In Silico Discovery and Characterization of a Novel Nuclear Transcription Factor‑Y (NF-Y) Inhibitor with Antimitogenic Properties

Nuclear Transcription Factor-Y (NF-Y) is a transcription factor that binds CCAAT motifs to regulate gene expression, controlling cell proliferation, metabolism, and differentiation. NF-Y dysregulation contributes to diverse pathologies, including cancer, neurological disorders, cardiovascular disease, and tissue fibrosis. Using in silico molecular docking, we screened a library of eight million compounds to identify molecules targeting a pocket on the NF-YB/NF-YC dimer. We identified one compound, designated NFYi5, that was able to reduce the NF-Y activity. NFYi5 reduced mRNA levels of NF-Y target genes, while sparing housekeeping gene expression, and inhibiting cell proliferation. Mechanistic studies revealed that NFYi5 impaired NF-Y–DNA binding and accelerated NF-YA protein degradation, reducing its half-life from 16.5 ± 1.5 h to 8.5 ± 0.7 h. Together, these data establish NFYi5 as a small-molecule that can reduce NF-Y activity and is associated with antimitogenic properties. This proof-of-concept study demonstrates that NF-Y is pharmacologically tractable and highlights NFYi5 as a potential lead compound for therapeutic development in NF-Y-driven diseases.