Function-specific virtual screening for GPCR ligands using a combined scoring method

The ability of scoring functions to correctly select and rank docking poses of small molecules in protein binding sites is highly target dependent, which presents a challenge for structure-based drug discovery. Here we describe a virtual screening method that combines an energy-based docking scoring function with a molecular interaction fingerprint (IFP) to identify new ligands based on G protein-coupled receptor (GPCR) crystal structures. The consensus scoring method is prospectively evaluated by: 1) the discovery of chemically novel, fragment-like, high affinity histamine H(1) receptor (H(1)R) antagonists/inverse agonists, 2) the selective structure-based identification of ß(2)-adrenoceptor (ß(2)R) agonists, and 3) the experimental validation and comparison of the combined and individual scoring approaches. Systematic retrospective virtual screening simulations allowed the definition of scoring cut-offs for the identification of H(1)R and ß(2)R ligands and the selection of an optimal ß-adrenoceptor crystal structure for the discrimination between ß(2)R agonists and antagonists. The consensus approach resulted in the experimental validation of 53% of the ß(2)R and 73% of the H(1)R virtual screening hits with up to nanomolar affinities and potencies. The selective identification of ß(2)R agonists shows the possibilities of structure-based prediction of GPCR ligand function by integrating protein-ligand binding mode information.