Combinatorial Anticancer Drug Screen Identifies Off-Target Effects of Epigenetic Chemical Probes
The response to anticancer drugs is influenced by both genetic and epigenetic factors. To explore the epigenetic regulators of anticancer drug efficacy, we performed a chemical epigenetic screen utilizing probes that target various epigenetic modulators. In this screening, we tested 31 epigenetic probes alongside 14 different anticancer agents and identified eight probes that significantly enhance the cytotoxic effects of TAK-243, a first-in-class inhibitor of ubiquitin-activating enzyme (UBA1) being evaluated in multiple solid and hematologic cancers. The effective probes included TP-472, GSK864, A-196, UNC1999, SGC-CBP30, and PFI-4 (along with its analogues GSK6853 and GSK5959), which target BRD9/7, mutant IDH1, SUV420H1/2, EZH2/1, p300/CBP, and BRPF1B, respectively. In contrast, negative control compounds did not significantly influence TAK-243’s cytotoxicity.
The enhancement of TAK-243’s cytotoxicity was linked to reduced ubiquitylation and increased apoptosis. Mechanistically, these epigenetic probes potentiated the effects of TAK-243 by inhibiting the efflux transporter ATP-binding cassette subfamily G member 2 (ABCG2), without causing notable changes in ubiquitylation pathways or ABCG2 expression levels. Docking analysis suggested that the identified probes may interact with ABCG2. Consequently, we developed a cell-based assay to quantitatively assess ABCG2 inhibition by drug candidates.
In summary, our study identifies specific epigenetic probes that significantly enhance the cytotoxicity of TAK-243 through off-target inhibition of ABCG2. We also provide experimental evidence that several negative control compounds do not rule out the possibility of off-target effects of chemical probes. Additionally, the potentiation of TAK-243’s cytotoxicity can be used as a quantitative measure of ABCG2-inhibitory activity.