Theoretical Insight into the Library Screening Approach for Binding of Intermolecular G-Quadruplex RNA and Small Molecules through Docking and Molecular Dynamics Simulation Studies

2021 ◽  
Author(s):  
Soma Roy ◽  
Asfa Ali ◽  
Santanu Bhattacharya
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Small Molecules ◽  
Dynamics Simulation ◽  
Library Screening ◽  
Simulation Studies ◽  
Screening Approach ◽  
G Quadruplex ◽  
Theoretical Insight ◽  
Insight Into

The effect of amino substituents on the interactions of quinazolone derivatives with c-KIT G-quadruplex: insight from molecular dynamics simulation study for rational design of ligands

RSC Advances ◽  
2015 ◽  
Vol 5 (93) ◽  
pp. 76642-76650 ◽  
Author(s):  
Kiana Gholamjani Moghaddam ◽  
Seyed Majid Hashemianzadeh
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Simulation Study ◽  
Rational Design ◽  
Ligand Design ◽  
Dynamics Simulation ◽  
Rational Ligand Design ◽  
G Quadruplex ◽  
Ligand Interactions ◽  
Insight Into

Our study provides insight into the effect of different substituents on the G-quadruplex–ligand interactions which helps us rational ligand design.

Insight into the adsorption profiles of the Saprolegnia monoica chitin synthase MIT domain on POPA and POPC membranes by molecular dynamics simulation studies

2016 ◽  
Vol 18 (7) ◽  
pp. 5281-5290 ◽  
Author(s):  
Guanglin Kuang ◽  
Lijun Liang ◽  
Christian Brown ◽  
Qi Wang ◽  
Vincent Bulone ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulation ◽  
Binding Free Energy ◽  
Binding Mode ◽  
Chitin Synthase ◽  
Dynamics Simulation ◽  
Simulation Methods ◽  
Simulation Studies ◽  
Insight Into

The binding mode and binding free energy of the Saprolegnia monoica chitin synthase MIT domain with the POPA membrane have been studied by molecular simulation methods.

scholarly journals Computational Investigations on the Binding Mode of Ligands for the Cannabinoid-Activated G Protein-Coupled Receptor GPR18

Biomolecules ◽  
2020 ◽  
Vol 10 (5) ◽  
pp. 686 ◽  
Author(s):  
Alexander Neumann ◽  
Viktor Engel ◽  
Andhika B. Mahardhika ◽  
Clara T. Schoeder ◽  
Vigneshwaran Namasivayam ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
G Protein ◽  
Phenyl Ring ◽  
Binding Mode ◽  
Dynamics Simulation ◽  
Simulation Studies ◽  
Binding Modes ◽  
G Protein Coupled Receptor ◽  
G Protein Coupled

GPR18 is an orphan G protein-coupled receptor (GPCR) expressed in cells of the immune system. It is activated by the cannabinoid receptor (CB) agonist ∆9-tetrahydrocannabinol (THC). Several further lipids have been proposed to act as GPR18 agonists, but these results still require unambiguous confirmation. In the present study, we constructed a homology model of the human GPR18 based on an ensemble of three GPCR crystal structures to investigate the binding modes of the agonist THC and the recently reported antagonists which feature an imidazothiazinone core to which a (substituted) phenyl ring is connected via a lipophilic linker. Docking and molecular dynamics simulation studies were performed. As a result, a hydrophobic binding pocket is predicted to accommodate the imidazothiazinone core, while the terminal phenyl ring projects towards an aromatic pocket. Hydrophobic interaction of Cys251 with substituents on the phenyl ring could explain the high potency of the most potent derivatives. Molecular dynamics simulation studies suggest that the binding of imidazothiazinone antagonists stabilizes transmembrane regions TM1, TM6 and TM7 of the receptor through a salt bridge between Asp118 and Lys133. The agonist THC is presumed to bind differently to GPR18 than to the distantly related CB receptors. This study provides insights into the binding mode of GPR18 agonists and antagonists which will facilitate future drug design for this promising potential drug target.

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