Deciphering the allosteric landscape of 5-HT2 receptors: integrated molecular dynamics and fragment molecular orbital analyses of activation mechanisms

Abstract Background The 5-HT 2 receptor subfamily (5-HT 2A , 5-HT 2B , and 5-HT 2C ) is a cornerstone of neuropsychiatric drug design, yet the precise molecular determinants of their activation and biased signaling remain only partially elucidated. This study aimed to investigate the conformational transitions and energetic landscapes across diverse functional states to provide a refined structural blueprint of the allosteric signaling mechanisms.

Methods: We integrated Molecular Dynamics (MD) simulations, Dynamical Network Analysis (DNA), and Fragment Molecular Orbital calculations combined with Pair Interaction Energy Decomposition Analysis (FMO/PIEDA). By applying FMO/PIEDA to MD-derived representative structures, we performed an ab initio evaluation of receptor–ligand complexes, quantifying individual residue-ligand pair interaction energies (PIE).

Results: Our results demonstrate that signal transduction is governed by a cooperative allosteric network rather than a single toggle switch, with the conserved R3.50 residue serving as a mandatory endpoint of ligand-induced communication. While agonists initiate the shift toward active-like states, G protein coupling acts as a directional amplifier, focusing communication pathways toward R3.50 and effectively stabilizing the E/DRY ionic lock against disruption. Subtype-specific analyses reveal that the 5-HT 2B receptor possesses the most intrinsically pre-organized communication network, while 5-HT 2A exhibits the highest sensitivity to perturbations in signal transmission. Furthermore, FMO analysis identified the highly conserved D3.32 as the primary stabilizing anchor, while residues such as S5.46 and W6.48 were found to be critical energetic determinants of ligand efficacy.

Conclusions: These integrated insights provide a refined structural blueprint of the TM5–TM6–TM7 allosteric landscape, moving beyond isolated residue descriptions. The findings facilitate the rational design of next-generation, non-hallucinogenic agonists or selective modulators by targeting specific energetic and dynamic pathways within the serotonin receptor family. Clinical trial number Not applicable.