Chromodomain Ligand Optimization via Target-Class Directed Combinatorial Repurposing

• Published in: ACS chemical biology Vol. 11; no. 9; pp. 2475 - 2483
• Main Authors: Barnash, Kimberly D, Lamb, Kelsey N, Stuckey, Jacob I, Norris, Jacqueline L, Cholensky, Stephanie H, Kireev, Dmitri B, Frye, Stephen V, James, Lindsey I
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 16.09.2016
• Subjects: Ligands; Molecular Probes - chemistry; Protein Binding; Proteins - chemistry; Structure-Activity Relationship
• ISSN: 1554-8929; 1554-8937; 1554-8937
• DOI: 10.1021/acschembio.6b00415

Efforts to develop strategies for small-molecule chemical probe discovery against the readers of the methyl-lysine (Kme) post-translational modification have been met with limited success. Targeted disruption of these protein–protein interactions via peptidomimetic inhibitor optimization is a promising alternative to small-molecule hit discovery; however, recognition of identical peptide motifs by multiple Kme reader proteins presents a unique challenge in the development of selective Kme reader chemical probes. These selectivity challenges are exemplified by the Polycomb repressive complex 1 (PRC1) chemical probe, UNC3866, which demonstrates submicromolar off-target affinity toward the non-PRC1 chromodomains CDYL2 and CDYL. Moreover, since peptidomimetics are challenging subjects for structure–activity relationship (SAR) studies, traditional optimization of UNC3866 would prove costly and time-consuming. Herein, we report a broadly applicable strategy for the affinity-based, target-class screening of chromodomains via the repurposing of UNC3866 in an efficient, combinatorial peptide library. A first-generation library yielded UNC4991, a UNC3866 analogue that exhibits a distinct selectivity profile while maintaining submicromolar affinity toward the CDYL chromodomains. Additionally, in vitro pull-down experiments from HeLa nuclear lysates further demonstrate the selectivity and utility of this compound for future elucidation of CDYL protein function.