Despite the availability of X-ray crystal structure data for several members of the G-protein-coupled receptor (GPCR) superfamily, structure-based discovery of GPCR ligands has been exclusively restricted to classA (rhodopsin-like) receptors. Herein we report the identification, by a docking-based virtual screening approach, of noncompetitive ligands for two related classB (secretin-like) GPCRs: the glucagon receptor (GLR) and the glucagon-like peptide1 receptor (GLP-1R). Starting from a knowledge-based three-dimensional model of the GLR, a database of 1.9 million commercially available drug-like compounds was screened for chemical similarity to existing GLR noncompetitive antagonists and docked to the transmembrane cavity of the GLR; 23 compounds were then selected based on protein-ligand interaction fingerprints, and were then purchased and evaluated for invitro binding to GLR and modulation of glucagon-induced cAMP release. Two of the 23 compounds inhibited the effect of glucagon in a dose-dependent manner, with one inhibitor exhibiting the same potency as L-168049, a reference noncompetitive GLR antagonist, in a whole-cell-based functional assay. Interestingly, one virtual hit that was inactive at the GLR was shown to bind to GLP-1R and potentiate the response to the endogenous GLP-1 ligand. Virtual reality: Although crystallographic structure data and related information have been reported for classA GPCRs, herein we report the first use of structure-based virtual screening to identify new allosteric modulators of classB GPCRs. Despite the modest activities of the identified compounds, this study provides a novel insilico approach for the discovery of future classB GPCR modulators. © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.