Nature 488, 404–408 (2012)

Jumonji (JMJ) family demethylases oxidatively remove methyl groups from lysine residues in histones and thereby regulate numerous gene expression pathways. To date, insights into the functions of JMJ demethylases have been hampered by the lack of potent and selective small-molecule inhibitors. A structure-based design approach now fills this gap by identifying a chemical probe that targets the KDM6 subfamily of JMJ enzymes (JMJD3 and UTX). Kruidenier et al. solved crystal structures of mouse and human forms of JMJD3 in complex with a peptide substrate. Building on their structural insights and subsequent mutational studies exploring substrate binding, the authors identified an inhibitor of JMJD3 and UTX activity (GSK-J1) and an inactive structural isomer (GSK-J2). Analysis of the JMJD3—GSK-J1 complex structure revealed that the compound's 2,2′-bipyridyl substructure ligates the catalytic metal ion while its propanoic acid moiety mimics the enzyme's α-ketoglutarate cofactor. Using chemical proteomics, the authors showed that immobilized GSK-J1, but not GSK-J2, specifically captured JMJD3 and UTX from whole cells. An esterified prodrug form of GSK-J1 with improved cellular efficacy maintained the amount of H3K27me3 in treated cells and was used to show that JMJD3 and UTX activity are required for the transcriptional regulation of proinflammatory genes in macrophages. In total, the studies expand the scope of chromatin-modifying enzyme inhibitors available to probe their complex cellular roles.