Prediction of the binding modes between BB-83698 and peptide deformylase from Bacillus stearothermophilus by docking and molecular dynamics simulation

2008 ◽  
Vol 134 (3) ◽  
pp. 178-184 ◽  
Author(s):  
Qiang Wang ◽  
Jianwu Wang ◽  
Zhengting Cai ◽  
Weiren Xu
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Bacillus Stearothermophilus ◽  
Dynamics Simulation ◽  
Peptide Deformylase ◽  
Binding Modes

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.

scholarly journals Multiple binding modes of a small molecule to human Keap1 revealed by X-ray crystallography and molecular dynamics simulation

FEBS Open Bio ◽  
2015 ◽  
Vol 5 (1) ◽  
pp. 557-570 ◽  
Author(s):  
Mikiya Satoh ◽  
Hajime Saburi ◽  
Tomoyuki Tanaka ◽  
Yoshinori Matsuura ◽  
Hisashi Naitow ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Small Molecule ◽  
Dynamics Simulation ◽  
Binding Modes ◽  
X Ray ◽  
X Ray Crystallography ◽  
Multiple Binding

Molecular Modeling and Molecular Dynamics Simulation of the Human A2BAdenosine Receptor. The Study of the Possible Binding Modes of the A2BReceptor Antagonists

2005 ◽  
Vol 48 (22) ◽  
pp. 6813-6820 ◽  
Author(s):  
Andrei A. Ivanov ◽  
Igor I. Baskin ◽  
Vladimir A. Palyulin ◽  
Laura Piccagli ◽  
Pier G. Baraldi ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Modeling ◽  
Molecular Dynamics Simulation ◽  
Dynamics Simulation ◽  
Binding Modes

A Molecular Dynamics Simulation of the Binding Modes of d-Glutamate and d-Glutamine to Glutamate Racemase

2005 ◽  
Vol 1 (4) ◽  
pp. 737-749 ◽  
Author(s):  
Eduard Puig ◽  
Mireia Garcia-Viloca ◽  
Àngels González-Lafont ◽  
Inés López ◽  
Xavier Daura ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Dynamics Simulation ◽  
Binding Modes ◽  
Glutamate Racemase
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