In silico discovery and characterisation of a novel nuclear transcription factor-Y (NF-Y) inhibitor with anti-mitogenic 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 NF-Y activity. NFYi5 reduced mRNA levels of NF-Y target genes, while sparing housekeeping gene expression, and inhibited 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 hours to 8.5±0.7. Together, these data establish NFYi5 as a small-molecule that can reduce NF-Y activity and is associated with anti-mitogenic 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.