What to do with an oncogene

Phospoinositide 3-kinase (PI3K) is an important cancer target. It shows gain of function by over-expression or mutation in numerous human cancers. More than 100 inhibitors of PI3K have been disclosed, but only five have received FDA approval. Of these, only one, BYL-719 (Alpelisib), is effective against solid tumors. All PI3K inhibitors compete with ATP binding to the active site of the enzyme, and all are directed against the wild type protein. Their clinical effectiveness is significantly reduced by resistance and by intolerable side effects. Targeting inhibitors to the cancer-specific mutants of PI3K is therefore an urgent necessity. It involves identification of mutant-specific ligands, a daunting goal considering that mutant and wild type proteins differ by only one amino acid substitution. We have been successful in this effort using new chemical space that has become accessible with DNA-encoded chemical libraries. Design of mutant-specific inhibitors also requires comprehensive structural information that includes the entire PI3K dimer consisting of the catalytic and regulatory subunit. Since only part of this molecule can be analyzed by X-ray crystallography, we have used single particle analysis by cryo-electron microscopy to gain access to the structure of the PI3K dimer. We were able to identify and localize all domains of PI3K in three distinct functional states. Further advances in the structural analysis were achieved by using nanobodies directed against PI3K in combination with chemical cross-linking. This work has led to novel insights into the structure and the function of PI3K.