Structure-Guided Discovery of Selective Antagonists for the Chromodomain of Polycomb Repressive Protein CBX7

Abstract

The chromobox 7 (CBX7) protein of the polycomb repressive complex 1 (PRC1) functions to repress transcription of tumor suppressor p16 (INK4a) through long noncoding RNA, ANRIL (antisense noncoding RNA in the INK4 locus) directed chromodomain (ChD) binding to trimethylated lysine 27 of histone H3 (H3K27me3), resulting in chromatin compaction at the INK4a/ARF locus. In this study, we report structure-guided discovery of two distinct classes of small-molecule antagonists for the CBX7ChD. Our Class A compounds, a series including analogues of the previously reported MS452, inhibit CBX7ChD/methyl-lysine binding by occupying the H3K27me3 peptide binding site, whereas our Class B compound, the newly discovered MS351, appears to inhibit H3K27me3 binding when CBX7ChD is bound to RNA. Our crystal structure of the CBX7ChD/MS351 complex reveals the molecular details of ligand recognition by the aromatic cage residues that typically engage in methyl-lysine binding. We further demonstrate that MS351 effectively induces transcriptional derepression of CBX7 target genes, including p16 (INK4a) in mouse embryonic stem cells and human prostate cancer PC3 cells. Thus, MS351 represents a new class of ChD antagonists that selectively targets the biologically active form of CBX7 of the PRC1 in long noncoding RNA- and H3K27me3-directed gene transcriptional repression.

Structure–Activity Relationships and Kinetic Studies of Peptidic Antagonists of CBX Chromodomains

“…Previous studies from the Zhou lab have reported weak, non-peptidic small molecule CBX7 ligands; however, SAR studies around these molecules struggled to produce significant improvements in potency. 21, 23 …”

Rational Adaptation of L3MBTL1 Inhibitors to Create Small‐Molecule Cbx7 Antagonists

“…State‐of‐the‐art Cbx inhibitors fall into two groups: high‐potency peptides and peptidomimetics, and low‐potency small‐molecule ligands. On an optimistic note, those low‐potency small‐molecule ligands include compounds like MS351, which has a 500 μ m affinity in solution but which shows cellular activities at only 5 μ m . The lack of significant traction gained by the approaches in this paper, and by the approaches of others, makes it clear that the creation of potent, low molecular weight, non‐peptidic inhibitors of Cbx proteins will continue to be challenging.…”

“…Successful approaches to Cbx7 inhibition have been driven by peptide‐based approaches– and high‐throughput screening for small‐molecule inhibitor approaches . Small‐molecule Cbx7 antagonists MS35472 and MS351 have been shown to de‐repress the p16 gene in PC3 prostate cancer cells …”

Chemical modulators for epigenome reader domains as emerging epigenetic therapies for cancer and inflammation

“…Further optimization lead to upto 7- fold increase ( K i = 4.8 μM) in potency but showed decreased cell permeability. [55] The same report[55] described another class of small molecule inhibitors of CBX7 that act by an allosteric mechanism and is represented by MS351 ( K D = 23.8 μM CBX7). The binding of this substituted benzimidazole to CBX7, induces binding of ANRIL RNA to a neighboring binding pocket on CBX7.…”