Discovery of a 53BP1 Small Molecule Antagonist Using a Focused DNA-Encoded Library Screen

J Med Chem. 2023 Oct 26;66(20):14133-14149. doi: 10.1021/acs.jmedchem.3c01192. Epub 2023 Oct 2.

Abstract

Methyl-lysine reader p53 binding protein 1 (53BP1) is a central mediator of DNA break repair and is associated with various human diseases, including cancer. Thus, high-quality 53BP1 chemical probes can aid in further understanding the role of 53BP1 in genome repair pathways. Herein, we utilized focused DNA-encoded library screening to identify the novel hit compound UNC8531, which binds the 53BP1 tandem Tudor domain (TTD) with an IC50 of 0.47 ± 0.09 μM in a TR-FRET assay and Kd values of 0.85 ± 0.17 and 0.79 ± 0.52 μM in ITC and SPR, respectively. UNC8531 was cocrystallized with the 53BP1 TTD to guide further optimization efforts, leading to UNC9512. NanoBRET and 53BP1-dependent foci formation experiments confirmed cellular target engagement. These results show that UNC9512 is a best-in-class small molecule 53BP1 antagonist that can aid further studies investigating the role of 53BP1 in DNA repair, gene editing, and oncogenesis.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA
  • DNA Repair*
  • Humans
  • Intracellular Signaling Peptides and Proteins* / metabolism
  • Tudor Domain
  • Tumor Suppressor p53-Binding Protein 1 / chemistry
  • Tumor Suppressor p53-Binding Protein 1 / genetics
  • Tumor Suppressor p53-Binding Protein 1 / metabolism

Substances

  • DNA
  • Intracellular Signaling Peptides and Proteins
  • Tumor Suppressor p53-Binding Protein 1