Conformation-selective inhibitors reveal differences in the activation and phosphate-binding loops of the tyrosine kinases Abl and Src

ACS Chem Biol. 2013 Dec 20;8(12):2734-43. doi: 10.1021/cb400663k. Epub 2013 Oct 29.

Abstract

Over the past decade, an increasingly diverse array of potent and selective inhibitors that target the ATP-binding sites of protein kinases have been developed. Many of these inhibitors, like the clinically approved drug imatinib (Gleevec), stabilize a specific catalytically inactive ATP-binding site conformation of their kinases targets. Imatinib is notable in that it is highly selective for its kinase target, Abl, over other closely related tyrosine kinases, such as Src. In addition, imatinib is highly sensitive to the phosphorylation state of Abl's activation loop, which is believed to be a general characteristic of all inhibitors that stabilize a similar inactive ATP-binding site conformation. In this report, we perform a systematic analysis of a diverse series of ATP-competitive inhibitors that stabilize a similar inactive ATP-binding site conformation as imatinib with the tyrosine kinases Src and Abl. In contrast to imatinib, many of these inhibitors have very similar potencies against Src and Abl. Furthermore, only a subset of this class of inhibitors is sensitive to the phosphorylation state of the activation loop of these kinases. In attempting to explain this observation, we have uncovered an unexpected correlation between Abl's activation loop and another flexible active site feature, called the phosphate-binding loop (p-loop). These studies shed light on how imatinib is able to obtain its high target selectivity and reveal how the conformational preference of flexible active site regions can vary between closely related kinases.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenosine Triphosphate / chemistry
  • Adenosine Triphosphate / metabolism
  • Antineoplastic Agents / chemistry*
  • Benzamides / chemistry*
  • Binding Sites
  • Enzyme Activation
  • Escherichia coli / genetics
  • Escherichia coli / metabolism
  • Gene Expression
  • Humans
  • Imatinib Mesylate
  • Kinetics
  • Ligands
  • Molecular Docking Simulation
  • Mutation
  • Phosphates / chemistry
  • Phosphates / metabolism
  • Phosphorylation
  • Piperazines / chemistry*
  • Protein Binding
  • Protein Kinase Inhibitors / chemistry*
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • Proto-Oncogene Proteins c-abl / antagonists & inhibitors
  • Proto-Oncogene Proteins c-abl / chemistry*
  • Proto-Oncogene Proteins c-abl / genetics
  • Proto-Oncogene Proteins c-abl / metabolism
  • Pyrimidines / chemistry*
  • Recombinant Proteins / chemistry
  • Recombinant Proteins / genetics
  • Recombinant Proteins / metabolism
  • Structure-Activity Relationship
  • src-Family Kinases / antagonists & inhibitors
  • src-Family Kinases / chemistry*
  • src-Family Kinases / genetics
  • src-Family Kinases / metabolism

Substances

  • Antineoplastic Agents
  • Benzamides
  • Ligands
  • Phosphates
  • Piperazines
  • Protein Kinase Inhibitors
  • Pyrimidines
  • Recombinant Proteins
  • Imatinib Mesylate
  • Adenosine Triphosphate
  • Proto-Oncogene Proteins c-abl
  • src-Family Kinases