Mechanistic deconvolution reveals DHODH as the key target of the KDM4 inhibitor QC6352 [RNA-Seq]

The small molecule QC6352, developed as an inhibitor of the histone demethylase KDM4, exhibits potent anti-cancer activity, and its derivative, zavondemstat, is currently being evaluated in cancer clinical trials. Here, we demonstrate that the anti-proliferative efficacy of QC6352 in glioblastoma models is independent of KDM4 inhibition. Transcriptomic analysis revealed that QC6352's gene expression signature in glioblastoma cells closely resembles that of drugs targeting dihydroorotate dehydrogenase (DHODH). Biochemical assays, protein crystallography, metabolomic analysis, and uridine rescue experiments confirmed that QC6352 inhibits DHODH and thereby disrupts the de novo pyrimidine biosynthesis pathway. Furthermore, we show that the therapeutic efficacy of zavondemstat is primarily driven by DHODH inhibition, rather than KDM4 inhibition. Lastly, by uncovering the mechanism of action of QC6352, we identify PRMT5 inhibitors as synergistic partners for DHODH inhibitors, providing the basis for maximising the therapeutic impact of DHODH inhibitors in cancer treatments.