Bidirectional Allosteric Communication between the ATP-Binding Site and the Regulatory PIF Pocket in PDK1 Protein Kinase

Cell Chem Biol. 2016 Oct 20;23(10):1193-1205. doi: 10.1016/j.chembiol.2016.06.017. Epub 2016 Sep 29.

Abstract

Allostery is a phenomenon observed in many proteins where binding of a macromolecular partner or a small-molecule ligand at one location leads to specific perturbations at a site not in direct contact with the region where the binding occurs. The list of proteins under allosteric regulation includes AGC protein kinases. AGC kinases have a conserved allosteric site, the phosphoinositide-dependent protein kinase 1 (PDK1)-interacting fragment (PIF) pocket, which regulates protein ATP-binding, activity, and interaction with substrates. In this study, we identify small molecules that bind to the ATP-binding site and affect the PIF pocket of AGC kinase family members, PDK1 and Aurora kinase. We describe the mechanistic details and show that although PDK1 and Aurora kinase inhibitors bind to the conserved ATP-binding site, they differentially modulate physiological interactions at the PIF-pocket site. Our work outlines a strategy for developing bidirectional small-molecule allosteric modulators of protein kinases and other signaling proteins.

Keywords: AGC kinase; Aurora; GSK2334470; PDK1; PIF pocket; adenosine; allosteric regulation; molecular dynamics; protein kinase; small compounds.

MeSH terms

  • Adenosine Triphosphate / metabolism*
  • Allosteric Regulation / drug effects*
  • Allosteric Site / drug effects
  • Aurora Kinases / antagonists & inhibitors
  • Aurora Kinases / chemistry
  • Aurora Kinases / metabolism
  • Binding Sites / drug effects
  • HEK293 Cells
  • Humans
  • Indazoles / chemistry
  • Indazoles / pharmacology*
  • Molecular Docking Simulation
  • Protein Kinase Inhibitors / chemistry
  • Protein Kinase Inhibitors / pharmacology*
  • Protein-Serine-Threonine Kinases / antagonists & inhibitors*
  • Protein-Serine-Threonine Kinases / chemistry
  • Protein-Serine-Threonine Kinases / metabolism
  • Pyrimidines / chemistry
  • Pyrimidines / pharmacology*
  • Pyruvate Dehydrogenase Acetyl-Transferring Kinase

Substances

  • GSK 2334470
  • Indazoles
  • PDK1 protein, human
  • Protein Kinase Inhibitors
  • Pyrimidines
  • Pyruvate Dehydrogenase Acetyl-Transferring Kinase
  • Adenosine Triphosphate
  • Aurora Kinases
  • Protein-Serine-Threonine Kinases