Combining the Allosteric ABL1 Tyrosine Kinase Inhibitor ABL001 with ATP-Competitive Inhibitors to Suppress Resistance in Chronic Myeloid Leukemia

The successful design and application of ABL1 tyrosine kinase inhibitors for the treatment of chronic myeloid leukemia (CML) has become a paradigm for molecularly targeted cancer therapies. However, resistance to therapy can develop and is most commonly attributed to acquired mutations within the kinase domain of the causative BCR-ABL1 oncoprotein. While the set of ABL1 kinase inhibitors currently available in the clinic facilitates management of many of these resistant BCR-ABL1 mutations, all clinically approved ABL1 kinase inhibitors for CML to date bind to the catalytic site within the kinase in an ATP-competitive manner. An alternative strategy to circumventing mutations in this region which has received recent attention involves the targeting of allosteric sites on BCR-ABL1 kinase. Here, we evaluated ABL001, a small-molecule inhibitor which binds highly selectively to the myristoyl pocket on ABL1 kinase, for its capacity to inhibit known imatinib-resistant BCR-ABL1 single and compound mutations. ABL001 potently inhibited the proliferation of Ba/F3 cells expressing native BCR-ABL1 or a variety of BCR-ABL1 point mutations (IC₅₀ range: 1.3-113.5 nM), with no observed toxicity to parental Ba/F3 cells up to 10 μM. Interestingly, however, ABL001 demonstrated little to no activity against a small panel of BCR-ABL1 compound mutations tested (G250E/T315I, E255K/T315I, E255V/T315I). Accelerated mutagenesis screens for ABL001 revealed dose-dependent reduction in the emergence of resistant clones, as well as novel BCR-ABL1 mutations at a subset of kinase domain and C-terminal residues lining the myristoyl pocket which are resistant to ABL001 but remain sensitive to ATP-competitive ABL1 kinase inhibitors. Intriguingly, similar mutagenesis screens conducted using ABL001 in combination with relevant ATP-competitive ABL1 kinase inhibitors showed marked suppression of resistant outgrowth compared to either drug alone, both in the setting of single and compound mutations. Furthermore, ABL001 demonstrated dose-dependent inhibition of myeloid colony formation of human CML cells, and this efficacy was further enhanced in the context of co-treatment with nilotinib or ponatinib. Together, these findings suggest that use of an allosteric ABL1 inhibitor such as ABL001 in combination with other currently approved ATP-competitive inhibitors may offer a meaningful strategy to further mitigate the emergence of resistance in CML patients both in a frontline and second-line treatment capacity.