Identification of substituted acetanilide compounds as small molecule CBX2 inhibitors via in silico screening

Abstract The chromodomain protein CBX2 binds directly to histone H3 trimethylation at lysine 27 (H3K27me3) and is a component of polycomb repressive complex 1 (PRC1). CBX2 plays a pivotal role in transcriptional repression by acting as a reader protein that recognizes H3K27me3. In this study, we performed in silico screening based on the crystal structure of CBX2 to identify small molecule compounds that target the chromodomain of CBX2. The ability of the selected compounds to inhibit the interaction between CBX2 and histone H3 in cells was validated. After three rounds of in silico screening, CG3-46 was ultimately identified as the most potent CBX2 inhibitor in this study. CG3-46 inhibited the growth of the triple-negative breast cancer cell line MDA-MB-231 in a concentration range comparable to that used to inhibit the interaction between CBX2 and H3K27me3. Our results indicate that CG3-46 represents the first nonpeptide small molecule inhibitor of CBX2, which not only serves as a valuable chemical tool for elucidating the role of CBX2 in cellular epigenetic regulation but also as a starting compound for the development of CBX2-targeted therapeutics for triple-negative breast cancer.