ATP-competitive inhibitors midostaurin and avapritinib have distinct resistance profiles in exon 17-mutant KIT

KIT is a type-3 receptor tyrosine kinasethat is frequently mutated at exon 11 or 17 in a variety of cancers. First generation KIT tyrosine kinaseinhibitors (TKIs) are ineffective against KIT exon 17 mutations, which favor an active conformation that prevents these TKIs from binding. The ATP-competitive inhibitors midostaurinand avapritinib, which target the active kinaseconformation, were developed to inhibit exon 17-mutant KIT. Because secondary kinasedomain mutations are a common mechanism of TKI resistance and guide ensuing TKI design, we sought to define problematic KIT kinasedomain mutations for these emerging therapeutics. Midostaurinand avapritinib displayed different vulnerabilities to secondary kinasedomain substitutions, with the T670I gatekeepermutation being selectively problematic for avapritinib. Though gatekeepermutations often directly disrupt inhibitor binding, we provide evidence that T670I confers avapritinib resistance indirectly by inducing distant conformational changes in the phosphate-binding loop. These findings suggest combining midostaurinand avapritinib may forestall acquired resistance mediated by secondary kinasedomain mutations.