Mechanistic Insights into the inhibition of Plasmodium falciparum DNA gyrase A by withanolides derivatives through integrated computational analysis

Malaria is a fatal disease affecting millions of people worldwide, primarily due to infection by Plasmodium falciparum. The emergence of multidrug-resistant parasite strains has necessitated the exploration of novel therapeutic targets, among which DNA gyrase represents a unique and underexploited enzyme in the parasites replication machinery. Plasmodium falciparum DNA gyrase A (pfDNA gyrase), an essential topoisomerase II that is not present in humans, has been identified as a promising target for antimalarial drug development. Present study deals with a structure based computational approach to characterize the binding mechanism and dynamic stability of three bioactive withanolide derivatives (D, E, and O) against pfDNA gyrase. Molecular docking revealed high binding affinities for withanolide D (-9.14kcal/mol), E (-9.73kcal/mol), and O (-9.00kcal/mol), with interactions mediated through key catalytic residues such as GLU648, LYS647, and TRY590 via hydrogen bonding and hydrophobic contacts. Stability of the ligand-protein complexes was further assessed through molecular dynamics simulations, where analyses of RMSD, RMSF, radius of gyration (Rg), and solvent accessible surface area (SASA) analysis confirmed the structural integrity and compactness of the complexes, notably withanolide O exhibited the most favorable dynamic profile, whereas withanolide E induced confirmational rigidity. MM/GBSA calculations are further supported by showing the lowest binding free energy for withanolide O and E ({Delta}Gbind =-20.89 and -20.22 kcal/mol). The ADME studies showed favorable pharmacokinetic and physiochemical properties of three ligands. Collectively, these findings highlight the potential of withanolide derivatives as promising inhibitors of pfDNA gyrase, thereby paving a way for the foundation of future antimalarial drug development.