Epigenetic Regulation of Wnt Signaling by Carboxamide-Substituted Benzhydryl Amines that Function as Histone Demethylase Inhibitors

Abstract

Aberrant activation of Wnt signaling triggered by mutations in either <i>Adenomatous Polyposis Coli</i> (<i>APC</i>) or <i>CTNNB1</i> (β-catenin) is a hallmark of colorectal cancers (CRC). As part of a program to develop epigenetic regulators for cancer therapy, we developed carboxamide-substituted benzhydryl amines (CBAs) bearing either aryl or heteroaryl groups that selectively targeted histone lysine demethylases (KDMs) and functioned as inhibitors of the Wnt pathway. A biotinylated variant of <i>N</i>-((5-chloro-8-hydroxyquinolin-7-yl) (4-(diethylamino)phenyl)-methyl)butyramide (CBA-1) identified KDM3A as a binding partner. KDM3A is a Jumonji (JmjC) domain-containing demethylase that is significantly upregulated in CRC. KDM3A regulates the demethylation of histone H3's lysine 9 (H3K9Me₂), a repressive marker for transcription. Inhibiting KDM3 increased H3K9Me₂ levels, repressed Wnt target genes, and curtailed <i>in vitro</i> CRC cell proliferation. CBA-1 also exhibited <i>in vivo</i> inhibition of Wnt signaling in a zebrafish model without displaying <i>in vivo</i> toxicity.