Ligand and Target Discovery by Fragment-Based Screening in Human Cells

Cell. 2017 Jan 26;168(3):527-541.e29. doi: 10.1016/j.cell.2016.12.029. Epub 2017 Jan 19.


Advances in the synthesis and screening of small-molecule libraries have accelerated the discovery of chemical probes for studying biological processes. Still, only a small fraction of the human proteome has chemical ligands. Here, we describe a platform that marries fragment-based ligand discovery with quantitative chemical proteomics to map thousands of reversible small molecule-protein interactions directly in human cells, many of which can be site-specifically determined. We show that fragment hits can be advanced to furnish selective ligands that affect the activity of proteins heretofore lacking chemical probes. We further combine fragment-based chemical proteomics with phenotypic screening to identify small molecules that promote adipocyte differentiation by engaging the poorly characterized membrane protein PGRMC2. Fragment-based screening in human cells thus provides an extensive proteome-wide map of protein ligandability and facilitates the coordinated discovery of bioactive small molecules and their molecular targets.

Keywords: FBLD; PGRMC2; adipogenesis; chemical probes; chemical proteomics; fragment-based ligand discovery; ligands; mass spectrometry; phenotypic screening; photoreactivity.

Publication types

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

MeSH terms

  • Adipocytes / cytology
  • Cell Differentiation
  • Crystallography, X-Ray
  • Drug Discovery / methods*
  • High-Throughput Screening Assays
  • Humans
  • Hydrolases / chemistry
  • Ligands
  • Membrane Proteins / antagonists & inhibitors
  • Oxidoreductases / chemistry
  • Protein Binding
  • Proteomics / methods*
  • Receptors, Progesterone / antagonists & inhibitors
  • Small Molecule Libraries


  • Ligands
  • Membrane Proteins
  • PGRMC2 protein, human
  • Receptors, Progesterone
  • Small Molecule Libraries
  • Oxidoreductases
  • Hydrolases