Small-molecule ligands of methyl-lysine binding proteins: optimization of selectivity for L3MBTL3

J Med Chem. 2013 Sep 26;56(18):7358-71. doi: 10.1021/jm400919p. Epub 2013 Sep 16.


Lysine methylation is a key epigenetic mark, the dysregulation of which is linked to many diseases. Small-molecule antagonism of methyl-lysine (Kme) binding proteins that recognize such epigenetic marks can improve our understanding of these regulatory mechanisms and potentially validate Kme binding proteins as drug-discovery targets. We previously reported the discovery of 1 (UNC1215), the first potent and selective small-molecule chemical probe of a methyl-lysine reader protein, L3MBTL3, which antagonizes the mono- and dimethyl-lysine reading function of L3MBTL3. The design, synthesis, and structure-activity relationship studies that led to the discovery of 1 are described herein. These efforts established the requirements for potent L3MBTL3 binding and enabled the design of novel antagonists, such as compound 2 (UNC1679), that maintain in vitro and cellular potency with improved selectivity against other MBT-containing proteins. The antagonists described were also found to effectively interact with unlabeled endogenous L3MBTL3 in cells.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA-Binding Proteins / antagonists & inhibitors
  • DNA-Binding Proteins / chemistry
  • DNA-Binding Proteins / metabolism*
  • Drug Design
  • HEK293 Cells
  • Humans
  • Inhibitory Concentration 50
  • Ligands
  • Lysine / metabolism*
  • Models, Molecular
  • Protein Structure, Tertiary
  • Small Molecule Libraries / chemistry
  • Small Molecule Libraries / metabolism*
  • Small Molecule Libraries / pharmacology
  • Structure-Activity Relationship
  • Substrate Specificity


  • DNA-Binding Proteins
  • L3MBTL3 protein, human
  • Ligands
  • Small Molecule Libraries
  • Lysine