Structural characterization of nonactive site, TrkA-selective kinase inhibitors

Proc Natl Acad Sci U S A. 2017 Jan 17;114(3):E297-E306. doi: 10.1073/pnas.1611577114. Epub 2016 Dec 30.


Current therapies for chronic pain can have insufficient efficacy and lead to side effects, necessitating research of novel targets against pain. Although originally identified as an oncogene, Tropomyosin-related kinase A (TrkA) is linked to pain and elevated levels of NGF (the ligand for TrkA) are associated with chronic pain. Antibodies that block TrkA interaction with its ligand, NGF, are in clinical trials for pain relief. Here, we describe the identification of TrkA-specific inhibitors and the structural basis for their selectivity over other Trk family kinases. The X-ray structures reveal a binding site outside the kinase active site that uses residues from the kinase domain and the juxtamembrane region. Three modes of binding with the juxtamembrane region are characterized through a series of ligand-bound complexes. The structures indicate a critical pharmacophore on the compounds that leads to the distinct binding modes. The mode of interaction can allow TrkA selectivity over TrkB and TrkC or promiscuous, pan-Trk inhibition. This finding highlights the difficulty in characterizing the structure-activity relationship of a chemical series in the absence of structural information because of substantial differences in the interacting residues. These structures illustrate the flexibility of binding to sequences outside of-but adjacent to-the kinase domain of TrkA. This knowledge allows development of compounds with specificity for TrkA or the family of Trk proteins.

Keywords: TrkA; inhibition; kinase; pain; selectivity.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Binding Sites
  • Crystallography, X-Ray
  • Drug Evaluation, Preclinical
  • Humans
  • Kinetics
  • Membrane Glycoproteins / antagonists & inhibitors
  • Membrane Glycoproteins / chemistry
  • Membrane Glycoproteins / genetics
  • Models, Molecular
  • Protein Conformation
  • Protein Kinase Inhibitors / chemical synthesis
  • Protein Kinase Inhibitors / chemistry*
  • Protein Kinase Inhibitors / pharmacology*
  • Receptor, trkA / antagonists & inhibitors*
  • Receptor, trkA / chemistry*
  • Receptor, trkA / genetics
  • Receptor, trkB / antagonists & inhibitors
  • Receptor, trkB / chemistry
  • Receptor, trkB / genetics
  • Receptor, trkC / antagonists & inhibitors
  • Receptor, trkC / chemistry
  • Receptor, trkC / genetics
  • Recombinant Proteins / chemistry
  • Recombinant Proteins / drug effects
  • Recombinant Proteins / genetics
  • Structure-Activity Relationship
  • Surface Plasmon Resonance


  • Membrane Glycoproteins
  • NTRK1 protein, human
  • Protein Kinase Inhibitors
  • Recombinant Proteins
  • Receptor, trkA
  • Receptor, trkB
  • Receptor, trkC
  • tropomyosin-related kinase-B, human

Associated data

  • PDB/5KMI
  • PDB/5KMJ
  • PDB/5KMK
  • PDB/5KML
  • PDB/5KMM
  • PDB/5KMN
  • PDB/5KMO