Limits of Ligand Selectivity from Docking to Models: In Silico Screening for A1 Adenosine Receptor Antagonists

Peter Kolb,Adam C Marko,Kenneth A Jacobson,Andrej Sali,Zhan-Guo Gao,Khai Phan,Roland Seifert

doi:10.1371/journal.pone.0049910

Abstract

G protein-coupled receptors (GPCRs) are attractive targets for pharmaceutical research. With the recent determination of several GPCR X-ray structures, the applicability of structure-based computational methods for ligand identification, such as docking, has increased. Yet, as only about 1% of GPCRs have a known structure, receptor homology modeling remains necessary. In order to investigate the usability of homology models and the inherent selectivity of a particular model in relation to close homologs, we constructed multiple homology models for the A1 adenosine receptor (A1AR) and docked ∼2.2 M lead-like compounds. High-ranking molecules were tested on the A1AR as well as the close homologs A2AAR and A3AR. While the screen yielded numerous potent and novel ligands (hit rate 21% and highest affinity of 400 nM), it delivered few selective compounds. Moreover, most compounds appeared in the top ranks of only one model. These findings have implications for future screens.

Highlights

G protein-coupled receptors (GPCRs) are one of the pharmaceutically most important protein families, and the targets of around one third of present day drugs [1]
Since the A2AAR structure was solved with the antagonist 1, water molecules, and stearic acid, these heteroatoms were included during A1 adenosine receptor (A1AR) model building to obtain a model conformation closer to the A2AAR Xray structure
Model A was the original model, refined with the two previously known ligands 5 and 6; model B was obtained by rebuilding extracellular loop 3 (ECL3) and adjacent residues around ligand 8; and models C and D were generated by further adapting the binding site to the most selective ligand previously identified in this study (8; binding mode shown in Fig. 2) using logAUC and side chain orientation diversity as model selection criteria

Summary

Introduction

G protein-coupled receptors (GPCRs) are one of the pharmaceutically most important protein families, and the targets of around one third of present day drugs [1]. They mediate the transmission of signals from the exterior to the interior of a cell by binding signaling agents and, via conformational changes, eliciting intracellular responses. The binding pockets of the native small molecule ligands, i.e. orthosteric binding sites, are situated in the middle of the helical bundle in the Class A GPCR structures that have been determined so far [2]. The accuracy of homology models is limited, by the uncertainty of modeling the extra- and intracellular loops, which greatly vary in length and amino acid composition, even between otherwise closely related GPCRs [7]

Methods

Results

Conclusion