Understanding the structural stability and plasticity of VPS34 protein determined by selective/nonselective inhibitors: insights from molecular dynamics simulations.

Vacuolar sorting protein 34 (VPS34), a sole member of class III phosphoinositide 3-kinase (PI3K), regulates critical cellular processes, such as endosomal trafficking and autophagosome biogenesis, making it a promising target for diseases such as cancer and neurodegenerative disorders. However, developing highly selective inhibitors for VPS34 is challenging due to the structural conservation of its ATP-binding site across PI3Ks. In this study, to elucidate the structural dynamics of selective ligand recognition, we performed molecular dynamics (MD) simulations to explore the conformational landscape of VPS34 in both its apo state and in complex with selective/nonselective ligands. MD simulations and trajectory analysis showed that the whole structural stability and rigidity of VPS34 were increased in the presence of selective ligands. Moreover, pocket dynamical analysis demonstrated that the binding pockets were more stable and conserved upon binding to selective ligands. Furthermore, our results indicated that the ligand selectivity was not determined by the ligand's ability to enter the pocket or residue-level interaction energetics. Overall, these results suggested that the ligand selectivity arose from limiting intrinsic dynamics of VPS34 and thereof increasing its rigidity. These findings offer a new mechanistic framework and structural criteria for the rational design and screening of next-generation selective VPS34 inhibitors.