MDM2 case study: Computational protocol utilizing protein flexibility and data mining improves ligand binding mode predictions

Abstract

Recovery of the P53 tumor suppressor pathway via small molecule inhibitors of oncoprotein MDM2 highlights the critical role of computational methodologies in targeted cancer therapies. Molecular docking programs in particular, have become essential during computer-aided drug design by providing a quantitative ranking of predicted binding geometries of small ligands to proteins based on binding free energy. In this study, we found improved ligand binding mode predictions of small medicinal compounds to MDM2 based on RMSD values using AutoDock and AutoDock Vina employing protein binding site flexibility. Additional analysis suggests a data mining protocol using linear regression can isolate the particular flexible bonds necessary for future optimum docking results. The implementation of a flexible receptor protocol based on a priori knowledge obtained from data mining will improve accuracy and reduce costs of high throughput virtual screenings of potential cancer drugs targeting MDM2.