Structure and mechanism of inhibition of lysine demethylase 2A (KDM2A) by compound 183c

Lysine demethylase 2A (KDM2A) is a key epigenetic regulator and promising target for inhibition since its loss is selectively lethal in cancers reliant on Alternative Lengthening of Telomeres (ALT). Here we investigated the mechanism of compound 183c, a potent KDM2A inhibitor described in the patent literature. Biophysical studies showed that 183c requires the co-factor 2-oxoglutarate (2OG) for binding. A 2.2 Å crystal structure of the KDM2A–183c–2OG ternary complex explained the selectivity of 183c and revealed how 183c occupies the H3K36me2 substrate pocket, with a crucial group mimicking dimethylated lysine 36. In proliferation assays, several ALT-positive cell lines were selectively sensitive to 183c. Comparing ALT-positive SAOS2 and ALT-negative SJSA1 cells, both showed repression of E2F-regulated genes, but only SJSA1 activated EMT, DNA repair, and mTOR pathways, indicating distinct adaptive responses. These structural and cellular insights establish a foundation for designing improved KDM2A inhibitors for ALT-positive cancers. Lysine demethylase 2A (KDM2A) is a critical epigenetic regulator and a promising target for cancers dependent on Alternative Lengthening of Telomeres (ALT). Here, the authors elucidate the mechanism of compound 183c, a potent KDM2A inhibitor, revealing the cofactor 2-oxoglutarate dependent binding to the H3K36me2 substrate pocket, demonstrating its efficacy in selectively inhibiting ALT-positive cancer cell proliferation.