Docking Simulations and Virtual Screening to find Novel Ligands for T3S in Yersinia pseudotuberculosis YPIII, A drug target for type III secretion (T3S) in the Gram-negative pathogen Yersinia pseudotuberculosis

An aggregate use of molecular docking, molecular dynamics simulations, and ADMET was successfully used to create salicylidene acyl hydrazides as inhibitors of type III secretion (T3S) in the Gram-negative pathogen Yersinia pseudotuberculosis and Chlamydia. Molecular docking study was performed on the simulated protein of cytidine monophosphate (CMP) which helped to correlate interactions of amino acids encompassed to the ligand. Molecular dynamics simulations study uncovered that the A-chain of CMP protein was stable at and above 100ps concerning temperature, Total energy, and kinetic energy. Virtual screening was executed dependent on pharmacophore modeling and molecular docking to distinguish the new inhibitors. Ten top-ranked compounds were discovered based on the Rerank score fitness function. ADME studies were executed on compounds retrieved from virtual screening in compliance with the standard ranges. All the results can offer us more valuable evidence for our further drug design.