Imatinib disassembles the regulatory core of Abelson kinase by binding to its ATP site and not by binding to its myristoyl pocket

Abstract. It was recently reported (Xie et al. Journal of Molecular Biology 2022, 434 (2), 167349) that the Abelson tyrosine kinase (Abl) ATP-site inhibitor imatinib also binds to Abl’s myristoyl binding pocket, which is the target of allosteric Abl inhibitors. This was based on a crystal structure of a truncated Abl kinase domain construct in complex with imatinib bound to the allosteric site as well as some further ITC, NMR, and kinase activity data. Albeit imatinib’s affinity for the allosteric site is significantly weaker (10 μM) than for the ATP site (10 nM), imatinib binding to the allosteric site may disassemble the regulatory core of Abl, thereby stimulating kinase activity, in particular for Abl mutants with reduced imatinib ATP-site affinity. It was argued that the previously observed imatinib-induced opening of the Abl regulatory core (Skora et al. PNAS 2013, 110 (47), E4437–E4445, Sonti et al. Journal of the American Chemical Society 2018, 140 (5), 1863–1869) may be caused by the binding of imatinib to the allosteric site and not to the ATP site. We show here that this is not the case, but that indeed imatinib binding to the ATP site induces the opening of the regulatory core at nanomolar concentrations. This agrees with findings that other type-II ATP site inhibitors (nilotinib, ponatinib) disassemble the regulatory core despite demonstrated negligible binding to the allosteric site.