Discovery of novel, potent, and selective inhibitors of 3-phosphoinositide-dependent kinase (PDK1)

J Med Chem. 2011 Dec 22;54(24):8490-500. doi: 10.1021/jm201019k. Epub 2011 Nov 23.


Analogues substituted with various amines at the 6-position of the pyrazine ring on (4-amino-7-isopropyl-7H-pyrrolo[2,3-d]pyrimidin-5-yl)pyrazin-2-ylmethanone were discovered as potent and selective inhibitors of PDK1 with potential as anticancer agents. An early lead with 2-pyridine-3-ylethylamine as the pyrazine substituent showed moderate potency and selectivity. Structure-based drug design led to improved potency and selectivity against PI3Kα through a combination of cyclizing the ethylene spacer into a saturated, five-membered ring and substituting on the 4-position of the aryl ring with a fluorine. ADME properties were improved by lowering the lipophilicity with heteroatom replacements in the saturated, five-membered ring. The optimized analogues have a PDK1 Ki of 1 nM and >100-fold selectivity against PI3K/AKT-pathway kinases. The cellular potency of these analogues was assessed by the inhibition of AKT phosphorylation (T308) and by their antiproliferation activity against a number of tumor cell lines.

MeSH terms

  • 3-Phosphoinositide-Dependent Protein Kinases
  • Antineoplastic Agents / chemical synthesis*
  • Antineoplastic Agents / chemistry
  • Antineoplastic Agents / pharmacology
  • Cell Line, Tumor
  • Crystallography, X-Ray
  • Drug Screening Assays, Antitumor
  • Ethylamines / chemical synthesis
  • Ethylamines / chemistry
  • Ethylamines / pharmacology
  • Humans
  • Models, Molecular
  • Phosphorylation
  • Protein Conformation
  • Protein-Serine-Threonine Kinases / antagonists & inhibitors*
  • Proto-Oncogene Proteins c-akt / metabolism
  • Pyridines / chemical synthesis*
  • Pyridines / chemistry
  • Pyridines / pharmacology
  • Pyrroles / chemical synthesis*
  • Pyrroles / chemistry
  • Pyrroles / pharmacology
  • Signal Transduction
  • Structure-Activity Relationship


  • Antineoplastic Agents
  • Ethylamines
  • Pyridines
  • Pyrroles
  • 3-Phosphoinositide-Dependent Protein Kinases
  • PDPK1 protein, human
  • Protein-Serine-Threonine Kinases
  • Proto-Oncogene Proteins c-akt

Associated data

  • PDB/3RWP
  • PDB/3RWQ