Reprogramming Cbx8-Prc1 Function With a Positive Allosteric Modulator

Abstract

Canonical targeting of Polycomb Repressive Complex 1 (PRC1) to repress developmental genes is mediated by cell type-specific, paralogous chromobox (CBX) proteins (CBX2, 4, 6, 7 and 8). Based on their central role in silencing and their misregulation associated with human disease including cancer, CBX proteins are attractive targets for small molecule chemical probe development. Here, we have used a quantitative and target-specific cellular assay to discover a potent positive allosteric modulator (PAM) of CBX8. The PAM activity of UNC7040 antagonizes H3K27me3 binding by CBX8 while increasing interactions with nucleic acids and participation in variant PRC1. We show that treatment with UNC7040 leads to efficient PRC1 chromatin eviction, loss of silencing and reduced proliferation across different cancer cell lines. Our discovery and characterization of UNC7040 not only revealed the most cellularly potent CBX8 specific chemical probe to date, but also corroborates a mechanism of polycomb regulation by non-histone lysine methylated interaction partners.

Discovery of Potent Peptidomimetic Antagonists for Heterochromatin Protein 1 Family Proteins

“…Owing to previous data from our group suggesting that C-terminal methyl ester derivatives of peptidomimetic compounds are more efficacious in cellular contexts than the corresponding amides, ,, we synthesized our top hit compound, UNC7047, as a methyl ester (UNC7560, Table ) for further analysis. Gratifyingly, UNC7560 maintains near identical potency toward CBX5 in comparison to the C-terminal amide compound, UNC7047, by both TR-FRET and ITC (Figure , Table , and Figure S5).…”

“…Structural diversity within the chromodomain family has resulted in specificity for one mark versus the other, as the Polycomb (Pc) sub-family of chromobox (CBX) proteins has been shown to primarily bind H3K27me3, while the heterochromatin protein 1 (HP1) family of CBX chromodomains and MPP8 chromodomain have shown specificity for H3K9me3. While the function of MPP8 has only recently been appreciated, the recognition of H3K9me3 and H3K27me3 by CBX chromodomains has been an active area of study among several groups, including ours. ,− …”

“…While we and others − have made progress toward high-quality chemical probes for the Polycomb CBX proteins, ligands for the HP1 family are lacking and a dedicated effort to create tools to explore the biology of HP1 chromodomains is warranted. The HP1 family includes HP1α (also known as CBX5), HP1β (CBX1), and HP1γ (CBX3), which contain a structurally conserved, N-terminal chromodomain consisting of a three-stranded anti-parallel β-sheet motif packed against a C-terminal α-helix.…”

Know when to fold ‘em: Polycomb complexes in oncogenic 3D genome regulation

“…More recently, Bell and colleagues reported UNC7040, a specific CBX8 compound that blocks CBX8 and RING1B recruitment to PRC2 targets while, similarly to the UNC4976, enhancing CBX8 affinity to DNA. Nonetheless, UNC7040 results in cPRC1 displacement from H3K27me3-enriched genes resulting in reduced cell proliferation of cancer cells (Suh et al, 2022).…”

Polycomb group proteins in cancer: multifaceted functions and strategies for modulation

“…A potent positive allosteric modulator of CBX8, UNC7040, can antagonize H3K27me3 binding to CBX8 while increasing interactions with nucleic acids and participation in variant PRC1 ( 290 ). It has increased potency against CBX8 binding in DLBCL cell compared to similar inhibitors that only inhibit H3K27me3 binding.…”