Ligand and structure-based models for the prediction of ligand-receptor affinities and virtual screenings: Development and application to the beta(2)-adrenergic receptor.
In this study, we evaluated the applicability of ligand-based and structure-based models to quantitative affinity predictions and virtual screenings for ligands of the beta(2)-adrenergic receptor, a G protein-coupled receptor (GPCR). We also devised and evaluated a number of consensus models obtained through partial least square regressions, to combine the strengths of the individual components. In all cases, the bioactive conformation of each ligand was derived from molecular docking at the crystal structure of the receptor. We identified the most effective models applicable to the different scenarios, in the presence or in the absence of a training set. For ranking the affinity of closely related analogs when a training set is available, a ligand-based consensus model (LI-CM) seems to be the best choice, while the structure-based MM-GBSA score seems the best alternative in the absence of a training set. For virtual screening purposes, the structure-based MM-GBSA score was found to be the method of choice. Consensus models consistently had performances superior or close to those of the best individual components, and were endowed with a significantly increased robustness. Given multiple models with no a priori knowledge of their predictive capabilities, constructing a consensus model ensures results very close to those that the best model alone would have yielded.
Vilar
Santiago
S
Laboratory of Biological Modeling, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, Maryland 20892, USA.
Karpiak
Joel
J
Costanzi
Stefano
S
D058666:Adrenergic beta-2 Receptor Agonists; D058672:Adrenergic beta-2 Receptor Antagonists; D001665:Binding Sites; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D016002:Discriminant Analysis; D004353:Drug Evaluation, Preclinical; D008024:Ligands; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D015394:Molecular Structure; D021281:Quantitative Structure-Activity Relationship; D018343:Receptors, Adrenergic, beta-2 / Q000737:chemistry* / Q000378:metabolism*
D058666:Adrenergic beta-2 Receptor Agonists; D058672:Adrenergic beta-2 Receptor Antagonists; D008024:Ligands; D018343:Receptors, Adrenergic, beta-2