Molecular dynamics simulation analysis of a modelled spermidine synthase from Yersinia pseudotuberculosis docked with cyclohexylamine

TL;DR

This paper studies the interaction between spermidine synthase from Yersinia pseudotuberculosis and cyclohexylamine using molecular docking and simulation.

Contribution

The study provides a novel molecular dynamics simulation analysis of spermidine synthase docked with cyclohexylamine for drug design.

Findings

Cyclohexylamine conformer 4-fluorocyclohexan-1-amine showed optimal binding with a score of -4.7 kcal/mol.

Molecular dynamics simulations confirmed the stability of the ligand binding pocket.

The protein structure analysis indicated high stability with specific amino acid composition and a GRAVY score of -0.125.

Abstract

The gram-negative bacterium Yersinia pestis is the causative agent of plague 1 and has been responsible for major pandemics in the
past. Therefore, it is of interest to document the molecular docking and simulation analysis of spermidine synthase from Yersinia
pseudotuberculosis with cyclohexylamine. The sequence and structure analysis showed an abundance of Leu, Val, Gly, Glu and Ala, the
least presence of Trp and Cys, higher negatively charged residues and a GRAVY score of -0.125, suggesting the stability of the protein.
The cyclohexylamine conformer 4-fluorocyclohexan-1-amine (CID 21027526) showed optimal binding features (-4.7 kcal/mol). Moreover,
molecular dynamics simulation confirmed the stability of the ligand binding pocket for further validation and consideration in drug
design and development.