Structure-based virtual fragment screening for ligands of the G protein-coupled histamine H4 receptor

The determination of the first set of crystal structures for the family of G protein-coupled receptors (GPCRs) has opened up new opportunities in structure-based ligand discovery for this pharmaceutically relevant protein family. We have explored the possibilities and challenges of structure-based virtual fragment screening (SBVFS) against the histamine H4 receptor (H4R), a key player in inflammatory responses. Several SBVFS strategies, employing different H4R ligand conformations, were validated and optimized with respect to their ability to discriminate small fragment-like H4R ligands from inactive fragments, and compared to ligand-based virtual screening (VS) approaches. Interestingly, structureand ligand-based methods performed equally well in terms of virtual screening accuracy while their hit lists were complementary. SBVFS experiments with an interaction fingerprint scoring method enabled the identification of H4R ligands that were not identified in ligand-based VS runs. Interestingly, SBVFS against H4R homology models based on the homologous histamine H1 receptor (H1R) crystal structure did not give higher VS enrichments than H4R models based on the more distantly related beta-2 adrenergic receptor (ADRB2). Optimized SBVFS methods were successfully used to find two new series of fragment-like H4R ligands. Of the 23 tested compounds, six fragments had affinities between 0.14 and 6.3 M at the H4R. The experimentally validated hits were inactive on ADRB2, but had approximately the same affinity for H1R, indicating that virtual screening for receptor subtype selective ligands is still challenging. The lessons learned from our comparative virtual fragment screening study can be used as a blueprint for future SBVFS campaigns.