Tetrazolylhydrazides as Selective Fragment‐Like Inhibitors of the JumonjiC‐Domain‐Containing Histone Demethylase KDM4A

Abstract

The JumonjiC-domain-containing histone demethylase 2A (JMJD2A, KDM4A) is a key player in the epigenetic regulation of gene expression. Previous publications have shown that both elevated and lowered enzyme levels are associated with certain types of cancer, and therefore the definite role of KDM4A in oncogenesis remains elusive. To identify a novel molecular starting point with favorable physicochemical properties for the investigation of the physiological role of KDM4A, we screened a number of molecules bearing an iron-chelating moiety by using two independent assays. In this way, we were able to identify 2-(1H-tetrazol-5-yl)acetohydrazide as a novel fragment-like lead structure with low relative molecular mass (Mr =142 Da), low complexity, and an IC50 value of 46.6 μm in a formaldehyde dehydrogenase (FDH)-coupled assay and 2.4 μm in an antibody-based assay. Despite its small size, relative selectivity against two other demethylases could be demonstrated for this compound. This is the first example of a tetrazole group as a warhead in JMJD demethylases.

Structure‐Based Screening of Tetrazolylhydrazide Inhibitors versus KDM4 Histone Demethylases

“…One such group is the tetrazole moiety. Given that, it seems surprising that no such structures of complexes have been reported for KDM4 proteins, to date, although tetrazolylhydrazide compounds in KDM4 inhibition were first reported in 2015 by Rüger et al …”

“…These small molecules constitute promising frameworks for early drug discovery stages because their initial selectivity has been reported . The structures presented herein show the specific binding of tetrazolylhydrazide ligands (Figure ) to the metal ion in the active site, serving as 2OG competitors. A series of molecules with hydrazide and tetrazole ring modifications show different modes of binding in the active center of the enzyme.…”

“…Herein, we present the first successful attempt to obtain high‐resolution X‐ray structures of both hydrazide and tetrazole moieties bound to the enzyme KDM4D. These small molecules constitute promising frameworks for early drug discovery stages because their initial selectivity has been reported . The structures presented herein show the specific binding of tetrazolylhydrazide ligands (Figure ) to the metal ion in the active site, serving as 2OG competitors.…”

4‐Biphenylalanine‐ and 3‐Phenyltyrosine‐Derived Hydroxamic Acids as Inhibitors of the JumonjiC‐Domain‐Containing Histone Demethylase KDM4A

“…With regard to KDM4A inhibition, we have recently reported the fragment‐like inhibitor 5‐tetrazolyl acetohydrazide (compound 2 , Figure ), which inhibits this demethylase with an IC 50 of 46.6 μ m . Compound 2 is a co‐substrate 2‐oxoglutarate mimic, with the tetrazole ring as a bioisosteric replacement of the carboxylic acid . A series of aminopyrimidylpyridine‐carboxylates were also prepared by our group.…”

Advances in histone demethylase KDM4 as cancer therapeutic targets

“…Zn 2+ ions, required for catalytic activity in KDM4A, can be locally released through the binding of Zn‐ejecting compounds such as disulfiram (IC 50 = 3.3 μM) and ebselen (IC 50 = 10.6 μM). In addition, 2‐(1H‐tetrazol‐5‐yl)acetohydrazide with an iron‐chelating moiety has a relatively low molecular weight, low complexity, and high affinity for the KDM4A metal‐binding site, with an IC 50 value of 46.6 μM in an FDH‐coupled assay and 2.4 μM by antibody‐based analysis . These metal cofactor disruptors may provide other inhibitory mechanisms that can be used to selectively target KDM4.…”