Rational design of methicillin resistance staphylococcus aureus inhibitors through 3D-QSAR, molecular docking and molecular dynamics simulations. (April 2018)

• Record Type: Journal Article
• Authors: Ballu, Srilata; Itteboina, Ramesh; Sivan, Sree Kanth; Manga, Vijjulatha
• Is Part Of: Computational biology and chemistry. Volume 73(2018)
• Page Start: 95
• Page End: 104
• Publication Date: 2018-04
• Subjects: 3D-QSAR (Three dimensional quantitative structure activity relationship) -- CoMFA (comparative molecular field analysis) -- CoMSIA (comparative molecular similarity indices analysis) -- PLS (Partial least square) MD (Molecular dynamics) -- XP (Extra precision); Chemistry -- Data processing -- Periodicals; Biology -- Data processing -- Periodicals; Biochemistry -- Data processing; Biology -- Data processing; Molecular biology -- Data processing; Periodicals; Electronic journals; 542.85
• DOI: 10.1016/j.compbiolchem.2017.12.007
• Languages: English
• ISSNs: 1476-9271

Abstract

Graphical abstract: Rational design of methicillin resistance staphylococcus aureus inhibitors through 3D-QSAR, molecular docking and molecular dynamics simulations. Highlights: Computational studies were done on topoisomerase inhibitors of methicillin resistance staphylococcus aureus. Molecular docking method was used to examine possible interactions between receptors and the compounds. Results of the docking studies and molecular dynamics simulations complement each other. Ten derivatives as potential candidates of topoisomerase inhibitors with good predicted activities were designed. Abstract: Staphylococcus aureus is a gram positive bacterium. It is the leading cause of skin and respiratory infections, osteomyelitis, Ritter's disease, endocarditis, and bacteraemia in the developed world. We employed combined studies of 3D QSAR, molecular docking which are validated by molecular dynamics simulations and in silico ADME prediction have been performed on Isothiazoloquinolones inhibitors against methicillin resistance Staphylococcus aureus . Three-dimensional quantitative structure-activity relationship (3D-QSAR) study was applied using comparative molecular field analysis (CoMFA) with Q 2 of 0.578, R 2 of 0.988, and comparative molecular similarity indices analysis (CoMSIA) with Q 2 of 0.554, R 2 of 0.975. The predictive ability of these model was determined using a test set of molecules that gave acceptable predictive correlation (r 2 Pred) values 0.55 and 0.57 of CoMFA and CoMSIA respectively. Docking, simulations were employed to position the inhibitors into protein active site to find out the most probable binding mode and most reliable conformations. Developed models and Docking methods provide guidance to design molecules with enhanced activity.