Crystal structure-based virtual screening for fragment-like ligands of the human histamine H(1) receptor

J Med Chem. 2011 Dec 8;54(23):8195-206. doi: 10.1021/jm2011589. Epub 2011 Nov 7.


The recent crystal structure determinations of druggable class A G protein-coupled receptors (GPCRs) have opened up excellent opportunities in structure-based ligand discovery for this pharmaceutically important protein family. We have developed and validated a customized structure-based virtual fragment screening protocol against the recently determined human histamine H(1) receptor (H(1)R) crystal structure. The method combines molecular docking simulations with a protein-ligand interaction fingerprint (IFP) scoring method. The optimized in silico screening approach was successfully applied to identify a chemically diverse set of novel fragment-like (≤22 heavy atoms) H(1)R ligands with an exceptionally high hit rate of 73%. Of the 26 tested fragments, 19 compounds had affinities ranging from 10 μM to 6 nM. The current study shows the potential of in silico screening against GPCR crystal structures to explore novel, fragment-like GPCR ligand space.

Publication types

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

MeSH terms

  • Databases, Factual
  • HEK293 Cells
  • Humans
  • Ligands*
  • Models, Molecular*
  • Molecular Structure
  • Quantitative Structure-Activity Relationship*
  • Radioligand Assay
  • Receptors, Histamine H1 / chemistry*
  • Receptors, Histamine H1 / metabolism


  • Ligands
  • Receptors, Histamine H1