Equally Potent Inhibition of c-Src and Abl by Compounds that Recognize Inactive Kinase Conformations

¹Howard Hughes Medical Institute and ²Department of Molecular and Cell Biology and Department of Chemistry, University of California; ³Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California; ⁴Department of Chemistry, University of Washington, Seattle, Washington; ⁵Division of Hematology/Oncology, Department of Medicine, University of California-San Francisco School of Medicine, San Francisco, California; and ⁶D. E. Shaw Research; ⁷Center for Computational Biology and Bioinformatics, Columbia University, New York, New York

^* To whom correspondence should be addressed. E-mail: maly{at}chem.washington.edu.

	Abstract

Imatinib is an inhibitor of the Abl tyrosine kinase domain that is effective in the treatment of chronic myelogenic leukemia. Although imatinib binds tightly to the Abl kinase domain, its affinity for the closely related kinase domain of c-Src is at least 2,000-fold lower. Imatinib recognition requires a specific inactive conformation of the kinase domain, in which a conserved Asp-Phe-Gly (DFG) motif is flipped with respect to the active conformation. The inability of c-Src to readily adopt this flipped DFG conformation was thought to underlie the selectivity of imatinib for Abl over c-Src. Here, we present a series of inhibitors (DSA compounds) that are based on the core scaffold of imatinib but which bind with equally high potency to c-Src and Abl. The DSA compounds bind to c-Src in the DFG-flipped conformation, as confirmed by crystal structures and kinetic analysis. The origin of the high affinity of these compounds for c-Src is suggested by the fact that they also inhibit clinically relevant Abl variants bearing mutations in a structural element, the P-loop, that normally interacts with the phosphate groups of ATP but is folded over a substructure of imatinib in Abl. Importantly, several of the DSA compounds block the growth of Ba/F3 cells harboring imatinib-resistant BCR-ABL mutants, including the Thr315Ile "gatekeeper" mutation, but do not suppress the growth of parental Ba/F3 cells. [Cancer Res 2009;69(6):2384–92]

Key Words: leukemia, Abl, imatinib, resistance mutations, structure