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

The gram-negative bacterium <i>Yersinia pestis</i> 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 <i>Yersinia</i> 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.