Title

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

Authors

Krishna Kuna¹, Srinivas Ganta², Pavan C. Akkiraju³, Sudheer Kumar Dokuparthi⁴, Sardar Hussain⁵ & Sreenivas Enaganti^6,*

Affiliation

¹Department of Chemistry, University College of Science, Saifabad, Osmania University, Hyderabad-500004, Telangana, India; ²Department of RNA Therapeutic, SciGen Pharmaceutical Inc., Hauppauge, NewYork-11788, United States of America; ³Department of Biotechnology, School of Allied Healthcare Sciences, Malla Reddy University, Hyderabad-500043, Telangana State, India; ⁴Biogenic Products Private Limited, Hyderabad-500007, Telangana State, India; ⁵Department of Biotechnology, Maharani's Science College for Women, Mysuru 570005, Karnataka, India; ⁶Department of Bioinformatics Averinbiotech Laboratories, No 208, 2nd Floor, Windsor Plaza, Nallakunta, Hyderabad-500044, Telangana, India; *Corresponding author

Email

Krishna Kuna - E - mail: Krishn.Kuna@gmail.com
Srinivas Ganta - E - mail: Srinivasg87@yahoo.com
Pavan C. Akkiraju - E - mail: drakkiraju_pavanchand@mallareddyuniversity.ac.in
Sudheer Kumar Dokuparthi - E - mail: sudheeroffice17@gmail.com
Sardar Hussain - E - mail: sardar1109@gmail.com
Sreenivas Enaganti - E - mail: sreenivas.bioinfo@gmail.com

Article Type

Research Article

Date

Received February 1, 2025; Revised February 28, 2025; Accepted February 28, 2025, Published February 28, 2025

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.

Keywords

Aminopropyl transferase spermidine synthase, spermidine synthase, Yersinia pseudotuberculosis, homology modeling, molecular docking, molecular dynamics

Citation

Kuna et al. Bioinformation 21(2): 210-219 (2025)

Edited by

P Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.