Small-molecule inhibitors as salvage therapy for CBFB::MYH11-associated acute myeloid leukemia

Acute myeloid leukemia (AML) is an aggressive blood cancer and the most common form of acute leukemia in adults. Although chemotherapy with cytarabine and an anthracycline induces high remission rates, it often causes severe side effects, and relapse is common. These limitations highlight the urgent need for new treatment options, particularly for relapsed disease, where therapeutic resistance remains a significant obstacle. Genetic rearrangements are major drivers of AML, generating fusion proteins that disrupt normal hematopoietic regulation in about 20-40% of cases. Among these, CBFB::MYH11, resulting from chromosome 16 inversion or t(16;16) translocation, occurs in 10-15% of adult AML. This fusion protein sequesters RUNX1 in the cytoplasm, impairing core-binding factor function, blocking myeloid differentiation, and promoting leukemic cell survival. Thus, CBFB::MYH11 represents an attractive therapeutic target in AML, including in the setting of relapsed disease. Using a comprehensive virtual screening pipeline that integrates chemical structures from FDA-approved drugs, natural products, the ZINC22 database, and experimental compounds, we systematically identified lead compounds targeting the CBFB component of the CBFB::MYH11 fusion protein. To experimentally validate our cheminformatics-based predictions, we established multiple cytarabine-resistant AML cell lines, including CBFB::MYH11, to model therapy-induced resistance. In parallel, we isolated mononuclear cells from peripheral blood and bone marrow samples from AML patients with and without CBFB::MYH11 at both diagnosis and relapse, enabling direct comparison between in vitro and patient-derived resistance mechanisms. Treatment with the experimental compound SM1, one of the predicted top-binding candidates, selectively induced cell cycle arrest and apoptotic cell death in chemoresistant and chemosensitive AML cells harboring CBFB::MYH11, while sparing AML cells with other chromosomal aberrations. Both primary and relapsed AML patient cells harboring CBFB::MYH11 were similarly affected. We then established xenograft and patient-derived mouse models of AML to evaluate the therapeutic efficacy of SM1 in vivo . Ongoing studies will assess SM1's impact on animal survival and aim to extend both in vitro and in vivo analyses to additional lead compounds identified in our in-silico screening. The success of this study could enable the development of a small-molecule therapeutic toolkit for chemoresistant AML harboring CBFB::MYH11 and support future applications in other AML subtypes with oncogenic fusions.