, Coimbatore, 641021, Tamil Nadu, India
| | - Basit Amin Shah
- Department of Biotechnology, University of Kashmir, Srinagar, 190006, Jammu & Kashmir, India
| | - Asif Lone
- Department of Biochemistry, Deshbandhu College, University of Delhi, 110019, New Delhi, India
| | - Faieza Arwa
- Department of Veterinary Physiology, SKUAST-J-180009, Jammu, Jammu & Kashmir, India
| | - Firdose Ahmad Malik
- College of Temperate Sericulture, SKUAST-Kashmir, Mirgund, 193121, Jammu & Kashmir, India
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Dewaker V, Srivastava PN, Verma S, Srivastava AK, Prabhakar YS. Non-bonding energy directed designing of HDAC2 inhibitors through molecular dynamics simulation. J Biomol Struct Dyn 2022; 40:13432-13455. [PMID: 34662251 DOI: 10.1080/07391102.2021.1989037] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Designing an inhibitor having strong affinity in the active site pocket is the cherished goal of structure based drug designing. To achieve this, it is considerably important to predict which structural scaffold is better suited for change to increase affinity. We have explored five HDAC2 co-crystals having PDB ligand code-SHH (vorinostat), LLX, 20Y, IWX (BRD4884) and 6EZ (BRD7232). For analyzing protein-ligand interaction at an atomistic level, we have employed the NAMD molecular dynamics (MD) package. The obtained 100 ns long MD trajectories were subjected to quantitative estimations of non-bonding energies (NBEs) for inferring their interactions with the whole protein or its composite active site (CAS). In addition, relative ΔGbind was calculated to rank the inhibitors. These inhibitors' NBEs reveal that the phenyl moieties are the major structural scaffold where modifications should be attempted. We designed new compounds (NCs) via introducing hydroxyl groups at 4,5 position of the phenyl moiety of 6EZ, called NC1. Improvement in NC1 further encouraged us for CAP modification by isochromane and isoindoline moieties in place of oxabicyclooctane in NC1, resulting in NC2 and NC3. We also explored trifluoromethyl oxadiazole in 6EZ (NC4 and NC5) and SHH (NC6 and NC7). This moiety acts as a ZBG in NC4 while acting as a part of the foot-pocket in the rest. NC2 and NC6 have highest favorable NBEs among all studied ligands due increased favorable electrostatic contribution. We expect these NBEs data will provide atomistic level insights and benefit in designing new and improved HDAC2 inhibitors. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Varun Dewaker
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - Pratik Narain Srivastava
- Molecular Parasitology and Immunology Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - Saroj Verma
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, Lucknow, India.,College of Pharmacy, Shree Guru Gobind Singh Tricentenary University, Gurugram, Haryana, India
| | - Ajay K Srivastava
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - Yenamandra S Prabhakar
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, Lucknow, India
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A neuronal cell-based reporter system for monitoring the activity of HDAC2. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2022; 27:440-447. [PMID: 36240996 DOI: 10.1016/j.slasd.2022.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/25/2022] [Accepted: 10/07/2022] [Indexed: 11/06/2022]
Abstract
Given that histone acetylation via histone acetyltransferases (HATs) and histone deacetylases (HDACs) is significant in memory formation, HDAC2 has been thoroughly investigated as a potential therapeutic target for the treatment of cognitive dysfunction. Although HDAC inhibitors have been discovered through in vitro enzyme assay, off-target effects on other HDACs are common due to their conserved catalytic domains. Each HDAC could be regulated by specific intracellular molecular mechanisms, raising the possibility that a cell-based assay could identify selective inhibitors targeting specific HDACs through their regulatory mechanisms. Here, we propose a versatile, cell-based reporter system for screening HDAC2 inhibitors. Through RNA-sequencing from human cultured neuronal cells, we determined that expression of a transcriptional repressor, inhibitor of DNA binding 1 (ID1), is increased by knockdown of HDAC2. We also established the knock-in neuronal cell lines of a bioluminescence reporter gene to ID1. The knock-in cell lines showed significant reporter activity by known HDAC inhibitors and by HDAC2-knockdown but not by HDAC1-knockdown. Thus, our neuronal cell-based reporter system is a promising method for screening the specific inhibitors of HDAC2 but not HDAC1, by potentially targeting not only HDAC2, but also the regulatory mechanisms of HDAC2 in neurons.
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Hamdy R, Hamoda AM, Al-Khalifa M, Menon V, El-Awady R, Soliman SSM. Efficient selective targeting of Candida CYP51 by oxadiazole derivatives designed from plant cuminaldehyde. RSC Med Chem 2022; 13:1322-1340. [PMID: 36439981 PMCID: PMC9667785 DOI: 10.1039/d2md00196a] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 09/19/2022] [Indexed: 07/24/2023] Open
Abstract
Candida infection represents a global threat with associated high resistance and mortality rate. Azoles such as the triazole drug fluconazole are the frontline therapy against invasive fungal infections; however, the emerging multidrug-resistant strains limit their use. Therefore, a series of novel azole UOSO1-15 derivatives were developed based on a modified natural scaffold to combat the evolved resistance mechanism and to provide improved safety and target selectivity. The antifungal screening against C. albicans and C. auris showed that UOSO10 and 12-14 compounds were the most potent derivatives. Among them, UOSO13 exhibited superior potent activity with MIC50 values of 0.5 and 0.8 μg mL-1 against C. albicans and C. auris compared to 25 and 600 μg mL-1 for fluconazole, respectively. UOSO13 displayed significant CaCYP51 enzyme inhibition activity in a concentration-dependent manner with an IC50 10-fold that of fluconazole, while exhibiting no activity against human CYP50 enzyme or toxicity to human cells. Furthermore, UOSO13 caused a significant reduction of Candida ergosterol content by 70.3% compared to a 35.6% reduction by fluconazole. Homology modeling, molecular docking, and molecular dynamics simulations of C. auris CYP51 enzyme indicated the stability and superiority of UOSO13. ADME prediction indicated that UOSO13 fulfils the drug-likeness criteria with good physicochemical properties.
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Affiliation(s)
- Rania Hamdy
- Research Institute for Medical and Health Sciences, University of Sharjah P.O. Box 27272 Sharjah United Arab Emirates
- Faculty of Pharmacy, Zagazig University Zagazig Egypt
| | - Alshaimaa M Hamoda
- Research Institute for Medical and Health Sciences, University of Sharjah P.O. Box 27272 Sharjah United Arab Emirates
- College of Medicine, University of Sharjah P.O. Box 27272 Sharjah United Arab Emirate
- Department of Pharmacognosy, Faculty of Pharmacy, Assiut University Assiut-71526 Egypt
| | - Mariam Al-Khalifa
- Research Institute for Medical and Health Sciences, University of Sharjah P.O. Box 27272 Sharjah United Arab Emirates
| | - Varsha Menon
- Research Institute for Medical and Health Sciences, University of Sharjah P.O. Box 27272 Sharjah United Arab Emirates
| | - Raafat El-Awady
- Research Institute for Medical and Health Sciences, University of Sharjah P.O. Box 27272 Sharjah United Arab Emirates
- College of Pharmacy, University of Sharjah P.O. Box 27272 Sharjah United Arab Emirates +97165057472
| | - Sameh S M Soliman
- Research Institute for Medical and Health Sciences, University of Sharjah P.O. Box 27272 Sharjah United Arab Emirates
- College of Pharmacy, University of Sharjah P.O. Box 27272 Sharjah United Arab Emirates +97165057472
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12
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Alov P, Stoimenov H, Lessigiarska I, Pencheva T, Tzvetkov NT, Pajeva I, Tsakovska I. In Silico Identification of Multi-Target Ligands as Promising Hit Compounds for Neurodegenerative Diseases Drug Development. Int J Mol Sci 2022; 23:13650. [PMID: 36362434 PMCID: PMC9655539 DOI: 10.3390/ijms232113650] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/25/2022] [Accepted: 10/31/2022] [Indexed: 09/29/2023] Open
Abstract
The conventional treatment of neurodegenerative diseases (NDDs) is based on the "one molecule-one target" paradigm. To combat the multifactorial nature of NDDs, the focus is now shifted toward the development of small-molecule-based compounds that can modulate more than one protein target, known as "multi-target-directed ligands" (MTDLs), while having low affinity for proteins that are irrelevant for the therapy. The in silico approaches have demonstrated a potential to be a suitable tool for the identification of MTDLs as promising drug candidates with reduction in cost and time for research and development. In this study more than 650,000 compounds were screened by a series of in silico approaches to identify drug-like compounds with predicted activity simultaneously towards three important proteins in the NDDs symptomatic treatment: acetylcholinesterase (AChE), histone deacetylase 2 (HDAC2), and monoamine oxidase B (MAO-B). The compounds with affinities below 5.0 µM for all studied targets were additionally filtered to remove known non-specifically binding or unstable compounds. The selected four hits underwent subsequent refinement through in silico blood-brain barrier penetration estimation, safety evaluation, and molecular dynamics simulations resulting in two hit compounds that constitute a rational basis for further development of multi-target active compounds against NDDs.
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Affiliation(s)
- Petko Alov
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Bl. 105, 1113 Sofia, Bulgaria
| | - Hristo Stoimenov
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Bl. 105, 1113 Sofia, Bulgaria
| | - Iglika Lessigiarska
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Bl. 105, 1113 Sofia, Bulgaria
| | - Tania Pencheva
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Bl. 105, 1113 Sofia, Bulgaria
| | - Nikolay T. Tzvetkov
- Institute of Molecular Biology “Acad. Roumen Tsanev”, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Bl. 21, 1113 Sofia, Bulgaria
| | - Ilza Pajeva
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Bl. 105, 1113 Sofia, Bulgaria
| | - Ivanka Tsakovska
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Bl. 105, 1113 Sofia, Bulgaria
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13
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Hamdy R, Mostafa A, Abo Shama NM, Soliman SSM, Fayed B. Comparative evaluation of flavonoids reveals the superiority and promising inhibition activity of silibinin against SARS-CoV-2. Phytother Res 2022; 36:2921-2939. [PMID: 35596627 PMCID: PMC9347486 DOI: 10.1002/ptr.7486] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 03/19/2022] [Accepted: 04/22/2022] [Indexed: 01/08/2023]
Abstract
Flavonoids are phenolic compounds naturally found in plants and commonly consumed in diets. Herein, flavonoids were sequentially evaluated by a comparative in silico study associated with systematic literature search. This was followed by an in vitro study and enzyme inhibition assays against vital SARS-CoV-2 proteins including spike (S) protein, main protease (Mpro ), RNA-dependent RNA-polymerase (RdRp), and human transmembrane serine protease (TMPRSS2). The results obtained revealed 10 flavonoids with potential antiviral activity. Out of them, silibinin showed promising selectivity index against SARS-CoV-2 in vitro. Screening against S protein discloses the highest inhibition activity of silibinin. Mapping the activity of silibinin indicated its excellent binding inhibition activity against SARS-CoV-2 S protein, Mpro and RdRP at IC50 0.029, 0.021, and 0.042 μM, respectively, while it showed no inhibition activity against TMPRSS2 at its IC50(SARS-CoV-2) . Silibinin was tested safe on human mammalian cells at >7-fold its IC50(SARS-CoV-2) . Additionally, silibinin exhibited >90% virucidal activity at 0.031 μM. Comparative molecular docking (MD) showed that silibinin possesses the highest binding affinity to S protein and RdRP at -7.78 and -7.15 kcal/mol, respectively. MDs showed that silibinin exhibited stable interaction with key amino acids of SARS-CoV-2 targets. Collectively, silibinin, an FDA-approved drug, can significantly interfere with SARS-CoV-2 entry and replication through multi-targeting activity.
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Affiliation(s)
- Rania Hamdy
- Research Institute for Medical and Health SciencesUniversity of SharjahSharjahUnited Arab Emirates
- Faculty of PharmacyZagazig UniversityZagazigEgypt
| | - Ahmed Mostafa
- Center of Scientific Excellence for Influenza VirusesNational Research CentreGizaEgypt
| | - Noura M. Abo Shama
- Center of Scientific Excellence for Influenza VirusesNational Research CentreGizaEgypt
| | - Sameh S. M. Soliman
- Research Institute for Medical and Health SciencesUniversity of SharjahSharjahUnited Arab Emirates
- College of PharmacyUniversity of SharjahSharjahUnited Arab Emirates
| | - Bahgat Fayed
- Research Institute for Medical and Health SciencesUniversity of SharjahSharjahUnited Arab Emirates
- Chemistry of Natural and Microbial Product DepartmentNational Research CentreCairoEgypt
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14
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Identification of novel leads as potent inhibitors of HDAC3 using ligand-based pharmacophore modeling and MD simulation. Sci Rep 2022; 12:1712. [PMID: 35110603 PMCID: PMC8810932 DOI: 10.1038/s41598-022-05698-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 01/03/2022] [Indexed: 02/08/2023] Open
Abstract
In the landscape of epigenetic regulation, histone deacetylase 3 (HDAC3) has emerged as a prominent therapeutic target for the design and development of candidate drugs against various types of cancers and other human disorders. Herein, we have performed ligand-based pharmacophore modeling, virtual screening, molecular docking, and MD simulations to design potent and selective inhibitors against HDAC3. The predicted best pharmacophore model ‘Hypo 1’ showed excellent correlation (R2 = 0.994), lowest RMSD (0.373), lowest total cost value (102.519), and highest cost difference (124.08). Hypo 1 consists of four salient pharmacophore features viz. one hydrogen bond acceptor (HBA), one ring aromatic (RA), and two hydrophobic (HYP). Hypo 1 was validated by Fischer's randomization with a 95% of confidence level and the external test set of 60 compounds with a good correlation coefficient (R2 = 0.970). The virtual screening of chemical databases, drug-like properties calculations followed by molecular docking resulted in identifying 22 representative hit compounds. Performed 50 ns of MD simulations on top three hits were retained the salient π-stacking, Zn2+ coordination, hydrogen bonding, and hydrophobic interactions with catalytic residues from the active site pocket of HDAC3. Total binding energy calculated by MM-PBSA showed that the Hit 1 and Hit 2 formed stable complexes with HDAC3 as compared to reference TSA. Further, the PLIP analysis showed a close resemblance between the salient pharmacophore features of Hypo 1 and the presence of molecular interactions in co-crystallized FDA-approved drugs. We conclude that the screened hit compounds may act as potent inhibitors of HDAC3 and further preclinical and clinical studies may pave the way for developing them as effective therapeutic agents for the treatment of different cancers and neurodegenerative disorders.
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15
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Vargas-Junior V, Antunes D, Guimarães AC, Caffarena E. In silico investigation of riboswitches in fungi: structural and dynamical insights into TPP riboswitches in Aspergillus oryzae. RNA Biol 2022; 19:90-103. [PMID: 34989318 PMCID: PMC8786325 DOI: 10.1080/15476286.2021.2015174] [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] [Indexed: 10/31/2022] Open
Abstract
Riboswitches are RNA sensors affecting post-transcriptional processes through their ability to bind to small molecules. Thiamine pyrophosphate (TPP) riboswitch plays a crucial role in regulating genes involved in synthesizing or transporting thiamine and phosphorylated derivatives in bacteria, archaea, plants, and fungi. Although TPP riboswitch is reasonably well known in bacteria, there is a gap in the knowledge of the fungal TPP riboswitches structure and dynamics, involving mainly sequence variation and TPP interaction with the aptamers. On the other hand, the increase of fungal infections and antifungal resistance raises the need for new antifungal therapies. In this work, we used computational approaches to build three-dimensional models for the three TPP riboswitches identified in Aspergillus oryzae, in which we studied their structure, dynamics, and binding free energy change (ΔGbind) with TPP. Interaction patterns between the TPP and the surrounding nucleotides were conserved among the three models, evidencing high structural conservation. Furthermore, we show that the TPP riboswitch from the A. oryzae NMT1 gene behaves similarly to the E. coli thiA gene concerning the ΔGbind. In contrast, mutations in the fungal TPP riboswitches from THI4 and the nucleoside transporter genes led to structural differences, affecting the binding-site volume, hydrogen bond occupancy, and ΔGbind. Besides, the number of water molecules surrounding TPP influenced the ΔGbind considerably. Notably, our ΔGbind estimation agreed with previous experimental data, reinforcing the relationship between sequence conservation and TPP interaction.
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Affiliation(s)
- Valdemir Vargas-Junior
- Computational Biophysics and Molecular Modeling Group, Scientific Computing Programme (Procc - Fiocruz), Rio de Janeiro, Brazil
| | - Deborah Antunes
- Laboratory of Functional Genomics and Bioinformatics, Oswaldo Cruz Institute (Ioc - Fiocruz), Rio de Janeiro, Brazil
| | - Ana Carolina Guimarães
- Laboratory of Functional Genomics and Bioinformatics, Oswaldo Cruz Institute (Ioc - Fiocruz), Rio de Janeiro, Brazil
| | - Ernesto Caffarena
- Computational Biophysics and Molecular Modeling Group, Scientific Computing Programme (Procc - Fiocruz), Rio de Janeiro, Brazil
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16
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Yadav V, Banerjee S, Baidya SK, Adhikari N, Jha T. Applying comparative molecular modelling techniques on diverse hydroxamate-based HDAC2 inhibitors: an attempt to identify promising structural features for potent HDAC2 inhibition. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2022; 33:1-22. [PMID: 34979835 DOI: 10.1080/1062936x.2021.2013317] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 11/29/2021] [Indexed: 06/14/2023]
Abstract
Histone deacetylase 2 (HDAC2) has been implicated in a variety of cardiovascular and neurodegenerative disorders as well as in cancers. Thus, HDAC2 has become an exclusive target for anticancer drug development. Therefore, the development of newer HDAC2 inhibitors in disease conditions is a prime goal to restrain such a scenario. Although a handful of HDAC inhibitors was accepted for the treatment of HDAC-related disease conditions, the non-selective nature of these entities is one of the major setbacks in the treatment of specific HDAC isoform-related pathophysiology. In this framework, the analyses of pre-existing molecules are essential to identify the important structural features that can fulfil the requirements for the cap and linker moieties to obtain potent and effective HDAC2 inhibition. Thus, in this study, the implementation of a combined comparative 2D and 3D molecular modelling techniques was done on a group of 92 diverse hydroxamate derivatives having a wide range of HDAC2 inhibitory potency. Besides other crucial features, this study upheld the importance of groups like triazole and benzyl moieties along with the molecular fields that are crucial for regulating HDAC2 inhibition. The outcomes of this study may be employed for the designing of HDAC2 inhibitors in future.
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Affiliation(s)
- V Yadav
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - S Banerjee
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - S K Baidya
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - N Adhikari
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - T Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
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17
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Hamdy R, Fayed B, Mostafa A, Shama NMA, Mahmoud SH, Mehta CH, Nayak Y, M. Soliman SS. Iterated Virtual Screening-Assisted Antiviral and Enzyme Inhibition Assays Reveal the Discovery of Novel Promising Anti-SARS-CoV-2 with Dual Activity. Int J Mol Sci 2021; 22:9057. [PMID: 34445763 PMCID: PMC8396542 DOI: 10.3390/ijms22169057] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/16/2021] [Accepted: 08/19/2021] [Indexed: 02/06/2023] Open
Abstract
Unfortunately, COVID-19 is still a threat to humankind and has a dramatic impact on human health, social life, the world economy, and food security. With the limited number of suggested therapies under clinical trials, the discovery of novel therapeutic agents is essential. Here, a previously identified anti-SARS-CoV-2 compound named Compound 13 (1,2,5-Oxadiazole-3-carboximidic acid, 4,4'-(methylenediimino) bis,bis[[(2-hydroxyphenyl)methylene]hydrazide) was subjected to an iterated virtual screening against SARS-CoV-2 Mpro using a combination of Ligand Designer and PathFinder. PathFinder, a computational reaction enumeration tool, was used for the rapid generation of enumerated structures via default reaction library. Ligand designer was employed for the computerized lead optimization and selection of the best structural modification that resulted in a favorable ligand-protein complex. The obtained compounds that showed the best binding to Mpro were re-screened against TMPRSS2, leading to the identification of 20 shared compounds. The compounds were further visually inspected, which resulted in the identification of five shared compounds M1-5 with dual binding affinity. In vitro evaluation and enzyme inhibition assay indicated that M3, an analogue of Compound 13 afforded by replacing the phenolic moiety with pyridinyl, possesses an improved antiviral activity and safety. M3 displayed in vitro antiviral activity with IC50 0.016 µM and Mpro inhibition activity with IC50 0.013 µM, 7-fold more potent than the parent Compound 13 and potent than the antivirals drugs that are currently under clinical trials. Moreover, M3 showed potent activity against human TMPRSS2 and furin enzymes with IC50 0.05, and 0.08 µM, respectively. Molecular docking, WaterMap analysis, molecular dynamics simulation, and R-group analysis confirmed the superiority of the binding fit to M3 with the target enzymes. WaterMap analysis calculated the thermodynamic properties of the hydration site in the binding pocket that significantly affects the biological activity. Loading M3 on zinc oxide nanoparticles (ZnO NPs) increased the antiviral activity of the compound 1.5-fold, while maintaining a higher safety profile. In conclusion, lead optimized discovery following an iterated virtual screening in association with molecular docking and biological evaluation revealed a novel compound named M3 with promising dual activity against SARS-CoV-2. The compound deserves further investigation for potential clinical-based studies.
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Affiliation(s)
- Rania Hamdy
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates; (R.H.); (B.F.)
- Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
| | - Bahgat Fayed
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates; (R.H.); (B.F.)
- Chemistry of Natural and Microbial Product Department, National Research Centre, Cairo 12622, Egypt
| | - Ahmed Mostafa
- Centre of Scientific Excellence for Influenza Viruses, National Research Centre, Giza 12622, Egypt; (A.M.); (N.M.A.S.); (S.H.M.)
| | - Noura M. Abo Shama
- Centre of Scientific Excellence for Influenza Viruses, National Research Centre, Giza 12622, Egypt; (A.M.); (N.M.A.S.); (S.H.M.)
| | - Sara Hussein Mahmoud
- Centre of Scientific Excellence for Influenza Viruses, National Research Centre, Giza 12622, Egypt; (A.M.); (N.M.A.S.); (S.H.M.)
| | - Chetan Hasmukh Mehta
- Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal 576104, India; (C.H.M.); (Y.N.)
| | - Yogendra Nayak
- Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal 576104, India; (C.H.M.); (Y.N.)
| | - Sameh S. M. Soliman
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates; (R.H.); (B.F.)
- College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates
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18
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Ganai SA, Srinivasan P, Rajamanikandan S, Shah BA, Mohan S, Gani M, Padder BA, Qadri RA, Bhat MA, Baba ZA, Yatoo MA. Delineating binding potential, stability of Sulforaphane-N-acetyl-cysteine in the active site of histone deacetylase 2 and testing its cytotoxicity against distinct cancer lines through stringent molecular dynamics, DFT and cell-based assays. Chem Biol Drug Des 2021; 98:363-376. [PMID: 33966346 DOI: 10.1111/cbdd.13854] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 03/29/2021] [Accepted: 04/25/2021] [Indexed: 12/12/2022]
Abstract
Histone deacetylase 2 (HDAC2), an isozyme of Class I HDACs has potent imputations in actuating neurodegenerative signaling. Currently, there are sizeable therapeutic disquiets with the use of synthetic histone deacetylase inhibitors in disease management. This strongly suggests the unfulfilled medical necessity of plant substitutes for therapeutic intervention. Sulforaphane-N-acetyl-cysteine (SFN-N-acetylcysteine or SFN-NAC), a sulforaphane metabolite has shown significantly worthier activity against HDACs under in vitro conditions. However, the atomistic studies of SFN-NAC against HDAC2 are currently lacking. Thus, the present study employed a hybrid strategy including extra-precision (XP) grid-based flexible molecular docking, molecular mechanics generalized born surface area (MM-GBSA), e-Pharmacophores method, and molecular dynamics simulation for exploring the binding strengh, mode of interaction, e-Pharmacophoric features, and stability of SFN-NAC towards HDAC2. Further, the globally acknowledged density functional theory (DFT) study was performed on SFN-NAC and entinostat individually in complex state with HDAC2. Apart from this, these inhibitors were tested against three distinct cancer cell models and one transformed cell line for cytotoxic activity. Moreover, double mutant of HDAC2 was generated and the binding orientation and interaction of SFN-NAC was scrutinized in this state. On the whole, this study unbosomed and explained the comparatively higher binding affinity of entinostat for HDAC2 and its wide spectrum cytotoxicity than SFN-NAC.
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Affiliation(s)
- Shabir Ahmad Ganai
- Division of Basic Sciences and Humanities, FoA, SKUAST-Kashmir, 193201, India
| | - Pappu Srinivasan
- Department of Animal Health and Management, Alagappa University, Karaikudi, India
| | - Sundaraj Rajamanikandan
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Bengaluru, India
| | - Basit Amin Shah
- Department of Biotechnology, University of Kashmir, Srinagar, India
| | - Suma Mohan
- SCBT, Shanmugha Arts Science Technology and Research Academy, 613401, India
| | - Mudasir Gani
- Division of Entomology, FoA, SKUAST-Kashmir, 193201, India
| | | | - Raies A Qadri
- Department of Biotechnology, University of Kashmir, Srinagar, India
| | - M A Bhat
- Division of Genetics and Plant Breeding, SKUAST-Kashmir, 193201, India
| | - Zahoor Ahmad Baba
- Division of Basic Sciences and Humanities, FoA, SKUAST-Kashmir, 193201, India
| | - Manzoor Ahmad Yatoo
- Division of Basic Sciences and Humanities, FoA, SKUAST-Kashmir, 193201, India
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19
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Shetty MG, Pai P, Deaver RE, Satyamoorthy K, Babitha KS. Histone deacetylase 2 selective inhibitors: A versatile therapeutic strategy as next generation drug target in cancer therapy. Pharmacol Res 2021; 170:105695. [PMID: 34082029 DOI: 10.1016/j.phrs.2021.105695] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 05/04/2021] [Accepted: 05/25/2021] [Indexed: 02/06/2023]
Abstract
Acetylation and deacetylation of histone and several non-histone proteins are the two important processes amongst the different modes of epigenetic modulation that are involved in regulating cancer initiation and development. Abnormal expression of histone deacetylases (HDACs) is often reported in various types of cancers. Few pan HDAC inhibitors have been approved for use as therapeutic interventions for cancer treatment including vorinostat, belinostat and panobinostat. However, not all the HDAC isoforms are abnormally expressed in certain cancers, such as in the case of, ovarian cancer where overexpression of HDAC1-3, lung cancer where overexpression of HDAC 1 and 3 and gastric cancer where overexpression of HDAC2 is seen. Therefore, pan-inhibition of HDAC is not an efficient way to combat cancer via HDAC inhibition. Hence, isoform-selective HDAC inhibition can be one of the best therapeutic strategies in the treatment of cancer. In this context since aberrant expression of HDAC2 largely contributes to cancer progression by silencing pro-apoptotic protein expressions such as NOXA and APAF1 (caspase 9-activating proteins) and inactivation of tumor suppressor p53, HDAC2 specific inhibitors may help to develop not only the direct targets but also indirect targets that are crucial for tumor development. However, to develop a HDAC2 specific and potent inhibitor, extensive knowledge of its structure and specific functions is essential. The present review updates details on the structural features, physiological functions, and roles of HDAC2 in different types of cancer, emphasizing the challenges and status of the development of HDAC2 selective inhibitors against various types of cancer.
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Affiliation(s)
| | - Padmini Pai
- Department of Biophysics, Manipal School of Life Sciences, MAHE, Manipal, India
| | - Renita Esther Deaver
- Department of Biotechnology, Manipal School of Life Sciences, MAHE, Manipal, India
| | - Kapaettu Satyamoorthy
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, MAHE, Manipal, India
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20
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Mehndiratta S, Chen MC, Chao YH, Lee CH, Liou JP, Lai MJ, Lee HY. Effect of 3-subsitution of quinolinehydroxamic acids on selectivity of histone deacetylase isoforms. J Enzyme Inhib Med Chem 2021; 36:74-84. [PMID: 33161799 PMCID: PMC7655065 DOI: 10.1080/14756366.2020.1839446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
A series of 3-subsituted quinolinehydroxamic acids has been synthesised and evaluated for their effect on human lung cancer cell line (A549), human colorectal cancer cell line (HCT116) and HDAC isoforms 1, 2, 6, and 8. The results indicated that substitution at C3 of quinoline is favoured for HDAC6 selectivity. Two compounds (25 and 26) were also found to be potent anti-proliferative compounds with IC50 values ranging from 1.29 to 2.13 µM against A549 and HCT116 cells. These compounds displayed remarkable selectivity for HDAC6 over other HDAC isoforms with nanomolar IC50 values. Western blot analysis revealed that compounds of this series activate apoptotic caspase pathway as indicated by cleavage of caspase 3, 8, and 9 and also increase phosphorylated H2AX thus inducing DNA double strand fragmentation in a concentration dependent manner. Flow cytometric analysis also displayed a dose dependent increase of cell population in sub G1 phase.
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Affiliation(s)
- Samir Mehndiratta
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Mei-Chuan Chen
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan.,Ph.D. Program in Clinical Drug Development of Herbal Medicine, College of Pharmacy, Taipei Medical University, Taipei, Taiwan.,Traditional Herbal Medicine Research Center of Taipei Medical University Hospital, Taipei, Taiwan
| | - Yuh-Hsuan Chao
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Cheng-Hsin Lee
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Jing-Ping Liou
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan.,Biomedical Commercialization Center, Taipei Medical University, Taipei, Taiwan
| | - Mei-Jung Lai
- Biomedical Commercialization Center, Taipei Medical University, Taipei, Taiwan
| | - Hsueh-Yun Lee
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan.,Ph.D. Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
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21
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Characterizing binding intensity and energetic features of histone deacetylase inhibitor pracinostat towards class I HDAC isozymes through futuristic drug designing strategy. In Silico Pharmacol 2021; 9:18. [PMID: 33628709 DOI: 10.1007/s40203-021-00077-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 01/16/2021] [Indexed: 02/07/2023] Open
Abstract
Pracinostat, an emerging hydroxamate histone deacetylase (HDAC) inhibitor has shown better efficacy than approved inhibitor suberoylanilide hydroxamic acid (SAHA). Apart from haematological malignancies, this inhibitor has shown promising results in preclinical models of solid tumours. Being pan-inhibitor pracinostat targets various classical HDACs and has demonstrated antiproliferative properties in a series of cancer cell lines. Currently, no energetic and structural studies are available about the pracinostat against four HDAC isozymes of Class I. Taking this into account, the current study involved flexible molecular docking for gaining insights regarding pracinostat-HDAC isozyme interactions, molecular mechanics generalized born surface area (MM-GBSA) for estimating binding affinity of this inhibitor towards these isozymes and energetically optimized pharmacophores (e-Pharmacophores) technique for delineating the critical e-pharmacophoric features of pracinostat in its least energy state in the binding pocket of these HDACs. The outcome from this study will help in further optimization of pracinostat towards better therapeutic and the e-Pharmacophores generated will serve as queries in e-Pharamcophores guided virtual screening.
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Rodrigues DA, Pinheiro PDSM, Sagrillo FS, Bolognesi ML, Fraga CAM. Histone deacetylases as targets for the treatment of neurodegenerative disorders: Challenges and future opportunities. Med Res Rev 2020; 40:2177-2211. [DOI: 10.1002/med.21701] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 06/02/2020] [Accepted: 06/09/2020] [Indexed: 12/15/2022]
Affiliation(s)
- Daniel A. Rodrigues
- Laboratório de Avaliação e Síntese de Substâncias Bioativas (LASSBio), Instituto de Ciências Biomédicas Universidade Federal do Rio de Janeiro Rio de Janeiro Brazil
- Programa de Pós‐Graduação em Química, Instituto de Química Universidade Federal do Rio de Janeiro Rio de Janeiro Brazil
| | - Pedro de S. M. Pinheiro
- Laboratório de Avaliação e Síntese de Substâncias Bioativas (LASSBio), Instituto de Ciências Biomédicas Universidade Federal do Rio de Janeiro Rio de Janeiro Brazil
- Programa de Pós‐Graduação em Farmacologia e Química Medicinal, Instituto de Ciências Biomédicas Universidade Federal do Rio de Janeiro Rio de Janeiro Brazil
- Department of Pharmacy and Biotechnology Alma Mater Studiorum‐University of Bologna Bologna Italy
| | - Fernanda S. Sagrillo
- Laboratório de Avaliação e Síntese de Substâncias Bioativas (LASSBio), Instituto de Ciências Biomédicas Universidade Federal do Rio de Janeiro Rio de Janeiro Brazil
| | - Maria L. Bolognesi
- Department of Pharmacy and Biotechnology Alma Mater Studiorum‐University of Bologna Bologna Italy
| | - Carlos A. M. Fraga
- Laboratório de Avaliação e Síntese de Substâncias Bioativas (LASSBio), Instituto de Ciências Biomédicas Universidade Federal do Rio de Janeiro Rio de Janeiro Brazil
- Programa de Pós‐Graduação em Química, Instituto de Química Universidade Federal do Rio de Janeiro Rio de Janeiro Brazil
- Programa de Pós‐Graduação em Farmacologia e Química Medicinal, Instituto de Ciências Biomédicas Universidade Federal do Rio de Janeiro Rio de Janeiro Brazil
- Department of Pharmacy and Biotechnology Alma Mater Studiorum‐University of Bologna Bologna Italy
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Exploring the inhibitory activity of valproic acid against the HDAC family using an MMGBSA approach. J Comput Aided Mol Des 2020; 34:857-878. [PMID: 32180123 DOI: 10.1007/s10822-020-00304-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Accepted: 03/07/2020] [Indexed: 12/30/2022]
Abstract
Valproic acid (VPA) is a compound currently used in clinical practice for the treatment of epilepsy as well as bipolar and mood disorders. VPA targets histone deacetylases (HDACs), which participate in the removal of acetyl groups from lysine in several proteins, regulating a wide variety of functions within the organism. An imbalance or malfunction of these enzymes is associated with the development and progression of several diseases, such as cancer and neurodegenerative diseases. HDACs are divided into four classes, but VPA only targets Class I (HDAC1-3 and 8) and Class IIa (HDAC4-5, 7 and 9) HDACs; however, structural and energetic information regarding the manner by which VPA inhibits these HDACs is lacking. Here, the structural and energetic features that determine this recognition were studied using molecular docking and molecular dynamics (MD) simulation. It was found that VPA reaches the catalytic site in HDAC1-3 and 7, whereas in HDAC6, VPA only reaches the catalytic tunnel. In HDAC4, VPA was bound adjacent to L1 and L2, a zone that participates in corepressor binding, and in HDAC8, VPA was bound to the hydrophobic active site channel (HASC), in line with previous reports.
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HDAC2 Inhibitor Valproic Acid Increases Radiation Sensitivity of Drug-Resistant Melanoma Cells. Med Sci (Basel) 2019; 7:medsci7030051. [PMID: 30909413 PMCID: PMC6473314 DOI: 10.3390/medsci7030051] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 03/15/2019] [Accepted: 03/18/2019] [Indexed: 01/22/2023] Open
Abstract
Resistance to anticancer drugs limits the effectiveness of chemotherapy in cancers. Melanoma cell lines B16F10C and A375C (parental) and B16F10R and A375R (drug-resistant sublines) were used to test radiation sensitization potential of valproic acid (VPA), an inhibitor of Histone deacetylase2 (HDAC2) and LDN193189 (BMP inhibitor). Inhibitors of other signaling pathways were tested for cross-resistance with the resistant cell lines. Cells were pretreated with low concentrations of VPA/ LDN193189 and exposed to 2 Gy radiation for radiation sensitization experiments. Assays-3-(4,5-Dimethylthiazol-2-yl)-2,5-Diphenyltetrazolium Bromide (MTT), live/dead, clonogenic, and melanin estimation were performed to test the effects of radiation sensitization. Interactions of VPA and HDAC2 were studied in silico. Dose-dependent growth inhibition was observed with all tested drugs. Radiation sensitization of melanoma cells with low dose of VPA induced synergistic cell death, decreased clonogenicity, and decreased melanin content. In silico docking showed two stable interactions between Arg39 of HDAC2 and VPA. In conclusion, pretreatment with low doses of VPA has a potential for sensitizing melanoma cells to low doses of radiation. The binding of VPA to HDAC2 reverses the drug resistance in melanoma and induces the cell death. Sensitization effects of VPA can be used for targeting drug-resistant cancers.
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Lu W, Zhang R, Jiang H, Zhang H, Luo C. Computer-Aided Drug Design in Epigenetics. Front Chem 2018; 6:57. [PMID: 29594101 PMCID: PMC5857607 DOI: 10.3389/fchem.2018.00057] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 02/23/2018] [Indexed: 12/31/2022] Open
Abstract
Epigenetic dysfunction has been widely implicated in several diseases especially cancers thus highlights the therapeutic potential for chemical interventions in this field. With rapid development of computational methodologies and high-performance computational resources, computer-aided drug design has emerged as a promising strategy to speed up epigenetic drug discovery. Herein, we make a brief overview of major computational methods reported in the literature including druggability prediction, virtual screening, homology modeling, scaffold hopping, pharmacophore modeling, molecular dynamics simulations, quantum chemistry calculation, and 3D quantitative structure activity relationship that have been successfully applied in the design and discovery of epi-drugs and epi-probes. Finally, we discuss about major limitations of current virtual drug design strategies in epigenetics drug discovery and future directions in this field.
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Affiliation(s)
- Wenchao Lu
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- Department of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
| | - Rukang Zhang
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- Department of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
| | - Hao Jiang
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- Department of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
| | - Huimin Zhang
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Cheng Luo
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- Department of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
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