Simulation and comparative analysis of binding modes of nucleoside and non-nucleoside agonists at the A(2B) adenosine receptor

PURPOSE: A(2B) receptor agonists are studied as possible therapeutic tools for a variety of pathological conditions. Unfortunately, medicinal chemistry efforts have led to the development of a limited number of potent agonists of this receptor, in most cases with a low or no selectivity versus the other adenosine receptor subtypes. Among the developed molecules, two structural families of compounds have been identified based on nucleoside and non-nucleoside (pyridine) scaffolds. The aim of this work is to analyse the binding mode of these molecules at 3D models of the human A(2B) receptor to identify possible common interaction features and the key receptor residues involved in ligand interaction. METHODS: The A(2B) receptor models are built by using two recently published crystal structures of the human A(2A) receptor in complex with two different agonists. The developed models are used as targets for molecular docking studies of nucleoside and non-nucleoside agonists. The generated docking conformations are subjected to energy minimization and rescoring by using three different scoring functions. Further analysis of top-score conformations are performed with a tool evaluating the interaction energy between the ligand and the binding site residues. RESULTS: Results suggest a set of common interaction points between the two structural families of agonists and the receptor binding site, as evidenced by the superimposition of docking conformations and by analysis of interaction energy with the receptor residues. CONCLUSIONS: The obtained results show that there is a conserved pattern of interaction between the A(2B) receptor and its agonists. These information and can provide useful data to support the design and the development of A(2B) receptor agonists belonging to nucleoside or non-nucleoside structural families. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/2193-9616-1-24) contains supplementary material, which is available to authorized users.