Free energy landscape of the PI3Kα C-terminal activation

The gene PIK3CA, encoding the catalytic subunit p110α of PI3Kα, is the second most frequently mutated gene in cancer, with the highest frequency oncogenic mutants occurring in the C-terminus of the kinase domain. The C-terminus has a dual function in regulating the kinase, playing a putative auto-inhibitory role for kinase activity and being absolutely essential for binding to the cell membrane. However, the molecular mechanisms by which these C-terminal oncogenic mutations cause PI3Kα overactivation remain unclear. To understand how a spectrum of C-terminal mutations of PI3Kα alter kinase activity compared to the WT, we perform unbiased and biased Molecular Dynamics simulations of several C-terminal mutants and report the free energy landscapes for the C-terminal “closed to open” transition in the WT, H1047R, G1049R, M1043L and N1068KLKR mutants Results are consistent with HDX-MS experimental data and  provide a molecular explanation why H1047R and G1049R reorient the C-terminus with a different mechanism compared to the WT and M1043L and N1068KLKR mutants. Moreover, we show that in the H1047R mutant, the cavity, where binds the allosteric ligands STX-478 and RLY-2608, bind is opened contrary to the WT. This study provides insights into the molecular mechanisms underlying activation of oncogenic PI3Kα by C-terminal mutations, and represent a valuable resource for continued efforts in the development of mutant selective inhibitors as therapeutics.

The "Free energy landscape of the PI3Kα C-terminal activation" container holds the input files for the unbiased and biased MD simulations performed with ACEMD software and the scripts used for the analysis of the trajectories.