Structural analysis of human KDM5B guides histone demethylase inhibitor development

Abstract

Members of the KDM5 (also known as JARID1) family are 2-oxoglutarate- and Fe(2+)-dependent oxygenases that act as histone H3K4 demethylases, thereby regulating cell proliferation and stem cell self-renewal and differentiation. Here we report crystal structures of the catalytic core of the human KDM5B enzyme in complex with three inhibitor chemotypes. These scaffolds exploit several aspects of the KDM5 active site, and their selectivity profiles reflect their hybrid features with respect to the KDM4 and KDM6 families. Whereas GSK-J1, a previously identified KDM6 inhibitor, showed about sevenfold less inhibitory activity toward KDM5B than toward KDM6 proteins, KDM5-C49 displayed 25-100-fold selectivity between KDM5B and KDM6B. The cell-permeable derivative KDM5-C70 had an antiproliferative effect in myeloma cells, leading to genome-wide elevation of H3K4me3 levels. The selective inhibitor GSK467 exploited unique binding modes, but it lacked cellular potency in the myeloma system. Taken together, these structural leads deliver multiple starting points for further rational and selective inhibitor design.

A KDM5 Inhibitor Increases Global H3K4 Trimethylation Occupancy and Enhances the Biological Efficacy of 5-Aza-2′-Deoxycytidine

“…1) as assayed by quantitative mass spectrometry. This KDM5i mediated increase in H3K4 methylation is similar in magnitude to those of previous studies using siRNA-mediated knockdown of KDM5B (6) or a distinct KDM5 inhibitor (7,34). Interestingly, increases in H3K9ac were also detected, but the mechanism driving these gains is unclear.…”

“…4F), indicating that this protein may be responsible for maintaining some of the borders of transcriptionally active regions. Key aspects of our findings thus fit those of others including data for another small molecule inhibitor of KDM5 (KDM5-C70) (7,34) which suggested a functional role for KDM5 proteins in regulating H3K4 methylation dynamics. Similarly, knockdown of KMD5B in MCF-7 led to subtle global increases in the H3K4me3/H3K4me2 ratio, and in mESC’s, KDM5B knockdown led to the spreading of H3K4me3 peaks into gene bodies (6,39).…”

“…A majority of these latter compounds competitively inhibit 2-OG binding in the JmJc domain (7,8). However, since this active site is strongly conserved in more than 30 distinct demethylases, many of these inhibitors lack specificity for a given family member (9,10).…”

JARID1/KDM5 demethylases as cancer targets?

“…Recent data indicate that a rethink about the contribution of the various domains to the demethylase activity and other functions of KDM5 family members may be required [2,3]. In KDM5 proteins, the JmjN domain is separated from the JmjC domain by the insertion of the ARID and PHD-1 domains, neither of which are required for demethylase activity, but the JmjN domain is.…”

“…The availability of the crystal structure of the KDM5 family members A, B, and C and studies on their interaction with the target histone mark is already guiding the development of more specific KDM5 inhibitors [2][3][4].…”