A selective jumonji H3K27 demethylase inhibitor modulates the proinflammatory macrophage response

Abstract

The jumonji (JMJ) family of histone demethylases are Fe2+- and α-ketoglutarate-dependent oxygenases that are essential components of regulatory transcriptional chromatin complexes1–4. These enzymes demethylate lysine residues in histones in a methylation-state and sequence-specific context5. Considerable effort has been devoted to gaining a mechanistic understanding of the roles of histone lysine demethylases in eukaryotic transcription, genome integrity and epigenetic inheritance2,4,6, as well as in development, physiology and disease3,7. However, because of the absence of any selective inhibitors, the relevance of the demethylase activity of JMJ enzymes in regulating cellular responses remains poorly understood. Here we present a structure-guided small-molecule and chemoproteomics approach to elucidating the functional role of the H3K27me3-specific demethylase subfamily (KDM6 subfamily members JMJD3 and UTX)8. The liganded structures of human and mouse JMJD3 provide novel insight into the specificity determinants for cofactor, substrate and inhibitor recognition by the KDM6 subfamily of demethylases. We exploited these structural features to generate the first small-molecule catalytic site inhibitor that is selective for the H3K27me3-specific JMJ subfamily. We demonstrate that this inhibitor binds in a novel manner and reduces lipopolysaccharide-induced proinflammatory cytokine production by human primary macrophages, a process that depends on both JMJD3 and UTX. Our results resolve the ambiguity associated with the catalytic function of H3K27-specific JMJs in regulating disease-relevant inflammatory responses and provide encouragement for designing small-molecule inhibitors to allow selective pharmacological intervention across the JMJ family.

Epigenetic modification in chromatin machinery and its deregulation in pediatric brain tumors: Insight into epigenetic therapies

“…GSK-J1/J4 were first discovered as JMJD3 (KMD6B) and UTX (KMD6A) inhibitors, and the treatment of human primary macrophages with these pharmacological substances reduces the lipopolysaccharide-induced pro-inflammatory response 107 Remarkably, GSK-J4 recently has been used successfully to treat brainstem gliomas in vitro and in vivo ( 108 and reviewed in [109][110][111][112] ). The mechanism of action of GSK-J4 is chelation of the Fe(II) active site and binding of a propanoic acid side-chain to the 2OG binding site.…”

“…Recent studies described that besides being a potent inhibitor of jumonji proteins, with activity toward H3K27me3/me2 (KDM6), GSK-J1 can also inhibit KDM5 activity on H3K4me3/me2 in U2OS cells in vitro. 141 Considering the effect of JMJD3 on several biologic functions (e.g., inflammatory response in macrophages 107 ) and those of KDM5, 142 optimizing the dose and frequency of administration of such inhibitors to maximize the therapeutic window and limit toxicity will be a key factor for reaching a successful clinical outcome. The combination of agents with different mechanisms of action, as recently proposed 117 may offer a better chance for tumor control with limited toxicity.…”

Metformin directly targets the H3K27me3 demethylase KDM6A/UTX

“…To gain insight into the inhibitory mechanism of metformin against KDM6A/UTX, we resolved the binding mode of metformin with the fragment corresponding to the C‐terminal region of KDM6A/UTX, which is known to exhibit demethylase activity against H3K27me3 (Sengoku & Yokoyama, 2011; Kruidenier et al., 2012). The metformin‐binding mode to KDM6A/UTX employed the crystal structure 3AVS in complex with N‐oxalylglycine (NOG, a nonreactive analog of AKG and Ni 2+ , which coordinates the Fe 2+ ‐binding site but does not support catalysis).…”

Discovery of a Highly Selective Cell‐Active Inhibitor of the Histone Lysine Demethylases KDM2/7

“…Currently, most inhibitors of the JmjC KDMs are iron‐chelating 2‐OG competitors (Figure 1). 8, 9, 10, 11, 12, 13, 14 Although many of these molecules achieve high levels of in vitro potency, they are frequently limited by a lack of selectivity and activity in cells. Peptide inhibitors that either mimic the histone substrate or bind KDMs allosterically have also been reported,15 however peptides are often limited by their low cellular permeability.…”