| PI3Kα is a promising target for anticancer drug design. Many human cancers show genetic aberrations in the phosphatidylinositol 3-kinaseα (PI3Kα) signaling pathway. PIK3CA, the gene encoding PI3Kα, is mutated, amplified, and overexpressed in numerous and diverse human cancers. Somatic mutations in PIK3CA cluster in the helical (E542K, E545K) and kinase (H1047R) domains. These mutations increase the lipid kinase activity of PI3Kα and stimulate the AKT signaling pathway.;In this study, we implemented structure-based and ligand-based drug design approaches to identify selective PI3Kα inhibitors. We investigated the coordinates of wild-type PI3Kα/γ and mutant (H1047R) PI3Kα to explore a structural basis of binding selectivity. Our docking studies against the crystal structures and molecular dynamic (MD) extracted trajectories showed that structural and size differences in the activation and hydrophobic domains of PI3Kα, PI3Kγ, and mutant (H1047R) PI3Kα could be exploited to direct the design of isoform- and/or mutant-specific PI3K inhibitors. Our ligand-based phamacophore model suggested that a PI3Kα selective inhibitor should harbor at least three aromatic rings and two H-bond acceptors. We searched the pharmacophore model against the National Cancer Institute (NCI) database of 260,071 compounds. Extensive refinement synchronous with biological assays identified NSC79888, NSC408120, and NSC675972 as new PI3Kα inhibitors. Our computational strategies have culminated in the discovery of a series of 4-hydroxy-2-quinolone-3-carboxamides as novel, potent, and selective MUT (H1047R) PI3Kα inhibitors. We performed energetic analysis using molecular mechanics/generalized born surface area (MM/GBSA) to estimate the binding free energy (ΔGbind) of the bound ligands in PI3Ks binding domains. The free energies of binding of PI3Kγ models (-9.39 and -9.58 Kcal/mol) are in a very good agreement with the experimental value (-9.10 Kcal/mol). We carried out computational alanine scanning to evaluate the relative changes in the binding free energies resulting from mutating key binding residues, and explored the contribution of individual residues on protein binding. Our data showed a significant loss in binding free energy when hydrophobic residues are mutated to alanine, suggesting that hydrophobic residues provide key interactions with the bound ligands. |
