MOLECULAR DYNAMICS SIMULATIONS OF SEVERAL SELECTED COMPOUNDS FROM THE HERBAL DATABASE OF INDONESIA RESULTS OF MOLECULAR DOCKING AGAINST DNA METHYLTRANSFERASE ENZYME

Objective: This study aimed to investigate the interactions of DNA methyltransferase (DNMT) enzymes and potential ligands as DNMT inhibitorsthrough molecular dynamics simulations.Methods: This study was conducted using tools in the form of hardware (primary and secondary computers) and software (OpenBabel, AutoDockTools, Amber MD, Amber Tools, VMD, PuTTY, LigandScout, and UCSF Chimera).Results: Results of molecular docking of cassiamin C, procyanidin B2, epicatechin-4alphaent-8-ent-epicatechin, epicatechin-4beta-8-epicatechin-3-O-gallate, neorhusflavanone, 3-O-galloylepigallocatechin -4beta-6-epicatechin-3-O-gallate, withanolide, 3-O-galloylepigallocatechin-4beta-6-epigallocatechin-3-O-gallate, cyanidin-3-6″-caffeylsophoroside-5-glucoside, epifriedelinol, gallocatechin-4alpha-8-epicatechin, scutellarein-7-glucosyl-1-4-rhamnoside, epigallocatechin-3-gallate (EGCG) (positive control), and sinefungin (co-crystal) compounds showed ΔG values −9.34,−10.95, −7.95, −11.01, −8.78, −8.87, −11.49, −7.98, −5.92, −8.92, −9.17, −8.76, −9.70, and −9.11 kcal/mol, respectively. Cassiamin C, procyanidin B2,epicatechin-4-beta-8-epicatechin-3-O-gallate, withanolide, and gallocatechin-4alpha-8-epicatechin compounds had lower ΔG than sinefungin (cocrystal)and EGCG (positive control) compounds. The results of molecular dynamic simulation of seven selected compounds showed the best overallactivities were procyanidin B2, epicatechin-4beta-8-epicatechin-3-O-gallate, and gallocatechin-4alpha-8-epi-catechin compounds.Conclusions: The best overall activities based on molecular docking and molecular dynamic simulation were procyanidin B2, epicatechin-4beta-8-epicatechin-3-O-gallate, and gallocatechin-4alpha-8-epi-catechin compounds. Amino acid residues that are important for the activity of DNMT1inhibitor are Phe1145, Glu1168, Met1169, Cys1191, Glu1266, Ala1579, and Val1580.

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Study on Nanolithography Process of Polycrystalline Copper Using Molecular Dynamic Simulation

Key Engineering Materials ◽

10.4028/www.scientific.net/kem.340-341.961 ◽

2007 ◽

Vol 340-341 ◽

pp. 961-966

Author(s):

Chan Il Kim ◽

Young Suk Kim ◽

Sang Il Hyun ◽

Seung Han Yang ◽

Jun Young Park ◽

...

Keyword(s):

Molecular Dynamics ◽

Grain Boundary ◽

Molecular Dynamic Simulation ◽

Molecular Dynamic ◽

Dynamic Simulation ◽

Diamond Like Carbon ◽

Polycrystalline Copper ◽

Berkovich Indenter ◽

Contact Surfaces ◽

Dynamics Simulations

Molecular dynamics simulations are performed to verify the effect of grain boundary on nanolithography process. The model with about two hundred thousand copper (Cu) atoms is composed of two different crystal orientations of which contact surfaces are (101) and (001) planes. The grain boundary is located on the center of model and has 45 degreeangle in xz-plane. The tool is made of diamond-like-carbon with the shape of Berkovich indenter. As the tool is indented and plowed on the surface, dislocations are generated. Moreover, during the plowing process, the steps as well as the typical pile-ups are formed in front of the tool. These defects propagate into the surface of the substrate. As the tool approaches to the grain boundary, the defects are seen to be accumulated near the grain boundary. The shape of the grain boundary is also significantly deformed after the tool passes it. We observed the forces exerted on the tool by the contact with substrate, so that the friction coefficients can be obtained to address the effect of the grain boundary on the friction characteristics.

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Ligand-based design, molecular dynamics and ADMET studies of suggested SARS-CoV-2 Mpro inhibitors

RSC Advances ◽

10.1039/d0ra10141a ◽

2021 ◽

Vol 11 (8) ◽

pp. 4523-4538

Author(s):

Nada M. Mohamed ◽

Eslam M. H. Ali ◽

Asmaa M. AboulMagd

Keyword(s):

Molecular Dynamics ◽

Molecular Docking ◽

Molecular Dynamic Simulation ◽

Molecular Dynamic ◽

Dynamic Simulation ◽

Pharmacophore Modeling ◽

Simulation Results

Compounds I–X were designed to inhibit SARS-CoV-2 Mpro based on pharmacophore modeling of SARS-CoV Mpro inhibitors. Compounds V and VI showed promising molecular docking and molecular dynamic simulation results that surpassed baicalein.

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