The mechanism of oncogenic PI3K lipid kinase variants at the membrane and their cryptic pockets

The emergence of cancer requires at least two mutations. The mutational profiles of cancer-prone alleles often include hotspot mutations. A cancer hotspot combined with a weak/moderate mutation can result in significant deviation from hotspot-only variants, suggesting a graded clinical phenotypic spectrum. PI3Kα variants can carry both oncogenic mutations and mutations associated with benign tumors and neurodevelopmental disorders. Statistics on same-allele double mutations and their single components in PI3Kα support the “one-two punch” cancer emergence hypothesis, in which cancer hotspots can pair with low-frequency, weak or moderate mutations. Atomistic MD simulations revealed expanded conformational profiles of PI3Kα variants with single and double mutations. The combination of hotspot and weak (moderate) mutations shifts the population of the conformational ensembles toward the active form, which has a more pronounced effect than a single mutation. Observable, potentially drug-targetable cryptic pockets are mutation-specific. Ab initio discovery of cryptic pockets by simulations can facilitate AI-aided virtual drug screening. A single drug may not be effective against PI3Kα variants with different conformational spectra. We propose combination of allosteric drugs with conformational selection strategy for PI3Kα variants with graded conformational spectrum, particularly those bearing strong double mutations, and we identified such allosteric potential co-existing pockets in double mutants.