G protein-coupled receptors: in silico drug discovery in 3D

Abstract

The application of structure-based in silico methods to drug discovery is still considered a major challenge, especially when the x-ray structure of the target protein is unknown. Such is the case with human G protein-coupled receptors (GPCRs), one of the most important families of drug targets, where in the absence of x-ray structures, one has to rely on in silico 3D models. We report repeated success in using ab initio in silico GPCR models, generated by the predict method, for blind in silico screening when applied to a set of five different GPCR drug targets. More than 100,000 compounds were typically screened in silico for each target, leading to a selection of <100 "virtual hit" compounds to be tested in the lab. In vitro binding assays of the selected compounds confirm high hit rates, of 12-21% (full dose-response curves, Ki < 5 microM). In most cases, the best hit was a novel compound (New Chemical Entity) in the 1- to 100-nM range, with very promising pharmacological properties, as measured by a variety of in vitro and in vivo assays. These assays validated the quality of the hits as lead compounds for drug discovery. The results demonstrate the usefulness and robustness of ab initio in silico 3D models and of in silico screening for GPCR drug discovery.

Fig. 1.

Enrichment graph for in silico screening of 26 known NK1 antagonists embedded in the 6,200-compound random drug-like library with similar physiochemical properties after docking into the predict 3D model of the NK1 receptor. Library compounds are ranked along the x axis, according to their docking score (best scorers on the left, worst scorers near the 100% mark). The curve shows the relative ranking of the known antagonists. Enrichment at 50% is 20-fold better than with random screening (dashed line).

Fig. 2.

Buspirone (a) and sunepitron (b), two 5-HT1A partial-agonist drugs, docked in the 5-HT1A receptor-binding pocket (transparent surface). The compounds are shown in space-fill-form to highlight their binding mode. Key protein residues responsible for ligand binding are shown. Also shown are the chemical structures of the two drugs.

Fig. 3.

GR-113808, a potent 5-HT4 ligand, docked in the receptor 3D model. The compound's amine group is 4.1 Å from Asp-100 (TM3), and the ester interacts with Ser-197 (TM5, 3.9 Å); Phe-297 (TM7) and Asn-279 (TM6) interact with the indole group of the ligand, and Tyr-302 (TM7) is within 5 Å from the sulfonamide. Also shown is the chemical structure of the compound.