Biased Ligands Differentially Shape the Conformation of the Extracellular Loop Region in 5-HT2B Receptors

Abstract

G protein-coupled receptors are linked to various intracellular transducers, each pathway associated with different physiological effects. Biased ligands, capable of activating one pathway over another, are gaining attention for their therapeutic potential, as they could selectively activate beneficial pathways whilst avoiding those responsible for adverse effects. We performed molecular dynamics simulations with known β-arrestin-biased ligands like lysergic acid diethylamide and ergotamine in complex with the 5-HT2B receptor and discovered that the extent of ligand bias is directly connected with the degree of closure of the extracellular loop region. Given a loose allosteric coupling of extracellular and intracellular receptor regions, we delineate a concept for biased signaling at serotonin receptors, by which conformational interference with binding pocket closure restricts the signaling repertoire of the receptor. Molecular docking studies of biased ligands gathered from the BiasDB demonstrate that larger ligands only show plausible docking poses in the ergotamine-bound structure, highlighting the conformational constraints associated with bias. This emphasizes the importance of selecting the appropriate receptor conformation on which to base virtual screening workflows in structure-based drug design of biased ligands. As this mechanism of ligand bias has also been observed for muscarinic receptors, our studies provide a general mechanism of signaling bias transferable between aminergic receptors.

Lysyl oxidase inhibitors attenuate cyclosporin A-induced nephropathy in mouse

“…Gels were electroblotted onto the Hybond nitrocellulose membrane (Amersham Pharmacia Biotech, Amersham, UK), and target proteins were captured by the corresponding primary-secondary antibody pairs. Primary antibodies, which have been validated in our previous studies 24 , 25 , are listed in Supplementary Table S2 . β-actin was used for loading control.…”

The Impact of the Secondary Binding Pocket on the Pharmacology of Class A GPCRs

“…A similar study aimed to clarify the molecular determinants of the bitopic binding mode of a negative allosteric modulator of the dopamine D 2 receptor ( Draper-Joyce et al, 2018 ). MDs combined with docking linked the degree of closure of the extracellular loop region to the extent of ligand bias and highlighted the importance of the appropriate receptor conformation for virtual screening at the 5-HT 2B receptor ( Denzinger et al, 2020 ). A similar concept was presented by Bermudez et al proposing that agonists with extended binding modes selectively interfere with binding pocket closure and through divergent allosteric coupling that leads to ligand bias ( Bermudez and Bock, 2019 ).…”

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“…This method allows statistical analysis of ligand-target interaction frequency and occurrence and provides an easily accessible dynamic view of interactions. The dynophore method has been successfully applied to GPCRs to describe complex phenomena of GPCR pharmacology such as partial agonism and has helped to elucidate ligand-dependent mechanistic understanding of GPCR function [97,138,139]. Complicated signaling events such as biased agonism can be difficult to capture via static models, so the incorporation of dynamics into 3D pharmacophores afforded by the dynophore method allows a deeper understanding of how pharmacophore interaction patterns relate to downstream signaling events.…”