Post-translational methylation of histone proteins is one of several major epigenetic modifications that regulate transcription factor recruitment and gene expression.1 Histone lysine methylation is partially controlled by the histone lysine demethylase (KDM) superfamily of proteins which catalyse the removal of repressive methyl marks from lysine residues in histone H3. KDM4A-E primarily target dimethylated and trimethylated H3K9 and H3K36, which are typically associated with gene activation. KDM protein expressions are generally tightly regulated in healthy tissues, however, many members of the KDM superfamily including KDM4A-E are regularly observed to be upregulated in a broad range of cancer cell lines and tissues, where they epigenetically activate multiple signalling pathways responsible for increased glucose metabolism, hormone response, angiogenesis, and tissue invasion.2 The recent completed phase 1 study of zavondemstat and the existence of several known inhibitory scaffolds suggest KDM4A-E are likely druggable targets, and highly potent and selective KDM4 inhibitors remain highly desirable as potential adjuvants to traditional chemotherapy.3,4
In this work, we report the development of analogues of existing fragments with enhanced inhibitory potency and selectivity for KDM4 over other non-KDM proteins from a computational and structure-based approach, and an expansion of existing SAR through bioisosteric replacement of key functional groups in existing fragments. Occupancy of the KDM4 active site by these analogues is supported by molecular modelling and acquired co-crystallised drug-protein structures, and the inhibitory activity is evidenced by in vitro demethylation assays.