Selective Inhibition of CBX6: A Methyllysine Reader Protein in the Polycomb Family.

The polycomb paralogs CBX2, CBX4, CBX6, CBX7, and CBX8 are epigenetic readers that rely on "aromatic cage" motifs to engage their partners' methyllysine side chains. Each CBX carries out distinct functions, yet each includes a highly similar methyllysine-reading chromodomain as a key element. CBX7 is the only chromodomain that has yet been targeted by chemical inhibition. We report a small set of peptidomimetic agents in which a simple chemical modification switches the ligands from one with promiscuity across all polycomb paralogs to one that provides selective inhibition of CBX6. The structural basis for this selectivity, which involves occupancy of a small hydrophobic pocket adjacent to the aromatic cage, was confirmed through molecular dynamics simulations. Our results demonstrate the increases in affinity and selectivity generated by ligands that engage extended regions of chromodomain binding surfaces.

[1]  C. Arrowsmith,et al.  Cbx2 targets PRC1 to constitutive heterochromatin in mouse zygotes in a parent-of-origin-dependent manner. , 2015, Molecular cell.

[2]  Yunxiang Mu,et al.  Identification of a fragment-like small molecule ligand for the methyl-lysine binding protein, 53BP1. , 2015, ACS chemical biology.

[3]  M. Bienz,et al.  Competitive Binding of a Benzimidazole to the Histone-Binding Pocket of the Pygo PHD Finger , 2014, ACS chemical biology.

[4]  Ming-Ming Zhou,et al.  Privileged diazepine compounds and their emergence as bromodomain inhibitors. , 2014, Chemistry & biology.

[5]  Zhaohui S. Qin,et al.  Therapeutic Targeting of BET Bromodomain Proteins in Castration-Resistant Prostate Cancer , 2014, Nature.

[6]  J. Wulff,et al.  Chromodomain antagonists that target the polycomb-group methyllysine reader protein chromobox homolog 7 (CBX7). , 2014, Journal of medicinal chemistry.

[7]  S. Knapp,et al.  Discovery of BET bromodomain inhibitors and their role in target validation , 2014 .

[8]  P. P. Sharp,et al.  BET bromodomain inhibitors: a patent review , 2014, Expert opinion on therapeutic patents.

[9]  S. Frye,et al.  The structure-activity relationships of L3MBTL3 inhibitors: flexibility of the dimer interface. , 2013, MedChemComm.

[10]  S. Frye,et al.  Small-molecule ligands of methyl-lysine binding proteins: optimization of selectivity for L3MBTL3. , 2013, Journal of medicinal chemistry.

[11]  P. Bamborough,et al.  Discovery of epigenetic regulator I-BET762: lead optimization to afford a clinical candidate inhibitor of the BET bromodomains. , 2013, Journal of medicinal chemistry.

[12]  P. Sandy,et al.  Discovery, Design, and Optimization of Isoxazole Azepine BET Inhibitors. , 2013, ACS medicinal chemistry letters.

[13]  Wei Wang,et al.  Identification of Methyllysine Peptides Binding to Chromobox Protein Homolog 6 Chromodomain in the Human Proteome* , 2013, Molecular & Cellular Proteomics.

[14]  K. Helin,et al.  Polycomb Cbx family members mediate the balance between haematopoietic stem cell self-renewal and differentiation , 2013, Nature Cell Biology.

[15]  K. Stegmaier,et al.  Targeting MYCN in neuroblastoma by BET bromodomain inhibition. , 2013, Cancer discovery.

[16]  L. Cozzuto,et al.  RYBP and Cbx7 define specific biological functions of polycomb complexes in mouse embryonic stem cells. , 2013, Cell reports.

[17]  A. Emili,et al.  Discovery of a chemical probe for the L3MBTL3 methyl-lysine reader domain , 2012, Nature chemical biology.

[18]  P. Sebastiani,et al.  BET bromodomain inhibition as a novel strategy for reactivation of HIV‐1 , 2012, Journal of leukocyte biology.

[19]  S. Knapp,et al.  Identification of a Chemical Probe for Bromo and Extra C-Terminal Bromodomain Inhibition through Optimization of a Fragment-Derived Hit , 2012, Journal of medicinal chemistry.

[20]  N. Nath,et al.  Identification and characterization of small molecule inhibitors of a plant homeodomain finger. , 2012, Biochemistry.

[21]  David M. Wilson,et al.  Fragment-based discovery of bromodomain inhibitors part 2: optimization of phenylisoxazole sulfonamides. , 2012, Journal of medicinal chemistry.

[22]  James M. Woolven,et al.  Fragment-based discovery of bromodomain inhibitors part 1: inhibitor binding modes and implications for lead discovery. , 2012, Journal of medicinal chemistry.

[23]  Edith Heard,et al.  MicroRNA Regulation of Cbx7 Mediates a Switch of Polycomb Orthologs during ESC Differentiation , 2012, Cell stem cell.

[24]  Matthieu Schapira,et al.  Druggability of methyl-lysine binding sites , 2011, J. Comput. Aided Mol. Des..

[25]  Jian Jin,et al.  Small-molecule ligands of methyl-lysine binding proteins. , 2011, Journal of medicinal chemistry.

[26]  Cen Gao,et al.  Biophysical probes reveal a "compromise" nature of the methyl-lysine binding pocket in L3MBTL1. , 2011, Journal of the American Chemical Society.

[27]  Shili Duan,et al.  Recognition and Specificity Determinants of the Human Cbx Chromodomains* , 2010, The Journal of Biological Chemistry.

[28]  William B. Smith,et al.  Selective inhibition of BET bromodomains , 2010, Nature.

[29]  R. Mishra,et al.  Novel motifs distinguish multiple homologues of Polycomb in vertebrates: expansion and diversification of the epigenetic toolkit , 2009, BMC Genomics.

[30]  M. Hendzel,et al.  Polycomb group protein gene silencing, non-coding RNA, stem cells, and cancer. , 2009, Biochemistry and cell biology = Biochimie et biologie cellulaire.

[31]  A. Shilatifard,et al.  An operational definition of epigenetics. , 2009, Genes & development.

[32]  Yi Zhang,et al.  Recognition of Histone H3 Lysine-4 Methylation by the Double Tudor Domain of JMJD2A , 2006, Science.

[33]  C. Allis,et al.  Mouse Polycomb Proteins Bind Differentially to Methylated Histone H3 and RNA and Are Enriched in Facultative Heterochromatin , 2006, Molecular and Cellular Biology.

[34]  Xinyi Huang.  Fluorescence Polarization Competition Assay: The Range of Resolvable Inhibitor Potency Is Limited by the Affinity of the Fluorescent Ligand , 2003 .

[35]  C. Allis,et al.  Translating the Histone Code , 2001, Science.

[36]  V. Stojanoff,et al.  Small-Molecule Modulators of Methyl-Lysine Binding for the CBX 7 Chromodomain Graphical Abstract Highlights , 2022 .

[37]  L. Cozzuto,et al.  RYBP and Cbx 7 Define Specific Biological Functions of Polycomb Complexes in Mouse Embryonic Stem Cells , 2022 .