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Published on: January 16, 2016
Molecular dynamics simulation analysis of a modelled spermidine synthase from Yersinia pseudotuberculosis docked with
Krishna Kuna1, Srinivas Ganta2, Pavan C Akkiraju3
1Department of Chemistry, University College of Science, Saifabad, Osmania University, Hyderabad-500004, Telangana, India.
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.
Insights
Researchers analyzed spermidine synthase from Yersinia pseudotuberculosis and its interaction with cyclohexylamine. This study provides insights into potential drug development for plague, caused by Yersinia pestis.
Area of Science:
- Microbiology and Molecular Biology
- Drug Discovery and Development
Background:
- Plague, caused by Yersinia pestis, is a re-emerging infectious disease with significant pandemic potential.
- Understanding the molecular mechanisms of Yersinia virulence factors is crucial for developing effective treatments.
Purpose of the Study:
- To perform molecular docking and simulation analysis of spermidine synthase from Yersinia pseudotuberculosis.
- To investigate the binding interaction between Yersinia spermidine synthase and cyclohexylamine derivatives for potential drug development.
Main Methods:
- Sequence and structural analysis of Yersinia spermidine synthase.
- Molecular docking of cyclohexylamine conformers with the target protein.
- Molecular dynamics simulation to assess ligand-protein complex stability.
Main Results:
- Sequence analysis revealed a stable protein structure with a GRAVY score of -0.125.
- The 4-fluorocyclohexan-1-amine conformer exhibited optimal binding affinity (-4.7 kcal/mol).
- Molecular dynamics simulations confirmed the stability of the ligand-binding pocket.
Conclusions:
- The Yersinia spermidine synthase-cyclohexylamine interaction is a promising target for anti-plague drug design.
- Further validation and development are warranted for therapeutic applications against Yersinia infections.
