A Novel Mode of Protein Kinase Inhibition Exploiting Hydrophobic Motifs of Autoinhibited Kinases

Protein kinase inhibitors with enhanced selectivity can be designed by optimizing binding interactions with less conserved inactive conformations because such inhibitors will be less likely to compete with ATP for binding and therefore may be less impacted by high intracellular concentrations of ATP...

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Bibliographic Details
Published in:The Journal of biological chemistry 2011-12, Vol.286 (23), p.20677-20687
Main Authors: Eathiraj, Sudharshan, Palma, Rocio, Hirschi, Marscha, Volckova, Erika, Nakuci, Enkeleda, Castro, Jennifer, Chen, Chang-Rung, Chan, Thomas C.K., France, Dennis S., Ashwell, Mark A.
Format: Article
Language:English
Subjects:
60 APPLIED LIFE SCIENCES
ATP
BASIC BIOLOGICAL SCIENCES
CRYSTALLOGRAPHY
DESIGN
Drug Design
DRUGS
FGFR
FIBROBLASTS
GROWTH FACTORS
INHIBITION
INTERACTIONS
Kinase Autoinhibition
Kinetics
NEOPLASMS
Non-competitive
OPTIMIZATION
PHOSPHOTRANSFERASES
Protein Phosphorylation
PROTEIN STRUCTURE
PROTEINS
Receptor Tyrosine Kinase
RECEPTORS
Small Molecule Protein Kinase Inhibitor
TYROSINE
X RADIATION
X-ray Crystallography
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Summary:Protein kinase inhibitors with enhanced selectivity can be designed by optimizing binding interactions with less conserved inactive conformations because such inhibitors will be less likely to compete with ATP for binding and therefore may be less impacted by high intracellular concentrations of ATP. Analysis of the ATP-binding cleft in a number of inactive protein kinases, particularly in the autoinhibited conformation, led to the identification of a previously undisclosed non-polar region in this cleft. This ATP-incompatible hydrophobic region is distinct from the previously characterized hydrophobic allosteric back pocket, as well as the main pocket. Generalized hypothetical models of inactive kinases were constructed and, for the work described here, we selected the fibroblast growth factor receptor (FGFR) tyrosine kinase family as a case study. Initial optimization of a FGFR2 inhibitor identified from a library of commercial compounds was guided using structural information from the model. We describe the inhibitory characteristics of this compound in biophysical, biochemical, and cell-based assays, and have characterized the binding mode using x-ray crystallographic studies. The results demonstrate, as expected, that these inhibitors prevent activation of the autoinhibited conformation, retain full inhibitory potency in the presence of physiological concentrations of ATP, and have favorable inhibitory activity in cancer cells. Given the widespread regulation of kinases by autoinhibitory mechanisms, the approach described herein provides a new paradigm for the discovery of inhibitors by targeting inactive conformations of protein kinases.
ISSN:0021-9258
1083-351X
DOI:10.1074/jbc.M110.213736