Chemical Proteomics and Structural Biology Define EPHA2 Inhibition by Clinical Kinase Drugs

The
receptor tyrosine kinase EPHA2 (Ephrin type-A receptor 2) plays
important roles in oncogenesis, metastasis, and treatment resistance,
yet therapeutic targeting, drug discovery, or investigation of EPHA2
biology is hampered by the lack of appropriate inhibitors and structural
information. Here, we used chemical proteomics to survey 235 clinical
kinase inhibitors for their kinase selectivity and identified 24 drugs
with submicromolar affinities for EPHA2. NMR-based conformational
dynamics together with nine new cocrystal structures delineated drug–EPHA2
interactions in full detail. The combination of selectivity profiling,
structure determination, and kinome wide sequence alignment allowed
the development of a classification system in which amino acids in
the drug binding site of EPHA2 are categorized into key, scaffold,
potency, and selectivity residues. This scheme should be generally
applicable in kinase drug discovery, and we anticipate that the provided
information will greatly facilitate the development of selective EPHA2
inhibitors in particular and the repurposing of clinical kinase inhibitors
in general.