Computer molecular dynamics simulation studies of grain‐boundary structures. II. Migration, sliding, and annihilation in a two‐dimensional solid

1982 ◽  
Vol 53 (8) ◽  
pp. 5609-5616 ◽  
Author(s):  
George H. Bishop ◽  
Ralph J. Harrison ◽  
Thomas Kwok ◽  
Sidney Yip
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Grain Boundary ◽  
Dynamics Simulation ◽  
Two Dimensional ◽  
Simulation Studies

Synthesis of the tetrasaccharide repeating unit of the O-antigen of the Escherichia coli O69 strain and its conformational analysis

RSC Advances ◽  
2014 ◽  
Vol 4 (70) ◽  
pp. 37079-37084 ◽  
Author(s):  
Manas Jana ◽  
Rajiv Kumar Kar ◽  
Anirban Bhunia ◽  
Anup Kumar Misra
Keyword(s):  
Escherichia Coli ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Conformational Analysis ◽  
Dynamics Simulation ◽  
Two Dimensional ◽  
Simulation Studies ◽  
One Pot ◽  
E Coli ◽  
O Antigen

A tetrasaccharide corresponding to theO-antigen of theE. coliO69 strain has been synthesized using iterative glycosylations in one pot. The conformational analysis of the tetrasaccharide was carried out using two-dimensional ROESY spectroscopy and molecular dynamics simulation studies.

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 Molecular Docking and Molecular Dynamics Simulation Studies of Triterpenes from Vernonia patula with the Cannabinoid Type 1 Receptor

2021 ◽  
Vol 22 (7) ◽  
pp. 3595
Author(s):  
Md Afjalus Afjalus Siraj ◽  
Md. Sajjadur Rahman ◽  
Ghee T. Tan ◽  
Veronique Seidel
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Molecular Dynamics Simulation ◽  
Binding Affinity ◽  
Docking Studies ◽  
Dynamics Simulation ◽  
Simulation Studies ◽  
Cannabinoid Type 1 Receptor ◽  
Docking Approach

A molecular docking approach was employed to evaluate the binding affinity of six triterpenes, namely epifriedelanol, friedelin, α-amyrin, α-amyrin acetate, β-amyrin acetate, and bauerenyl acetate, towards the cannabinoid type 1 receptor (CB1). Molecular docking studies showed that friedelin, α-amyrin, and epifriedelanol had the strongest binding affinity towards CB1. Molecular dynamics simulation studies revealed that friedelin and α-amyrin engaged in stable non-bonding interactions by binding to a pocket close to the active site on the surface of the CB1 target protein. The studied triterpenes showed a good capacity to penetrate the blood–brain barrier. These results help to provide some evidence to justify, at least in part, the previously reported antinociceptive and sedative properties of Vernonia patula.

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