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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.

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