Rational Design and Optimization of m6A-RNA Demethylase FTO Inhibitors as Anticancer Agents

Aberrant regulation of N⁶-methyladenosine (m⁶A) RNA modification has been implicated in the progression of multiple diseases, including Cancer. Previously, we identified a small molecule inhibitor of the m⁶A demethylase fat mass- and obesity-associated protein (FTO), which removes both m⁶A and N⁶,2'-O-dimethyladenosine (m⁶A_m) RNA modifications. In this work, we describe the rational design and optimization of a new class of FTO inhibitors derived from our previous lead FTO-04 with nanomolar potency and high selectivity against the homologous m⁶A RNA demethylase ALKBH5. The oxetanyl class of compounds comprise competitive inhibitors of FTO with potent antiproliferative effects in glioblastoma, acute myeloid leukemia, and gastric Cancer models where lead FTO-43 demonstrated potency comparable to clinical chemotherapeutic 5-fluorouracil. Furthermore, FTO-43 increased m⁶A and m⁶A_m levels in a manner comparable to FTO knockdown in gastric Cancer cells and regulated Wnt/PI3K-Akt signaling pathways. The oxetanyl class contains significantly improved Anticancer agents with a variety of applications beyond glioblastoma.