scholarly journals New Insights into the Binding Mode of Melanin Concentrating Hormone Receptor-1 Antagonists: Homology Modeling and Explicit Membrane Molecular Dynamics Simulation Study

2011 ◽  
Vol 51 (3) ◽  
pp. 635-646 ◽  
Author(s):  
Mohamed A. Helal ◽  
Amar G. Chittiboyina ◽  
Mitchell A. Avery
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Homology Modeling ◽  
Simulation Study ◽  
Hormone Receptor ◽  
Binding Mode ◽  
Dynamics Simulation ◽  
Melanin Concentrating Hormone

Identification of the inhibitory mechanism of FDA approved selective serotonin reuptake inhibitors: an insight from molecular dynamics simulation study

2016 ◽  
Vol 18 (4) ◽  
pp. 3260-3271 ◽  
Author(s):  
Weiwei Xue ◽  
Panpan Wang ◽  
Bo Li ◽  
Yinghong Li ◽  
Xiaofei Xu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Major Depression ◽  
Computational Methods ◽  
Simulation Study ◽  
Serotonin Reuptake ◽  
Selective Serotonin Reuptake Inhibitors ◽  
Binding Mode ◽  
Dynamics Simulation ◽  
Inhibitory Mechanism

The binding mode shared by 4 FDA approved SSRIs treating major depression was identified by integrating multiple computational methods.

scholarly journals Title should read as “Homology modeling and molecular dynamics simulation study of β carbonic anhydrase of Ascaris lumbricoides” in Yadav & Khandelwal, (2019)

2021 ◽  
Vol 17 (4) ◽  
pp. 528-529
Author(s):  
Yadav M
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Carbonic Anhydrase ◽  
Homology Modeling ◽  
Simulation Study ◽  
Ascaris Lumbricoides ◽  
Dynamics Simulation

Title should read as “Homology modeling and molecular dynamics simulation study of β carbonic anhydrase of Ascaris lumbricoides” in Yadav & Khandelwal, (2019)

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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