Molecular Modeling and Docking of Potential Inhibitors

The compound was designed using ChembioDraw Professional 13.0 [56 ] and was converted to 2D by using BIOVIA Discover Studio Visualizer 17.2.0.16349 [57 ]. Structure optimization was achieved by applying the Hahn forcefield [58 (link)]. Optimized structures were used for the docking study. Crystal structure of dihydropteroate synthase, 5uoy [59 (link)], DNA topoisomerase II gyrase; 5mmn [60 (link)], and SARS-CoV-2 spike; 6vsb [61 (link)] were retrieved from protein data bank with resolutions 1.82 Å, 1.90 Å and 3.46 Å respectively. Protein editing was done by means of Discovery Studio[57 ] which included the deletion of co-crystallized ligands, multiple chains, hetero atoms, the water of crystallization, the addition of polar hydrogens, energy minimization, and structure optimization [58 (link)]. Enhanced proteins were used for molecular docking.

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Ugwu D.I., Eze F.U., Ezeorah C.J., Rhyman L., Ramasami P., Tania G., Eze C.C., Uzoewulu C.P., Ogboo B.C, & Okpareke O.C. (2023). Synthesis, Structure, Hirshfeld Surface Analysis, Non-Covalent Interaction, and In Silico Studies of 4-Hydroxy-1-[(4-Nitrophenyl)Sulfonyl]Pyrrolidine-2-Carboxyllic Acid. Journal of Chemical Crystallography.

Publication 2023

Crystallization Deletion Dihydropteroate synthase Dna gyrase Hydrogens Ligands Proteins Sars cov 2 Topoisomerase ii

Corresponding Organization : North Carolina State University

Other organizations : University of South Carolina, University of Johannesburg, University of Mauritius, University of Auckland, University at Buffalo, State University of New York

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Variable analysis

independent variables

Chemical structure design using ChembioDraw Professional 13.0
2D conversion using BIOVIA Discover Studio Visualizer 17.2.0.16349
Structure optimization using Hahn forcefield

dependent variables

Molecular docking of optimized structures against dihydropteroate synthase, DNA topoisomerase II gyrase, and SARS-CoV-2 spike

control variables

Protein editing using Discovery Studio, including deletion of co-crystallized ligands, multiple chains, hetero atoms, water of crystallization, addition of polar hydrogens, energy minimization, and structure optimization

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