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Molecular dynamics simulation and QM/MM calculation reveal the selectivity mechanism of type I 1/2 kinase inhibitors: the effect of intramolecular H-bonds and conformational restriction for improved
TLDR
Computational methods including protein comparison, molecular docking, QM/MM, molecular dynamics simulations, and density functional theory (DFT) calculation revealed the crucial factors accounting for selective inhibition of PAK4 over NIK, including different protein-ligand interactions, the positions and conformations of key residues, and the ligands flexibilities.
Quinone–thioether metabolites of hydroquinone play a dual role in promoting a vicious cycle of ROS generation: in vitro and in silico insights
TLDR
Quinone–thioether metabolites of HQ afforded high affinity to the above proteins that purportedly cause a surge in the generation of ROS, providing a prospective insight into the mechanisms of ROS motivation, expanding HQ-mediated toxicology profiles.
Computational insights into the sorption mechanism of environmental contaminants by carbon nanoparticles through molecular dynamics simulation and density functional theory.
TLDR
It is proposed that CNTs and graphene- carbon nanoparticles can be used for the sorption of hydrophobic contaminants, and the GO-carbon nanoparticles are more suitable for the Sorption of polar and ionic contaminants.
Molecular docking, 3D-QSAR, and molecular dynamics simulations of thieno[3,2-b]pyrrole derivatives against anticancer targets of KDM1A/LSD1
TLDR
A molecular modeling study on a set of 43 thieno[3,2-b]pyrrole competitive inhibitors of LSD1 using three-dimensional quantitative structure-activity relationship (3D-QSAR), molecular docking and molecular dynamics simulations indicated the good predictive power and statistical reliability of this model.
Sacubitril-valsartan cocrystal revisited: role of polymer excipients in the formulation
TLDR
It is found that unappreciated excipients in the formulation, especially some polymers, might compete with the intermolecular hydrogen bonding among the cocrystals components and provide unexpected affinity, and thus leverage the therapeutic benefits.
Computational investigation reveals Picrasidine C as selective PPARα lead: binding pattern, selectivity mechanism and ADME/tox profile
TLDR
The detailed information of binding pattern and affinity for Picrasidine C elucidated here will be valuable for chemical modification and for finding more potent, safe and selective PPARα agonists during structural optimization.
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