Identification of a fragment-like small molecule ligand for the methyl-lysine binding protein, 53BP1

ACS Chem Biol. 2015 Apr 17;10(4):1072-81. doi: 10.1021/cb500956g. Epub 2015 Jan 28.


Improving our understanding of the role of chromatin regulators in the initiation, development, and suppression of cancer and other devastating diseases is critical, as they are integral players in regulating DNA integrity and gene expression. Developing small molecule inhibitors for this target class with cellular activity is a crucial step toward elucidating their specific functions. We specifically targeted the DNA damage response protein, 53BP1, which uses its tandem tudor domain to recognize histone H4 dimethylated on lysine 20 (H4K20me2), a modification related to double-strand DNA breaks. Through a cross-screening approach, we identified UNC2170 (1) as a micromolar ligand of 53BP1, which demonstrates at least 17-fold selectivity for 53BP1 as compared to other methyl-lysine (Kme) binding proteins tested. Structural studies revealed that the tert-butyl amine of UNC2170 anchors the compound in the methyl-lysine (Kme) binding pocket of 53BP1, making it competitive with endogenous Kme substrates. X-ray crystallography also demonstrated that UNC2170 binds at the interface of two tudor domains of a 53BP1 dimer. Importantly, this compound functions as a 53BP1 antagonist in cellular lysates and shows cellular activity by suppressing class switch recombination, a process which requires a functional 53BP1 tudor domain. These results demonstrate that UNC2170 is a functionally active, fragment-like ligand for 53BP1.

Publication types

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

MeSH terms

  • Animals
  • B-Lymphocytes / drug effects
  • Benzamides / chemistry
  • Benzamides / metabolism*
  • Benzamides / pharmacology
  • Binding Sites
  • Chromatin / metabolism
  • Crystallography, X-Ray
  • Diamines / chemistry
  • Diamines / metabolism*
  • Diamines / pharmacology
  • HEK293 Cells
  • Histones / genetics
  • Histones / metabolism
  • Humans
  • Intracellular Signaling Peptides and Proteins / chemistry*
  • Intracellular Signaling Peptides and Proteins / metabolism*
  • Ligands
  • Lysine / metabolism*
  • Magnetic Resonance Spectroscopy
  • Mice, Inbred C57BL
  • Protein Structure, Tertiary
  • Small Molecule Libraries / chemistry
  • Small Molecule Libraries / metabolism
  • Structure-Activity Relationship
  • Tumor Suppressor p53-Binding Protein 1


  • 3-bromo-N-(3-(tert-butylamino)propyl)benzamide
  • Benzamides
  • Chromatin
  • Diamines
  • Histones
  • Intracellular Signaling Peptides and Proteins
  • Ligands
  • Small Molecule Libraries
  • TP53BP1 protein, human
  • Tumor Suppressor p53-Binding Protein 1
  • Lysine

Associated data

  • PDB/4RG2