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

Year: 2025

Type: article

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 dyanmics simulation confirmed the stability of the ligand binding pocket for further validation and consideration in drug design and development.

Source: Bioinformation

DOI: 10.6026/973206300210210

Authors: Krishna Kuna, Srinivas Ganta, Pavan C. Akkiraju, Sudheer Kumar Dokuparthi, Biogenic Products Private Limited, Hyderabad-500007, Telangana State, India, Sardar Hussain, Sreenivas Enaganti

Institutions: Osmania University, Malla Reddy University, Malla Reddy Vishwavidyapeeth, University of Mysore

Language: English

Topic: Computational Drug Discovery Methods

Subfield: Computational Theory and Mathematics

Field: Computer Science

Domain: Physical Sciences

Open Access status: hybrid

OpenAlex ID: W4408633670

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