A hinge motif unveils the cryptic structural determinants of selective inhibitors towards PI3Kα and VPS34

Abstract

Isoform-selective PI3K inhibitors have garnered attention for precise cancer therapy, particularly targeting PI3Kα and VPS34, which share highly homologous ATP-binding pockets. Due to their broad expression and critical physiological roles, these isoforms pose challenges of off-target inhibition in non-disease tissues. This study elucidates the selective mechanisms of PI3Kα and VPS34 inhibitors by analyzing their interactions with highly selective ligands. Despite its high sequence homology, PI3Kα features a narrow hydrophobic active pocket, while that of VPS34 is quadrate. Rationally designing ligands with spatially optimized scaffolds can improve selectivity. Energy mapping revealed that VAL851, SER854, and GLN859 in PI3Kα's hinge motif and ILE685 in VPS34's hinge motif play pivotal roles in selectivity. Additionally, hydrophobic interactions were critical for inhibitor binding, while water bridges significantly enhanced VPS34's selective inhibition. These findings provide valuable insights into the selectivity mechanisms of PI3Kα and VPS34 inhibitors, offering a foundation for developing highly selective inhibitors for future therapeutic applications.