DFT, Molecular Docking and Molecular Dynamics Simulation Studies on Some Newly Introduced Natural Products for Their Potential Use Against SARS-CoV-2.
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TLDR
In this article, density functional theory (DFT) calculations were performed on the investigated compounds and geometry optimized structures were subjected to molecular docking calculations with the use of SARS-CoV-2 main protease (pdb id: 5r80) and top-scoring ligand-receptor complexes were obtained.About:
This article is published in Journal of Molecular Structure.The article was published on 2021-05-22 and is currently open access. It has received 19 citations till now. The article focuses on the topics: Molecular dynamics.read more
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Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2
TL;DR: There is a tsunami of literature on the molecular modeling, simulations, and predictions of SARS-CoV-2 and related developments of drugs, vaccines, antibodies, and diagnostics as discussed by the authors .
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Comparative study of the interaction of ivermectin with proteins of interest associated with SARS-CoV-2: A computational and biophysical approach.
Lenin A. González-Paz,Lenin A. González-Paz,María Laura Hurtado-León,Carla A. Lossada,Francelys V. Fernández-Materán,Joan Vera-Villalobos,Marcos Loroño,José Luis Paz,Laura Jeffreys,Ysaias J. Alvarado +9 more
TL;DR: In this article, a comparative analysis of the potential theoretical inhibitory effect of avermectins on biomolecules associated with COVID-19, and suggest that ivermectin through its homologs, has a multiobjective behavior.
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(2E)-2-(4-ethoxybenzylidene)-3,4-dihydro-2H-naphthalen-1-one single crystal: Synthesis, growth, crystal structure, spectral characterization, biological evaluation and binding interactions with SARS-CoV-2 main protease
TL;DR: In this paper, a new α-Tetralone based chalcone compound, (2E)-2-(4-ethoxybenzylidene)-3,4-dihydro-2H-naphthalen-1-one (EBDN), has been synthesized by Claisen-Schmidt condensation reaction of α tetralone (1) with 4-ethoxbenzaldehyde (2) in basic medium.
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Discovery of novel 3-butyl-6-benzyloxyphthalide Mannich base derivatives as multifunctional agents against Alzheimer's disease.
TL;DR: Based on the multitarget-directed ligands strategy, a series of 3-butyl-6-benzyloxyphthalide Mannich base derivatives were designed, synthesized and identified for Alzheimer's disease (AD) as mentioned in this paper .
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Interaction of panduratin A and derivatives with the SARS-CoV-2 main protease (mpro): a molecular docking study
Gérard Vergoten,Christian Bailly +1 more
TL;DR: The interaction of Pa-A, and 26 panduratin analogues with the main protease (Mpro) of SARS-CoV-2 using molecular docking is modeled, providing novel ideas to guide the design of new molecules interacting with Mpro.
References
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Journal ArticleDOI
AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
Oleg Trott,Arthur J. Olson +1 more
TL;DR: AutoDock Vina achieves an approximately two orders of magnitude speed‐up compared with the molecular docking software previously developed in the lab, while also significantly improving the accuracy of the binding mode predictions, judging by tests on the training set used in AutoDock 4 development.
Journal ArticleDOI
AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility
Garrett M. Morris,Ruth Huey,William Lindstrom,Michel F. Sanner,Richard K. Belew,David S. Goodsell,Arthur J. Olson +6 more
TL;DR: AutoDock4 incorporates limited flexibility in the receptor and its utility in analysis of covalently bound ligands is reported, using both a grid‐based docking method and a modification of the flexible sidechain technique.
Journal ArticleDOI
Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings
TL;DR: Experimental and computational approaches to estimate solubility and permeability in discovery and development settings are described in this article, where the rule of 5 is used to predict poor absorption or permeability when there are more than 5 H-bond donors, 10 Hbond acceptors, and the calculated Log P (CLogP) is greater than 5 (or MlogP > 415).
Journal ArticleDOI
GROMACS: Fast, flexible, and free
David van der Spoel,Erik Lindahl,Berk Hess,Gerrit Groenhof,Alan E. Mark,Herman J. C. Berendsen +5 more
TL;DR: The software suite GROMACS (Groningen MAchine for Chemical Simulation) that was developed at the University of Groningen, The Netherlands, in the early 1990s is described, which is a very fast program for molecular dynamics simulation.
Journal ArticleDOI
Electrostatics of nanosystems: Application to microtubules and the ribosome
TL;DR: The application of numerical methods are presented to enable the trivially parallel solution of the Poisson-Boltzmann equation for supramolecular structures that are orders of magnitude larger in size.