title: A small-molecule mimic of a peptide docking motif inhibits the protein kinase PDK1.
abstract: There is great interest in developing selective protein kinase inhibitors by targeting allosteric sites, but these sites often involve protein-protein or protein-peptide interfaces that are very challenging to target with small molecules. Here we present a systematic approach to targeting a functionally conserved allosteric site on the protein kinase PDK1 called the PDK1-interacting fragment (PIF)tide-binding site, or PIF pocket. More than two dozen prosurvival and progrowth kinases dock a conserved peptide tail into this binding site, which recruits them to PDK1 to become activated. Using a site-directed chemical screen, we identified and chemically optimized ligand-efficient, selective, and cell-penetrant small molecules (molecular weight ∼ 380 Da) that compete with the peptide docking motif for binding to PDK1. We solved the first high-resolution structure of a peptide docking motif (PIFtide) bound to PDK1 and mapped binding energy hot spots using mutational analysis. We then solved structures of PDK1 bound to the allosteric small molecules, which revealed a binding mode that remarkably mimics three of five hot-spot residues in PIFtide. These allosteric small molecules are substrate-selective PDK1 inhibitors when used as single agents, but when combined with an ATP-competitive inhibitor, they completely suppress the activation of the downstream kinases. This work provides a promising new scaffold for the development of high-affinity PIF pocket ligands, which may be used to enhance the anticancer activity of existing PDK1 inhibitors. Moreover, our results provide further impetus for exploring the helix αC patches of other protein kinases as potential therapeutic targets even though they involve protein-protein interfaces.
authors.affiliation: Chemistry and Chemical Biology Graduate Program, Department of Pharmaceutical Chemistry.
authors.forename: T Justin
authors.initials: TJ
authors.lastname: Rettenmaier
authors.affiliation: Department of Pharmaceutical Chemistry.
authors.forename: Jack D
authors.initials: JD
authors.lastname: Sadowsky
authors.affiliation: Department of Pharmaceutical Chemistry.
authors.forename: Nathan D
authors.initials: ND
authors.lastname: Thomsen
authors.affiliation: Small Molecule Discovery Center, and.
authors.forename: Steven C
authors.initials: SC
authors.lastname: Chen
authors.affiliation: Department of Pharmaceutical Chemistry.
authors.forename: Allison K
authors.initials: AK
authors.lastname: Doak
authors.affiliation: Small Molecule Discovery Center, and.
authors.forename: Michelle R
authors.initials: MR
authors.lastname: Arkin
authors.affiliation: Department of Pharmaceutical Chemistry, Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158 jim.wells@ucsf.edu.
authors.forename: James A
authors.initials: JA
authors.lastname: Wells
mesh_terms: D064413:3-Phosphoinositide-Dependent Protein Kinases / Q000037:antagonists & inhibitors / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D000494:Allosteric Regulation / Q000187:drug effects; D000495:Allosteric Site; D020816:Amino Acid Motifs; D000970:Antineoplastic Agents / Q000737:chemistry / Q000494:pharmacology; D018360:Crystallography, X-Ray; D057809:HEK293 Cells; D006801:Humans; D062105:Molecular Docking Simulation; D009363:Neoplasm Proteins / Q000037:antagonists & inhibitors / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D009369:Neoplasms / Q000188:drug therapy / Q000201:enzymology / Q000235:genetics / Q000473:pathology; D010455:Peptides / Q000737:chemistry / Q000494:pharmacology; D047428:Protein Kinase Inhibitors / Q000737:chemistry / Q000494:pharmacology; D017433:Protein Structure, Secondary
chemical_list: D000970:Antineoplastic Agents; D009363:Neoplasm Proteins; D010455:Peptides; D047428:Protein Kinase Inhibitors; D064413:3-Phosphoinositide-Dependent Protein Kinases; C578562:PDPK1 protein, human
keywords: allostery; drug discovery; peptide mimicry; protein–protein interaction