Kinases are crucial components in numerous cell signaling pathways. Aberrant expression and activation of
protein kinases are known to be accompanied by many types of
cancer, and more than 30 small-molecule
kinase inhibitors have been approved by the Food and Drug Administration (FDA) for
cancer chemotherapy. Biological and clinical applications of small-molecule
kinase inhibitors require comprehensive characterizations about how these inhibitors modulate the
protein expression and activities of
kinases at the entire
proteome scale. In this study, we developed a parallel-reaction monitoring (PRM)-based targeted proteomic method to monitor the alterations in
protein expression of
kinases in K-562
chronic myelocytic leukemia (CML) cells elicited by treatment with
imatinib, an ABL
kinase inhibitor approved by the FDA for CML treatment. By employing
isotope-coded
ATP affinity probes together with liquid chromatography-multiple-reaction monitoring (LC-MRM) analysis, we also examined the modulation of the
ATP-binding affinities of
kinases induced by
imatinib treatment. The results revealed profound increases in
protein expression levels of a large number of
kinases in K-562 cells upon treatment with
imatinib, which is accompanied by substantial decreases in
ATP-binding capacities of many
kinases. Apart from ABL
kinases, we identified a number of other
kinases whose
ATP-binding affinities are markedly diminished upon
imatinib treatment, including CHK1, a checkpoint
kinase involved in DNA damage response signaling. Together, our targeted quantitative proteomic methods enabled, for the first time, dual assessments of small-molecule
kinase inhibitor-induced changes in
protein expression and
ATP-binding affinities of
kinases in live cells.