Microsecond molecular dynamics simulations provide insight into the ATP‐competitive inhibitor‐induced allosteric protection of Akt kinase phosphorylation

Akt is a serine/threonine protein kinase, a critical mediator of growth factor‐induced survival in key cellular pathways. Allosteric signaling between protein intramolecular domains requires long‐range communication mediated by hotspot residues, often triggered by ligand binding. Here, based on extensive 3 μs explicit solvent molecular dynamics (MD) simulations of Akt1 kinase domain in the unbound (apo) and ATP‐competitive inhibitor, GDC‐0068‐bound states, we propose a molecular mechanism for allosteric regulation of Akt1 kinase phosphorylation by GDC‐0068 binding to the ATP‐binding site. MD simulations revealed that the apo Akt1 is flexible with two disengaged N‐ and C‐lobes, equilibrated between the open and closed conformations. GDC‐0068 occupancy of the ATP‐binding site shifts the conformational equilibrium of Akt1 from the open conformation toward the closed conformation and stabilizes the closed state. This effect enables allosteric signal propagation from the GDC‐0068 to the phosphorylated T308 (pT308) in the activation loop and restrains phosphatase access to pT308, thereby protecting the pT308 in the GDC‐0068‐bound Akt1. Importantly, functional hotspots involved in the allosteric communication from the GDC‐0068 to the pT308 are identified. Our analysis of GDC‐0068‐induced allosteric protection of Akt kinase phosphorylation yields important new insights into the molecular mechanism of allosteric regulation of Akt kinase activity.