Design, Synthesis and Characterization of Covalent KDM5 Inhibitors

Abstract

Histone lysine demethylases (KDMs) are involved in the dynamic regulation of gene expression and they play a critical role in several biological processes. Achieving selectivity over the different KDMs has been a major challenge for KDM inhibitor development. Here we report potent and selective KDM5 covalent inhibitors designed to target cysteine residues only present in the KDM5 sub‐family. The covalent binding to the targeted proteins was confirmed by MS and time‐dependent inhibition. Additional competition assays show that compounds were non 2‐OG competitive. Target engagement and ChIP‐seq analysis showed that the compounds inhibited the KDM5 members in cells at nano‐ to micromolar levels and induce a global increase of the H3K4me3 mark at transcriptional start sites.

The Clinically Used Iron Chelator Deferasirox Is an Inhibitor of Epigenetic JumonjiC Domain-Containing Histone Demethylases

“…JmjC histone demethylases have emerged as promising drug targets, ,− with inhibitor discovery programs being reported by us − and others, − as recently reviewed. ,,− A majority of reported JmjC KDM inhibitors function by active site metal chelation and competitive displacement of the co-substrate 2OG. − Very recently, covalent KDM5 inhibitors , and inhibitors of both the lysyl- and arginyl-demethylase activities have also been reported.…”

Targeting Epigenetic Regulators with Covalent Small-Molecule Inhibitors

“…As discussed above, Cys481 of KDM5A is conserved in the KDM5 subfamily and corresponds to Cys497 of KDM5B. Therefore, another series of covalent KDM5 subfamily inhibitors targeting Cys497 of KDM5B were also designed by Brennan and co-workers, as exemplified by compound 81 , which was generated by incorporating 2-chloroacetamide into the pyrazolyl moiety of compound 73 via an ethylamine linker . Covalent binding of compound 81 with KDM5B was confirmed by mass spectrometry labeling experiments, and a protein–inhibitor adduct in the mass spectra was detected after incubation of 81 with KDM5B.…”

“…On the other hand, Cys480 is identified as a unique residue in KDM5B and corresponds to Ser464 in KDM5A, Ser485 in KDM5C, and Ser495 in KDM5D, providing an opportunity to develop selective covalent inhibitors of KDM5B over KDM5A/C/D and KDM4s . Therefore, a series of KDM5B-selective covalent inhibitors based on the core structure of compound 74 were designed, as exemplified by compounds 82 and 83 (Figure ).…”

The Clinically Used Iron Chelator Deferasirox is an Inhibitor of Epigenetic JumonjiC Domain-Containing Histone Demethylases

“…17,19,[36][37][38][39][40] The majority of reported JmjC KDM inhibitors function by active site metal chelation and competitive displacement of the co-substrate 2OG. [36][37][38][39] Very recently, covalent KDM5 inhibitors 41,42 and inhibitors of both the lysyl-and arginyl-demethylase activities 43 have also been reported.…”