Abstract
G protein-coupled receptors (GPCRs) are a main drug target and therefore a hot topic in pharmaceutical research. One important prerequisite to understand how a certain ligand affects a GPCR is precise knowledge about its binding mode and the specific underlying interactions. If no crystal structure of the respective complex is available, computational methods can be used to deduce the binding site. One of them are metadynamics simulations which have the advantage of an enhanced sampling compared to conventional molecular dynamics simulations. However, the enhanced sampling of higher-energy states hampers identification of the preferred binding mode. Here, we present a novel protocol based on clustering of multiple walker metadynamics simulations which allows identifying the preferential binding mode from such conformational ensembles. We tested this strategy for three different model systems namely the histamine H1 receptor in combination with its physiological ligand histamine, as well as the adrenoceptor with its agonist adrenaline and its antagonist alprenolol. For all three systems, the proposed protocol was able to reproduce the correct binding mode known from the literature suggesting that the approach can more generally be applied to the prediction of GPCR ligand binding in future.
Highlights
G protein-coupled receptors (GPCRs) are a family of membrane proteins with seven transmembrane helices
For the metadynamics simulation itself, we adapted the protocol of Saleh et al [28], which relies on a common collective variable (CV) to study GPCR-ligand interactions
To apply this protocol to the prediction of ligand binding modes, one conceptual change had to be made: Saleh et al mainly investigated the energy landscape of the binding process, which allowed starting the simulations from the ligand-bound GPCR structure [28]
Summary
G protein-coupled receptors (GPCRs) are a family of membrane proteins with seven transmembrane helices. There exist more than 800 different members in humans [1,2] most of which are regulated by extracellular ligands Binding of such a ligand results in structural changes thereby modulating the interaction between the GPCR and its intracellular binding partners like G proteins or β-arrestin [3]. The method has drawbacks like the limited ability to treat protein flexibility [2,12,16] This may in particular become problematic if the docked ligands differ significantly from the ligand that was used for the determination of the reference GPCR crystal structure [17]. We present a clustering-based strategy, which facilitates the detection of the most stable ligand binding mode from GPCR metadynamics simulations. Reference Binding Mode unbiased MD study [14] crystal structure PDB 4LDO [30] crystal structure PDB 3NYA [31]
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