Molecular dynamics and virtual screening
Homology modeling, molecular dynamics, and virtual screening of NorA efflux pump inhibitors of <em>Staphylococcus aureus</em>
... 1PW4). Molecular dynamics (MD) simulation was performed using ...helices. Molecular docking of reser- pine, totarol, ferruginol, salvin, thioxanthene, phenothiazine, omeprazole, verapamil, nalidixic ...
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Identification of polyketide synthase 13 inhibitor: Pharmacophore-based virtual screening and molecular dynamics simulation
... perform virtual screening on ZINC database to identify small molecules of Pks13 ...obtained virtual hits of 107 small molecules were subjected to molecular docking studies employing iDock ...
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ENERGY BASED PHARMACOPHORE MODELING, VIRTUAL SCREENING, AND MOLECULAR DYNAMICS TO IDENTIFY POTENTIAL INHIBITORS FOR GLYCOGEN SYNTHASE KINASE 3 BETA
... Comparative molecular docking of nitrofurazone, sulfathiazole (standard drugs) and entagenic acid, triterpenoid lupeol, and oleanolic acid (phytocompounds) with GSK3β was ...by molecular dynamics ...
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Virtual screening for potential inhibitors of Mcl-1 conformations sampled by normal modes, molecular dynamics, and nuclear magnetic resonance
... is part of the AMBER package, were used. Clustering is a means of partitioning data so that data points inside a cluster are more similar to each other than they are to points out- side a cluster. In the context of ...
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Virtual screening and molecular dynamics simulation suggest Valproic acid Co-A could bind to SARS-CoV2 RNA depended RNA polymerase
... Similar contact patterns from the two virtual docking supports valproic acid co-A as a potential RdRp blocker. Valproic acid Co-A generates from prodrug valproic acid by one stem metabolic pathway (Fig. 3) by ...
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Virtual Screening and Molecular Dynamics Study on Blockage of Key Drug Targets as Treatment for COVID-19 caused by SARS-CoV-2
... Docking and then calculating binding free energy were performed as workflow against four key anti-SARS-CoV-2 drug targets, 3CLpro, PLpro and RdRp from SARS-CoV- 2, and AAK1 from hum[r] ...
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Virtual Screening of Natural Products, Molecular Docking and Dynamics Simulations on M.tuberculosis S-adenosyl-L-homocysteine Hydrolase
... Since in vitro and in vivo testing of binding affinities of a vast collection of compounds to TB protein targets are time consuming and expensive, computer-aided drug discovery has been used as a more practical and ...
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IN-SILICO APPROACH FOR THE IDENTIFICATION OF NEW MOLECULES FOR ALZHEIMER’S DISEASE (AD)
... pharmacophore-based virtual screening, molecular docking, rescoring for validation of molecular docking and ADMET analysis and binding interaction was ...Finally, molecular ...
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Computational Modeling on Aquaporin-3 as Skin Cancer Target: A Virtual Screening and Molecular Dynamic Simulation Study
... stability, dynamics, reliability, and underlying molecular interactions of the docked poses at the atomic level, the top 20 docked poses were submitted for molecular dynamics ...the ...
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High-throughput virtual screening with e-pharmacophore and molecular simulations study in the designing of pancreatic lipase inhibitors
... Based on these observations, huge deviations were noted in the RMSD of the protein–ligand docked complex, lead- ing to the instability in the hydrogen-bond network between complexes except in 1LPB–zinc 85893731. The ...
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DESIGN, SYNTHESIS AND VIRTUAL SCREENING OF CERTAIN 2 PYRAZOLIN 5 ONE AND PYRAZOLIDINE 3, 5 DIONE DERIVATIVES AS POTENTIAL PPAR AGONISTS
... of Molecular Modeling Studies: Comparing the Fit values of the virtual screening of the generated and validated PPAR agonist hypothesis obtained by using Catalyst HipHop modules, together with the ...
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Pharmacoinformatic and molecular docking studies reveal potential novel antidepressants against neurodegenerative disorders by targeting HSPB8
... Comparative molecular docking studies were analyzed by AutoDock 4 and AutoDock Vina, which revealed the ligand–receptor interactions of the most representative ...in molecular docking studies of selected ...
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Structure-Based Design of Inhibitors Against Maltosyltransferase Glge
... employed. The top three lead compounds, ZINC39010596, ZINC31163371 and ZINC31166471 were the ones modified using the De Novo Evolution protocol. In the De Novo Evolution protocol of DS2.5, modifications (i.e. addition of ...
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In silico identification of novel ligand molecules for rabies nucleoprotein using structure-based method.
... protein. Molecular docking study of Nucleoprotein with ligands derived from virtual screening divulges that ZINC01530604 and ZINC01530605 ligands molecules could be the potential lead molecule ...
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IVSPlat 1.0: an integrated virtual screening platform with a molecular graphical interface
... is used to identify candidate lead compounds. Thus, SBVS is not dependent on the existence of known active com- pounds, which increases the prospects for identifying new active lead compounds [3]. Several docking ...
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3D Pharmacophore-based Virtual Screening, Docking Approaches toward the Discovery of Novel HPPD Inhibitors
... useful molecular target in treating life-threatening tyrosinemia type I, but also an important target for chemical ...and molecular docking based virtual screening were performed to identify ...
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CVDHD: a cardiovascular disease herbal database for drug discovery and network pharmacology
... The lead generation is a crucial step in drug discovery [32]. Nowadays, HTS has become the major paradigm for lead discovery from chemical libraries [32,33]. Lipinski’s “rule of five” (molecular weight less than ...
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Combining structure-based pharmacophore modeling, virtual screening, and in silico ADMET analysis to discover novel tetrahydro-quinoline based pyruvate kinase isozyme M2 activators with antitumor activity
... An in vitro pyruvate kinase enzymatic assay was performed. Hit Compound 8, which was identified from the virtual screen, possessed the highest AC 50 (activation concentration 50%) value versus 0.111 μ M PKM2. ...
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In silico discovery and in vitro activity of inhibitors against <em>Mycobacterium tuberculosis</em> 7,8-diaminopelargonic acid synthase (<em>Mtb</em> BioA)
... The docking experiment with ACM returned a binding energy of - 158.81 kcal/mol, which was set as the threshold value in our screening. Out of over 4 million compounds, 45 turned out to have better binding energies ...
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INSILICO PHARMACOPHORE ANALYSIS OF POTENTIAL INHIBITORS TO TREAT THE COMPLICATIONS OF EMERGING INFECTIOUS BOURBON VIRUS
... using virtual screening and molecular docking approaches to a specific target of Bourbon virus (Matrix Protein), which was modeled using computational ...their molecular properties and ...
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