In silico studies of 2-aryloxy-1,4- naphthoquinone derivatives as antibacterial agents against Escherichia coli using 3D-QSAR, ADMET properties, molecular docking, and molecular dynamics
{"title":"In silico studies of 2-aryloxy-1,4- naphthoquinone derivatives as antibacterial agents against Escherichia coli using 3D-QSAR, ADMET properties, molecular docking, and molecular dynamics","authors":"Khaoula Mkhayar , Rachid Haloui , Ossama Daoui , Kaouakeb Elkhattabi , Samir Chtita , Souad Elkhattabi","doi":"10.1016/j.cdc.2023.101060","DOIUrl":null,"url":null,"abstract":"<div><p>In this study, we investigated 30 derivatives of naphthoquinone using 3D-QSAR, drug-likeness, ADMET, molecular docking, and dynamics techniques in silico. The objective is carried out to elaborate the robust 3D-QSAR models using the CoMFA to discover new antibacterial agents against Escherichia coli. High predictive power has been demonstrated by the QSAR models based on their evaluations (Q<sup>2</sup> = 0.613, R<sup>2</sup> = 0.902, SEE = 0.063). Using the QSAR model predictions, new four molecular structures are designed. As a next step, we examined the four compounds' drug-likeness and ADMET predictions. Two compounds have excellent ADMET predictions and drug-likeness. Molecular docking was used to examine the bindings established between the newly designed molecule 1 and 2 with the protein. Based on the obtained results, the compound 2 exhibits high stability. To confirm this stability, we performed molecular dynamics during 100 ns under three different temperature conditions. High stability was confirmed by molecular dynamics simulations.</p></div>","PeriodicalId":269,"journal":{"name":"Chemical Data Collections","volume":null,"pages":null},"PeriodicalIF":2.2180,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"1","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Chemical Data Collections","FirstCategoryId":"1085","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S240583002300071X","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"Chemistry","Score":null,"Total":0}
引用次数: 1
Abstract
In this study, we investigated 30 derivatives of naphthoquinone using 3D-QSAR, drug-likeness, ADMET, molecular docking, and dynamics techniques in silico. The objective is carried out to elaborate the robust 3D-QSAR models using the CoMFA to discover new antibacterial agents against Escherichia coli. High predictive power has been demonstrated by the QSAR models based on their evaluations (Q2 = 0.613, R2 = 0.902, SEE = 0.063). Using the QSAR model predictions, new four molecular structures are designed. As a next step, we examined the four compounds' drug-likeness and ADMET predictions. Two compounds have excellent ADMET predictions and drug-likeness. Molecular docking was used to examine the bindings established between the newly designed molecule 1 and 2 with the protein. Based on the obtained results, the compound 2 exhibits high stability. To confirm this stability, we performed molecular dynamics during 100 ns under three different temperature conditions. High stability was confirmed by molecular dynamics simulations.
期刊介绍:
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