A design approach for bitopic kinase inhibitors.

Traditional kinase inhibitors face a trade-off between potency and selectivity because their affinity depends on limited molecular interactions in a single highly conserved binding site. Bitopic inhibitors overcome this limitation by engaging multiple sites on the same target1. Here, using ABL1 and EGFR as model kinases, we systematically explore the bitopic-specific design parameters of ligand choice, linkage vector and linker length and show that they affect potency through inter-ligand cooperativity and linker entropy. We apply this approach to address an unmet clinical need: existing inhibitors of ABL1, an important target in BCR::ABL1-driven leukaemias, are constrained by resistance mutations and off-target effects2. The third-generation inhibitor ponatinib overcomes many resistance mutations, but cardiovascular toxicity limits its clinical use3. We design a bitopic ABL1 inhibitor, PonatiLink-2, that maintains or surpasses the potency of ponatinib against resistance mutants. Moreover, it has an enhanced therapeutic window in vitro and in vivo, which enables increased dosing without apparent toxicity. PonatiLink-2 outperforms clinically relevant treatments in mouse models of BCR::ABL1-driven cancer, both in combination with dasatinib against wild-type BCR::ABL1 and as a single agent against ponatinib-resistant disease. These findings indicate that the bitopic design approach is a promising strategy for developing potent, well-tolerated clinical inhibitors of ABL1 and other targets.