Molecular basis of the constitutive activity and STI571 resistance of Asp816Val mutant KIT receptor tyrosine kinase

J Mol Graph Model. 2004 Oct;23(2):139-52. doi: 10.1016/j.jmgm.2004.04.003.

Abstract

The receptor tyrosine kinase, KIT, displays activating mutations in the kinase domain, which are associated with various cancers. We have used homology modelling based on the crystal structures of the insulin receptor kinase in active and inactive conformations to predict the corresponding structures of the KIT kinase domain. We have prepared four KIT models, one each for the active and inactive conformations of the wild-type and of the Asp816Val mutant proteins. We have also placed ATP into the active conformations and the inhibitor, STI571, into the inactive conformations. All models have been fully energy minimised. The molecular modelling studies described here explain (i) why Asp816Val KIT is constitutively active, (ii) why the nature of the substituting amino acid at residue 816 is relatively unimportant, and (iii) why the Asp816Val substitution confers resistance to the KIT-inhibitory drug STI571. The models will be valuable for predicting other kinase inhibitory drugs that may be active on wild-type and mutant forms of KIT. During the course of this work, a crystal structure of the active conformation of the KIT kinase domain has been published. Our model of the active conformation of the Asp816Val mutant is strikingly similar to this crystal structure, whereas our model of the active conformation of the wild-type kinase domain of KIT differs from the crystal structure in some respects. The reasons for this apparent discrepancy are discussed.

Publication types

  • Comparative Study

MeSH terms

  • Amino Acid Sequence
  • Amino Acid Substitution
  • Benzamides
  • Binding Sites
  • Computer Simulation
  • Drug Resistance / genetics
  • Humans
  • Hydrogen Bonding
  • Imatinib Mesylate
  • In Vitro Techniques
  • Models, Molecular
  • Molecular Sequence Data
  • Mutation
  • Piperazines / pharmacology*
  • Protein Conformation
  • Protein Kinase Inhibitors / pharmacology*
  • Proto-Oncogene Proteins c-kit / chemistry*
  • Proto-Oncogene Proteins c-kit / genetics*
  • Proto-Oncogene Proteins c-kit / metabolism
  • Pyrimidines / pharmacology*
  • Sequence Homology, Amino Acid

Substances

  • Benzamides
  • Piperazines
  • Protein Kinase Inhibitors
  • Pyrimidines
  • Imatinib Mesylate
  • Proto-Oncogene Proteins c-kit