Binding pose depth modulates photoswitchable ligands’ efficacy at the 5-HT2A receptor
Verena Weber, Giacomo Salvadori, Federico Natale, Hubert Gerwe, Michael Decker, Paolo Carloni, Giulia Rossetti
Communications Chemistry February 12, 2026 DOI: 10.1038/s42004-026-01936-5 (opens in new tab)
Study at a glance
AI-extracted from the abstract| Characteristics | Computational simulation study Peer reviewed |
|---|---|
| Topics | Serotonin |
| Keywords | Moiety Steric effects G protein-coupled receptor Ligand biochemistry Substituent Hydrogen bond Allosteric regulation Molecular switch Stereochemistry Biophysics Binding pocket Molecular dynamics Antagonist Internalization Anchoring Binding site Cricetulus Protein structure Hek 293 cells Signal transduction |
| Key points | The vertical depth of ligand insertion into the orthosteric binding pocket, determined by the position of a methoxy substituent, is a critical determinant of efficacy for azobenzene-based human 5-HT2A receptor ligands. |
Abstract
Abstract Photoswitchable ligands enable reversible control of receptor signaling through light-induced cis – trans isomerization, yet predicting how subtle structural modifications affect efficacy remains challenging. Here, we use molecular dynamics simulations to investigate two azobenzene-based human 5–HT 2A receptor ligands differing only by a methoxy substituent position ( para – vs meta –methoxy). Compound 1 ( para –methoxy) switches from acting as a weak antagonist ( trans ) to a moderate agonist ( cis ), whereas compound 2 ( meta -methoxy) maintains agonist activity in both forms, with cis - 2 exhibiting the highest efficacy. Our simulations reveal that the key determinant of these efficacy differences lies in the vertical depth of ligand insertion into the orthosteric binding pocket. The para –methoxy moiety of trans – 1 forms hydrogen bonds with Asp231 5.35 and Thr160 3.37 , anchoring the ligand deeper than typical tryptamine agonists and preventing engagement with activation-critical residues, thereby stabilizing the inactive receptor. Conversely, trans – 2 lacks these anchoring interactions and adopts a shallower, agonist-compatible pose. In the active receptor, cis – 2 forms a persistent Thr160 3.37 hydrogen bond that allows deeper penetration between TM4 and TM5, whereas cis – 1 ’s para –methoxy causes steric hindrances limiting this interaction. Based on these findings, we suggest that ligand insertion depth is a critical determinant of efficacy. This provides a framework for designing light-sensitive GPCR ligands with tunable signaling properties.