Mechanistic Insights into the Inhibition of Plasmodium falciparum DNA Gyrase A by Withanolide Derivatives through Integrated Computational Analysis
Bini Chhetri Soren, Soujanya J. Vastrad, Syed Junied, Diya Srikanth, Aparna Chimalamari, BJ Mahender Kumar Jayappa, Jagadish Babu DasariIntroduction:
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. Plasmodium falciparum DNA gyrase A (pfDNA gyrase A), an essential topoisomerase II that is not present in humans, is a promising antimalarial drug target. This study explores the inhibitory potential of three Withania somnifera withanolide derivatives, D, E, and O, against pfDNA gyrase A
Methods:
An integrated structure-based computational analysis was conducted to explore the inhibitory potential of three withanolides (D, E, and O) against pfDNA gyrase A. Molecular docking, Molecular Dynamics (MD) simulations, and Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) free energy calculations were performed. Pharmacokinetic properties were analysed using SWISS ADME and pkCSM tools.
Results:
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. MD simulations confirmed the structural integrity and compactness of the complexes through Root Mean Square Deviation (RMSD), Root Mean Square Fluctuation (RMSF), Radius of Gyration (Rg), and Solvent Accessible Surface Area (SASA). MM/GBSA calculations are further supported by showing the lowest binding free energy for withanolide O and E (ΔGbind =-20.89 and -20.22 kcal/mol). The ADME studies showed favourable pharmacokinetic and physicochemical properties
Discussion:
This study identifies pfDNA gyrase A as a potential molecular target of Withania somnifera-derived withanolides and elucidates their inhibitory mechanism. Withanolides O and E exhibited strong binding affinity, favorable energetics, and distinct dynamic effects, acting through activesite occlusion and allosteric modulation, respectively. Molecular dynamics and free-energy analyses suggest that effective inhibition results from both structural stabilization and the disruption of critical enzyme motions.
Conclusion:
Withanolide derivatives were identified as promising inhibitors of pfDNA gyrase A, highlighting their potential as antimalarial agents for addressing drug-resistant malaria.