{"title":"Molecular dynamics simulation analysis of a modelled spermidine synthase from <i>Yersinia pseudotuberculosis</i> docked with cyclohexylamine.","authors":"Krishna Kuna, Srinivas Ganta, Pavan C Akkiraju, Sudheer Kumar Dokuparthi, Sardar Hussain, Sreenivas Enaganti","doi":"10.6026/973206300210210","DOIUrl":null,"url":null,"abstract":"<p><p>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.</p>","PeriodicalId":8962,"journal":{"name":"Bioinformation","volume":"21 2","pages":"210-219"},"PeriodicalIF":1.9000,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12044185/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Bioinformation","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.6026/973206300210210","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2025/1/1 0:00:00","PubModel":"eCollection","JCR":"","JCRName":"","Score":null,"Total":0}
引用次数: 0
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.
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