Allosteric modulation of YTHDFs by ellagic acid suppresses triple-negative breast cancer via non-canonical activation of the HIF-1α pathway.

Abstract

Triple-negative breast cancer (TNBC) lacks effective targeted therapies, and YTHDF proteins are frequently overexpressed in this malignancy, which correlates with adverse prognosis. Through high-throughput drug screening, we identify ellagic acid (EA) as a compound that binds to YTHDF proteins and disrupts their interaction with N6-methyladenosine (m6A)-modified RNAs. Structural and biochemical analyses show that EA targets a conserved, histidine-dependent allosteric site shared among YTHDF paralogs. This interaction induces conformational changes that disrupt m6A recognition and impair RNA binding, effectively inhibiting all three YTHDF proteins without compensatory escape. Phenotypically, EA suppresses TNBC cell proliferation and migration in vitro and in vivo. Mechanistically, EA enhances global mRNA stability, while selectively suppressing translation. In TNBC, EA-induced YTHDF2 inhibition stabilizes PFKFB4 mRNA, thereby increasing PFKFB4 protein, which blocks ubiquitin-dependent degradation of HIF-1α, resulting in BNIP3 induction and ultimately triggering apoptosis and necrosis. Collectively, our work unveils EA as a natural YTHDF inhibitor with compelling therapeutic potential for TNBC.