Structural Superimposition

Abstact

Histone lysine demethylase 4 (KDM4) enzymes are frequently overexpressed in cancer and are considered to be promising therapeutic targets. QC6352, which is widely used as a best-in-class KDM4 chemical probe, shows potent antitumor activity across cancer models. Using comprehensive chemical biology approaches in glioblastoma models, we demonstrate that the efficacy of QC6352 and that of its clinical analog zavondemstat are independent of KDM4 inhibition. Instead, we identify dihydroorotate dehydrogenase (DHODH), a key enzyme in de novo pyrimidine biosynthesis, as the functional target driving their antiproliferative activity. Uridine supplementation and expression of an inhibitor-resistant DHODH mutant fully abrogate growth inhibition, whereas the orthogonal KDM4 inhibitor ML324, which lacks DHODH inhibition, fails to phenocopy QC6352. These findings establish QC6352 and zavondemstat as dual KDM4-DHODH inhibitors and identify DHODH inhibition as the dominant driver of their antiglioblastoma efficacy, as well as demonstrating the need for orthogonal chemical probes to accurately define drug mechanisms in cells.