Predicting Novel Binding Modes of Agonists to β Adrenergic Receptors Using All-Atom Molecular Dynamics Simulations

Understanding the binding mode of agonists to adrenergic receptors is crucial to enabling improved rational design of new therapeutic agents. However, so far the high conformational flexibility of G protein-coupled receptors has been an obstacle to obtaining structural information on agonist binding at atomic resolution. In this study, we report microsecond classical molecular dynamics simulations of β1 and β2 adrenergic receptors bound to the full agonist isoprenaline and in their unliganded form. These simulations show a novel agonist binding mode that differs from the one found for antagonists in the crystal structures and from the docking poses reported by in silico docking studies performed on rigid receptors. Internal water molecules contribute to the stabilization of novel interactions between ligand and receptor, both at the interface of helices V and VI with the catechol group of isoprenaline as well as at the interface of helices III and VII with the ethanolamine moiety of the ligand. Despite the fact that the characteristic N-C-C-OH motif is identical in the co-crystallized ligands and in the full agonist isoprenaline, the interaction network between this group and the anchor site formed by Asp(3.32) and Asn(7.39) is substantially different between agonists and inverse agonists/antagonists due to two water molecules that enter the cavity and contribute to the stabilization of a novel network of interactions. These new binding poses, together with observed conformational changes in the extracellular loops, suggest possible determinants of receptor specificity.
Author Summary G-protein coupled receptors are the largest family of membrane proteins in the human genome and they constitute the largest class of drug targets. Amongst them, beta adrenergic receptors are involved in the regulation of muscular and vascular tone and are thus molecular targets for the treatment of various diseases including hypertension, heart failure and asthma. The function of these receptors is regulated via the binding of endogenous or exogenous ligands that can either lead to activation (agonists) or inactivation (inverse agonists/antagonists). However, structure determination of these receptors has been very elusive, and the few atomic resolution structures that are available so far have only been obtained in the presence of inverse agonists or antagonists. In order to study the binding mode of agonists inside the binding pocket, we employ all-atom molecular dynamics. This facilitates the study of the details of the interaction between agonist and receptor in full atomistic detail. We find that agonists binding to beta adrenergic receptors require the formation of a highly structured hydrogen bond network that is further stabilized by the presence of internal water molecules. The observed local rearrangements also help provide insights into the molecular origin of the differences between agonist and inverse agonist binding.