Development of PRC1 Inhibitors Employing Fragment-Based Approach and NMR-Guided Optimization

J Med Chem. 2025 Jan 23;68(2):1382-1396. doi: 10.1021/acs.jmedchem.4c01955. Epub 2025 Jan 2.

Abstract

Polycomb Repressive Complex 1 (PRC1) is associated with transcriptional silencing, and its dysregulation plays an important role in various cancers. Well-characterized PRC1 inhibitors can facilitate the exploration of PRC1 inhibition as therapeutic agents. By employing an NMR-based fragment screening approach, we have previously identified a very weak millimolar ligand RB-1, which directly binds to RING1B-BMI1. Then, we reported a low-micromolar PRC1 inhibitor, RB-3, which is active in leukemic cells, showing inhibition of H2A ubiquitylation and modulation of target genes. Here, we describe details of the optimization campaign of RB-1 into potent PRC1 inhibitors by guiding the SAR employing two NMR approaches and a probe-based biochemical assay. These efforts, combined with medicinal chemistry optimization, resulted in the development of RB-3 and slightly improved RB-4. We have demonstrated that RB-4 binds to both RING1A and RING1B proteins and inhibits the activity of RING1B-BMI1 and RING1B-PCGF1, representing both canonical and noncanonical PRC1 complexes.

Publication types

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

MeSH terms

  • Cell Cycle Proteins
  • Humans
  • Magnetic Resonance Spectroscopy
  • Polycomb Repressive Complex 1* / antagonists & inhibitors
  • Polycomb Repressive Complex 1* / metabolism
  • Structure-Activity Relationship

Substances

  • Polycomb Repressive Complex 1
  • PRC1 protein, human
  • Cell Cycle Proteins