Bidirectional Allosteric Communication between the ATP-Binding Site and the Regulatory PIF Pocket in PDK1 Protein Kinase.
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.
Research Group PhosphoSites, Department of Internal Medicine I, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany.
Jörg O
JO
Schulze
Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK.
Giorgio
G
Saladino
Research Group PhosphoSites, Department of Internal Medicine I, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany.
Katrien
K
Busschots
Research Group PhosphoSites, Department of Internal Medicine I, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany.
Sonja
S
Neimanis
Research Group PhosphoSites, Department of Internal Medicine I, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany.
Evelyn
E
Süß
Research Group PhosphoSites, Department of Internal Medicine I, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany.
Dalibor
D
Odadzic
Research Group PhosphoSites, Department of Internal Medicine I, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany.
Stefan
S
Zeuzem
Research Group PhosphoSites, Department of Internal Medicine I, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany.
Valerie
V
Hindie
Research Group PhosphoSites, Department of Internal Medicine I, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany.
Amanda K
AK
Herbrand
Structural Biochemistry Unit, Pasteur Institute, Rue du Docteur Roux 25, 75724 Paris, France.
María-Natalia
MN
Lisa
Structural Biochemistry Unit, Pasteur Institute, Rue du Docteur Roux 25, 75724 Paris, France.
Pedro M
PM
Alzari
Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK; Research Department of Structural and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK. Electronic address: f.l.gervasio@ucl.ac.uk.
Francesco L
FL
Gervasio
Research Group PhosphoSites, Department of Internal Medicine I, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany; German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany. Electronic address: biondi@med.uni-frankfurt.de.
Ricardo M
RM
Biondi
D000255:Adenosine Triphosphate / Q000378:metabolism*; D000494:Allosteric Regulation / Q000187:drug effects*; D000495:Allosteric Site / Q000187:drug effects; D064127:Aurora Kinases / Q000037:antagonists & inhibitors / Q000737:chemistry / Q000378:metabolism; D001665:Binding Sites / Q000187:drug effects; D057809:HEK293 Cells; D006801:Humans; D007191:Indazoles / Q000737:chemistry / Q000494:pharmacology*; D062105:Molecular Docking Simulation; D047428:Protein Kinase Inhibitors / Q000737:chemistry / Q000494:pharmacology*; D017346:Protein Serine-Threonine Kinases / Q000037:antagonists & inhibitors* / Q000737:chemistry / Q000378:metabolism; D011743:Pyrimidines / Q000737:chemistry / Q000494:pharmacology*; D000081382:Pyruvate Dehydrogenase Acetyl-Transferring Kinase
C555257:GSK 2334470; D007191:Indazoles; C000631429:PDK1 protein, human; D047428:Protein Kinase Inhibitors; D011743:Pyrimidines; D000081382:Pyruvate Dehydrogenase Acetyl-Transferring Kinase; D000255:Adenosine Triphosphate; D064127:Aurora Kinases; D017346:Protein Serine-Threonine Kinases
AGC kinase; Aurora; GSK2334470; PDK1; PIF pocket; adenosine; allosteric regulation; molecular dynamics; protein kinase; small compounds