Molecular Docking Study of Aminoacyl-tRNA Synthetases with Ligand Molecules from Four Different Scaffolds

Abstract

Aminoacyl-tRNA synthetases (aaRSs) play vital roles in protein biosynthesis of living organisms and are interesting antibacterial drug targets. In order to find out new inhibitor candidate molecules as antibacterial agent, the binding modes of the candidate molecules were investigated at the active sites of aaRSs by molecular docking study. The docking simulations were performed with 48 compounds from four different scaffolds into the eight different aaRSs. The results show that scaffolds 3 and 4 compounds have consistently better binding capabilities, specifically for HisRS (E. coli) and IleRS (S. aureus). The binding modes of the best compounds with the proteins were well compatible with those of two ligands in crystal structures. Therefore, we expect that the final compounds we present may have reasonable aaRS inhibitory activity.

Macromolecular Docking Simulation to Identify Binding Site of FGB1 for Antifungal Compounds

“…Two methods are usually applied to define a binding site for a protein: (i) Based on the shape of receptor using "eraser" algorithm and (ii) Based on volume occupied by the known ligand pose already in an active site. 41,42 Here the first method was used to define the binding pocket of FGB1. We set the maximum poses retained as 10, RMS threshold for diversity as 1.5 Å and score threshold for diversity 20.0 kcal/mol.…”