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Structural and biochemical studies of the PDGFRA kinase domain

Ling Liang1, Xiao-E Yan2, Yuxin Yin3

  • 1Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, PR China; Department of Pathology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, PR China.

Biochemical and Biophysical Research Communications
|June 29, 2016
PubMed

Insights

The D842V mutation in Platelet-Derived Growth Factor Receptor Alpha (PDGFRA) causes imatinib resistance in gastrointestinal stromal tumors by altering kinase conformation and increasing ATP affinity. This structural insight aids in developing new targeted therapies.

Area of Science:

  • Molecular Biology
  • Structural Biology
  • Oncology

Background:

  • Platelet-Derived Growth Factor Receptor Alpha (PDGFRA) is a key target for gastrointestinal stromal tumors (GIST).
  • Mutations in PDGFRA, particularly in the activation loop (A-loop) and juxtamembrane (JM) domain, lead to constitutive activation and drug resistance.
  • The D842V mutation confers imatinib resistance in PDGFRA-mutated GIST.

Purpose of the Study:

  • To elucidate the structural mechanism underlying PDGFRA drug resistance, focusing on the D842V mutation.
  • To understand how the JM domain stabilizes the auto-inhibited state of PDGFRA.
  • To provide a structural basis for developing novel inhibitors targeting both active and resistant PDGFRA mutations.

Main Methods:

  • Determined the crystal structure of the PDGFRA kinase domain in its auto-inhibited conformation.
  • Performed kinetic studies to analyze the D842V mutation's effect on kinase activity and drug binding.
  • Utilized structural analysis to understand the role of Asp842 in maintaining the inactive state.

Main Results:

  • The auto-inhibited PDGFRA structure reveals stabilization by the JM domain inserting into the active site.
  • The conserved Asp842 residue is crucial for maintaining the inactive "DFG out" conformation, facilitating imatinib binding.
  • The D842V mutation is shown to destabilize the "DFG out" conformation, leading to kinase activation and reduced imatinib efficacy.
  • Kinetic data indicate that the D842V mutation also increases ATP affinity, contributing to drug resistance.

Conclusions:

  • The crystal structure of auto-inhibited PDGFRA provides critical insights into its regulation and the mechanism of imatinib resistance.
  • The D842V mutation activates PDGFRA and hinders imatinib binding by disrupting the auto-inhibited conformation and increasing ATP affinity.
  • This study lays the groundwork for designing new therapeutic agents effective against both wild-type and mutated PDGFRA, including drug-resistant forms.
Keywords:
AutoinhibitionCrystal structureD842VDrug-resistancePDGFRA

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