Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Perspective
  • Published:

Targeting non-bromodomain chromatin readers

Abstract

Chromatin regulatory proteins are increasingly recognized as potential new drug targets. Many of these proteins harbor one or more so called ‘reader domains’ that recognize covalent modifications of lysine and arginine residues, typically on histones, which mediate specific interactions within chromatin. Here we review recent progress in the discovery of drug-like small molecules that antagonize the function of methyl-lysine and methyl-arginine reader domains (Royal family, plant homeodomain (PHD) and WD40 domains) as well as the acyl-lysine-binding YEATS domain.

This is a preview of subscription content, access via your institution

Access options

Buy this article

Prices may be subject to local taxes which are calculated during checkout

Fig. 1: MBT, chromodomain and Tudor domain antagonists.
Fig. 2: PWWP, PHD and YEATS domain ligands.
Fig. 3: WDR domain antagonists.

Similar content being viewed by others

References

  1. Arrowsmith, C. H., Bountra, C., Fish, P. V., Lee, K. & Schapira, M. Epigenetic protein families: a new frontier for drug discovery. Nat. Rev. Drug Discov. 11, 384–400 (2012).

    Article  CAS  Google Scholar 

  2. Jeltsch, A., Broche, J. & Bashtrykov, P. Molecular processes connecting DNA methylation patterns with DNA methyltransferases and histone modifications in mammalian genomes. Genes 9, E566 (2018).

    Article  Google Scholar 

  3. Zaware, N. & Zhou, M.-M. Bromodomain biology and drug discovery. Nat. Struct. Mol. Biol. https://doi.org/10.1038/s41594-019-0309-8 (2019).

  4. Maurer-Stroh, S. et al. The Tudor domain ‘Royal Family’: Tudor, plant Agenet, Chromo, PWWP and MBT domains. Trends Biochem. Sci. 28, 69–74 (2003).

    Article  CAS  Google Scholar 

  5. Gayatri, S. & Bedford, M. T. Readers of histone methylarginine marks. Biochim. Biophys. Acta 1839, 702–710 (2014).

    Article  CAS  Google Scholar 

  6. Collins, R. E. et al. The ankyrin repeats of G9a and GLP histone methyltransferases are mono- and dimethyllysine binding modules. Nat. Struct. Mol. Biol. 15, 245–250 (2008).

    Article  CAS  Google Scholar 

  7. Sanchez, R. & Zhou, M.-M. The PHD finger: a versatile epigenome reader. Trends Biochem. Sci. 36, 364–372 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  8. Schapira, M., Tyers, M., Torrent, M. & Arrowsmith, C. H. WD40 repeat domain proteins: a novel target class? Nat. Rev. Drug Discov. 16, 773–786 (2017).

    Article  CAS  Google Scholar 

  9. Trojer, P. et al. L3MBTL1, a histone-methylation-dependent chromatin lock. Cell 129, 915–928 (2007).

    Article  CAS  Google Scholar 

  10. Nady, N. et al. Histone recognition by human malignant brain tumor domains. J. Mol. Biol. 423, 702–718 (2012).

    Article  CAS  Google Scholar 

  11. Min, J. et al. L3MBTL1 recognition of mono- and dimethylated histones. Nat. Struct. Mol. Biol. 14, 1229–1230 (2007).

    Article  CAS  Google Scholar 

  12. Taverna, S. D., Li, H., Ruthenburg, A. J., Allis, C. D. & Patel, D. J. How chromatin-binding modules interpret histone modifications: lessons from professional pocket pickers. Nat. Struct. Mol. Biol. 14, 1025–1040 (2007).

    Article  CAS  Google Scholar 

  13. Meier, K. & Brehm, A. Chromatin regulation: how complex does it get? Epigenetics 9, 1485–1495 (2014).

    Article  Google Scholar 

  14. Santiago, C., Nguyen, K. & Schapira, M. Druggability of methyl-lysine binding sites. J. Comput. Aided Mol. Des. 25, 1171–1178 (2011).

    Article  CAS  Google Scholar 

  15. Herold, J. M. et al. Small-molecule ligands of methyl-lysine binding proteins. J. Med. Chem. 54, 2504–2511 (2011).

    Article  CAS  Google Scholar 

  16. James, L. I. et al. Discovery of a chemical probe for the L3MBTL3 methyllysine reader domain. Nat. Chem. Biol. 9, 184–191 (2013). First biologically active antagonist of a Kme reader domain, demonstrating proof of concept for this class of protein.

    Article  CAS  Google Scholar 

  17. Lu, J. et al. L3MBTL1 regulates ALS/FTD-associated proteotoxicity and quality control. Nat. Neurosci. 22, 875–886 (2019).

    Article  CAS  Google Scholar 

  18. Kaustov, L. et al. Recognition and specificity determinants of the human cbx chromodomains. J. Biol. Chem. 286, 521–529 (2011).

    Article  CAS  Google Scholar 

  19. Ren, C. et al. Small-molecule modulators of methyl-lysine binding for the CBX7 chromodomain. Chem. Biol. 22, 161–168 (2015).

    Article  CAS  Google Scholar 

  20. Simhadri, C. et al. Chromodomain antagonists that target the polycomb-group methyllysine reader protein chromobox homolog 7 (CBX7). J. Med. Chem. 57, 2874–2883 (2014).

    Article  CAS  Google Scholar 

  21. Stuckey, J. I. et al. A cellular chemical probe targeting the chromodomains of Polycomb repressive complex 1. Nat. Chem. Biol. 12, 180–187 (2016).

    Article  CAS  Google Scholar 

  22. Botuyan, M. V. et al. Structural basis for the methylation state-specific recognition of histone H4-K20 by 53BP1 and Crb2 in DNA repair. Cell 127, 1361–1373 (2006).

    Article  CAS  Google Scholar 

  23. Lee, J., Thompson, J. R., Botuyan, M. V. & Mer, G. Distinct binding modes specify the recognition of methylated histones H3K4 and H4K20 by JMJD2A-tudor. Nat. Struct. Mol. Biol. 15, 109–111 (2008).

    Article  CAS  Google Scholar 

  24. Roy, S. et al. Structural insight into p53 recognition by the 53BP1 tandem Tudor domain. J. Mol. Biol. 398, 489–496 (2010).

    Article  CAS  Google Scholar 

  25. Bian, C. et al. Sgf29 binds histone H3K4me2/3 and is required for SAGA complex recruitment and histone H3 acetylation. EMBO J. 30, 2829–2842 (2011).

    Article  CAS  Google Scholar 

  26. Arita, K. et al. Recognition of modification status on a histone H3 tail by linked histone reader modules of the epigenetic regulator UHRF1. Proc. Natl Acad. Sci. USA 109, 12950–12955 (2012).

    Article  CAS  Google Scholar 

  27. Tripsianes, K. et al. Structural basis for dimethylarginine recognition by the Tudor domains of human SMN and SPF30 proteins. Nat. Struct. Mol. Biol. 18, 1414–1420 (2011).

    Article  CAS  Google Scholar 

  28. Liu, K. et al. Structural basis for recognition of arginine methylated Piwi proteins by the extended Tudor domain. Proc. Natl Acad. Sci. USA 107, 18398–18403 (2010).

    Article  CAS  Google Scholar 

  29. Sikorsky, T. et al. Recognition of asymmetrically dimethylated arginine by TDRD3. Nucleic Acids Res. 40, 11748–11755 (2012).

    Article  CAS  Google Scholar 

  30. Perfetti, M. T. et al. Identification of a fragment-like small molecule ligand for the methyl-lysine binding protein, 53BP1. ACS Chem. Biol. 10, 1072–1081 (2015).

    Article  CAS  Google Scholar 

  31. Jurkowska, R. Z. et al. H3K14ac is linked to methylation of H3K9 by the triple Tudor domain of SETDB1. Nat. Commun. 8, 2057 (2017).

    Article  Google Scholar 

  32. Mader, P. et al. Identification and characterization of the first fragment hits for SETDB1 Tudor domain. Bioorg. Med. Chem. 27, 3866–3878 (2019).

    Article  CAS  Google Scholar 

  33. Senisterra, G. et al. Discovery of small-molecule antagonists of the H3K9me3 binding to UHRF1 tandem Tudor domain. SLAS Discov. 23, 930–940 (2018).

    CAS  PubMed  Google Scholar 

  34. Houliston, R. S. et al. Conformational dynamics of the TTD-PHD histone reader module of the UHRF1 epigenetic regulator reveals multiple histone-binding states, allosteric regulation, and druggability. J. Biol. Chem. 292, 20947–20959 (2017).

    Article  CAS  Google Scholar 

  35. Su, X. et al. Molecular basis underlying histone H3 lysine-arginine methylation pattern readout by Spin/Ssty repeats of Spindlin1. Genes Dev. 28, 622–636 (2014).

    Article  CAS  Google Scholar 

  36. Fagan, V. et al. A chemical probe for Tudor domain protein Spindlin1 to investigate chromatin functions. https://doi.org/10.26434/chemrxiv.7673129.v2 (2019). First-in-class chemical probe for a Tudor domain protein.

  37. Wagner, T. et al. Identification of a small-molecule ligand of the epigenetic reader protein Spindlin1 via a versatile screening platform. Nucleic Acids Res. 44, e88 (2016).

    Article  Google Scholar 

  38. Sweis, R. F. et al. Discovery and development of potent and selective inhibitors of histone methyltransferase g9a. ACS Med. Chem. Lett. 5, 205–209 (2014).

    Article  CAS  Google Scholar 

  39. Bae, N. et al. Developing Spindlin1 small-molecule inhibitors by using protein microarrays. Nat. Chem. Biol. 13, 750–756 (2017).

    Article  CAS  Google Scholar 

  40. Xiong, Y. et al. Discovery of a potent and selective fragment-like inhibitor of methyllysine reader protein spindlin 1 (SPIN1). J. Med. Chem. (2019).

  41. Qin, S. & Min, J. Structure and function of the nucleosome-binding PWWP domain. Trends Biochem. Sci. 39, 536–547 (2014).

    Article  CAS  Google Scholar 

  42. Böttcher, J. et al. Fragment-based discovery of a chemical probe for the PWWP1 domain of NSD3. Nat. Chem. Biol. 15, 822–829 (2019). First-in-class PWWP inhibitor, with demonstrated impact on relevant biology.

    Article  Google Scholar 

  43. Shen, C. et al. NSD3-Short is an adaptor protein that couples BRD4 to the CHD8 chromatin remodeler. Mol. Cell 60, 847–859 (2015).

    Article  CAS  Google Scholar 

  44. Klein, B. J. et al. Recognition of histone H3K14 acylation by MORF. Structure 25, 650–654.e2 (2017).

    Article  CAS  Google Scholar 

  45. Amato, A., Lucas, X., Bortoluzzi, A., Wright, D. & Ciulli, A. Targeting ligandable pockets on plant homeodomain (PHD) zinc finger domains by a fragment-based approach. ACS Chem. Biol. 13, 915–921 (2018).

    Article  CAS  Google Scholar 

  46. Miller, T. C. R. et al. Competitive binding of a benzimidazole to the histone-binding pocket of the Pygo PHD finger. ACS Chem. Biol. 9, 2864–2874 (2014).

    Article  CAS  Google Scholar 

  47. Wagner, E. K., Nath, N., Flemming, R., Feltenberger, J. B. & Denu, J. M. Identification and characterization of small molecule inhibitors of a plant homeodomain finger. Biochemistry 51, 8293–8306 (2012).

    Article  CAS  Google Scholar 

  48. Horton, J. R. et al. Enzymatic and structural insights for substrate specificity of a family of jumonji histone lysine demethylases. Nat. Struct. Mol. Biol. 17, 38–43 (2010).

    Article  CAS  Google Scholar 

  49. Andrews, F. H. et al. The Taf14 YEATS domain is a reader of histone crotonylation. Nat. Chem. Biol. 12, 396–398 (2016).

    Article  CAS  Google Scholar 

  50. Li, Y. et al. Molecular coupling of histone crotonylation and active transcription by AF9 YEATS domain. Mol. Cell 62, 181–193 (2016).

    Article  CAS  Google Scholar 

  51. Zhao, D. et al. YEATS2 is a selective histone crotonylation reader. Cell Res. 26, 629–632 (2016).

    Article  CAS  Google Scholar 

  52. Moustakim, M. et al. Discovery of an MLLT1/3 YEATS domain chemical probe. Angew. Chem. Int. Edn Engl. 57, 16302–16307 (2018).

    Article  CAS  Google Scholar 

  53. Li, X. et al. Structure-guided development of YEATS domain inhibitors by targeting π-π-π stacking. Nat. Chem. Biol. 14, 1140–1149 (2018).

    Article  CAS  Google Scholar 

  54. Schuetz, A. et al. Structural basis for molecular recognition and presentation of histone H3 by WDR5. EMBO J. 25, 4245–4252 (2006).

    Article  CAS  Google Scholar 

  55. Couture, J.-F., Collazo, E. & Trievel, R. C. Molecular recognition of histone H3 by the WD40 protein WDR5. Nat. Struct. Mol. Biol. 13, 698–703 (2006).

    Article  CAS  Google Scholar 

  56. Ruthenburg, A. J. et al. Histone H3 recognition and presentation by the WDR5 module of the MLL1 complex. Nat. Struct. Mol. Biol. 13, 704–712 (2006).

    Article  CAS  Google Scholar 

  57. Han, Z. et al. Structural basis for the specific recognition of methylated histone H3 lysine 4 by the WD-40 protein WDR5. Mol. Cell 22, 137–144 (2006).

    Article  CAS  Google Scholar 

  58. Song, J.-J. & Kingston, R. E. WDR5 interacts with mixed lineage leukemia (MLL) protein via the histone H3-binding pocket. J. Biol. Chem. 283, 35258–35264 (2008).

    Article  CAS  Google Scholar 

  59. Avdic, V. et al. Structural and biochemical insights into MLL1 core complex assembly. Structure 19, 101–108 (2011).

    Article  CAS  Google Scholar 

  60. Patel, A., Vought, V. E., Dharmarajan, V. & Cosgrove, M. S. A conserved arginine-containing motif crucial for the assembly and enzymatic activity of the mixed lineage leukemia protein-1 core complex. J. Biol. Chem. 283, 32162–32175 (2008).

    Article  CAS  Google Scholar 

  61. Dias, J. et al. Structural analysis of the KANSL1/WDR5/KANSL2 complex reveals that WDR5 is required for efficient assembly and chromatin targeting of the NSL complex. Genes Dev. 28, 929–942 (2014).

    Article  CAS  Google Scholar 

  62. Grebien, F. et al. Pharmacological targeting of the Wdr5-MLL interaction in C/EBPα N-terminal leukemia. Nat. Chem. Biol. 11, 571–578 (2015). First small-molecule chemical probe to a chromatin WDR protein with demonstrated activity on target biology.

    Article  CAS  Google Scholar 

  63. Aho, E. R. et al. Displacement of WDR5 from Chromatin by a WIN Site Inhibitor with Picomolar Affinity. Cell Rep. 26, 2916–2928.e13 (2019).

    Article  CAS  Google Scholar 

  64. Karatas, H. et al. High-affinity, small-molecule peptidomimetic inhibitors of MLL1/WDR5 protein-protein interaction. J. Am. Chem. Soc. 135, 669–682 (2013). First cell-permeant modulator of a chromatin-associated WDR domain with effects on relevant biology.

    Article  CAS  Google Scholar 

  65. Karatas, H. et al. Discovery of a highly potent, cell-permeable macrocyclic peptidomimetic (MM-589) targeting the WD repeat domain 5 protein (WDR5)-mixed lineage leukemia (MLL) protein-protein interaction. J. Med. Chem. 60, 4818–4839 (2017).

    Article  CAS  Google Scholar 

  66. Zhu, J. et al. Gain-of-function p53 mutants co-opt chromatin pathways to drive cancer growth. Nature 525, 206–211 (2015).

    Article  CAS  Google Scholar 

  67. Xu, C. et al. Binding of different histone marks differentially regulates the activity and specificity of polycomb repressive complex 2 (PRC2). Proc. Natl Acad. Sci. USA 107, 19266–19271 (2010).

    Article  CAS  Google Scholar 

  68. Lee, C.-H. et al. Allosteric activation dictates PRC2 activity independent of its recruitment to chromatin. Mol. Cell 70, 422–434.e6 (2018).

    Article  CAS  Google Scholar 

  69. Justin, N. et al. Structural basis of oncogenic histone H3K27M inhibition of human polycomb repressive complex 2. Nat. Commun. 7, 11316 (2016).

    Article  CAS  Google Scholar 

  70. Jiao, L. & Liu, X. Structural basis of histone H3K27 trimethylation by an active polycomb repressive complex 2. Science 350, aac4383 (2015).

    Article  Google Scholar 

  71. He, Y. et al. The EED protein-protein interaction inhibitor A-395 inactivates the PRC2 complex. Nat. Chem. Biol. 13, 389–395 (2017). First (along with ref. 72) small-molecule allosteric modulation of a chromatin enzyme.

    Article  CAS  Google Scholar 

  72. Qi, W. et al. An allosteric PRC2 inhibitor targeting the H3K27me3 binding pocket of EED. Nat. Chem. Biol. 13, 381–388 (2017). First (along with ref. 71) small-molecule allosteric modulation of a chromatin enzyme complex by targeting its Kme reader domain.

    Article  CAS  Google Scholar 

  73. Suh, J. L. et al. Discovery of selective activators of PRC2 mutant EED-I363M. Sci. Rep. 9, 6524 (2019).

    Article  Google Scholar 

  74. Lai, A. C. & Crews, C. M. Induced protein degradation: an emerging drug discovery paradigm. Nat. Rev. Drug Discov. 16, 101–114 (2017).

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Cheryl H. Arrowsmith.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Peer review information Anke Sparmann was the primary editor on this article and managed its editorial process and peer review in collaboration with the rest of the editorial team.

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Arrowsmith, C.H., Schapira, M. Targeting non-bromodomain chromatin readers. Nat Struct Mol Biol 26, 863–869 (2019). https://doi.org/10.1038/s41594-019-0290-2

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41594-019-0290-2

This article is cited by

Search

Quick links

Nature Briefing: Translational Research

Sign up for the Nature Briefing: Translational Research newsletter — top stories in biotechnology, drug discovery and pharma.

Get what matters in translational research, free to your inbox weekly. Sign up for Nature Briefing: Translational Research