Mechanistic insights into sodium ion-mediated ligand binding affinity and modulation of 5-HT2B GPCR activity: implications for drug discovery and development

Abstract

Purpose

The G-protein coupled receptor (GPCR) family, implicated in neurological disorders and drug targets, includes the sensitive serotonin receptor subtype, 5-HT2B. The influence of sodium ions on ligand binding at the receptor’s allosteric region is being increasingly studied for its impact on receptor structure.

Methods

High-throughput virtual screening of three libraries, specifically the Asinex-GPCR library, which contains 8,532 compounds and FDA-approved (2466 compounds) and investigational compounds (2731)) against the modeled receptor [4IB4-5HT_2BR_M] using the standard agonist/antagonist (Ergotamine/Methysergide), as previously selected from our studies based on ADMET profiling, and further on basis of binding free energy a single compound – dihydroergotamine is chosen.

Results

This compound displayed strong interactions with the conserved active site. Ions influence ligand binding, with stronger interactions (3-H-bonds and 1-π-bond around 3.35 Å) observed when an agonist and ions are present. Ions entry is guided by conserved motifs in helices III, IV, and VII, which regulate the receptor. Dihydroergotamine, the selected drug, showed binding variance based on ions presence/absence, affecting amino acid residues in these motifs. DCCM and PCA confirmed the stabilization of ligands, with a greater correlation (∼46.6%-PC1) observed with ions. Dihydroergotamine-modified interaction sites within the receptor necessary for activation, serving as a potential 5HT_2BR_M agonist. RDF analysis showed the sodium ions density around the active site during dihydroergotamine binding.

Conclusion

Our study provides insights into sodium ion mobility’s role in controlling ligand binding affinity in 5HT_2BR, offering therapeutic development insights.

Graphical Abstract

Keywords:

• 5HT_2BR
• allosteric site
• conserved motifs
• G-protein-coupled receptors (GPCRs)
• sodium ions

Acknowledgments

One of the authors, Ms. Arushi Chauhan, would like to thank the Council of Scientific & Industrial Research (CSIR), New Delhi, India, for providing a fellowship under the scheme CSIR-UGC NET-SRF (File no-09/141(0216)/2019-EMR-I).

Ethical approval and consent to participate

This is an in silico study and, therefore, does not require human and animal approval.

Disclosure statement

The research in this paper is computational, involving only computer simulations and analyses without human or animal subjects. Therefore, it does not require review board approval or compliance with the declaration of Helsinki, as it falls outside the scope of clinical or in vivo study ethical review. The authors have no known competing financial interests or personal relationships that could have affected the work reported in this paper.

Data and software availability statement

The downloaded X-RAY crystal structure of 4IB4 was a chimera with mutations so the structure was downloaded (https://www.rcsb.org/structure/4IB4) and modeled to depict the un-mutated and non-chimera’. Homology modeling is done via open-source software SWISS-MODEL (https://swissmodel.expasy.org/interactive), validated by using SAVESv5.0 (https://servicesn.mbi.ucla.edu/SAVES/). The enrichment analysis, protein preparation, modeling, and molecular docking simulations operations were performed on Maestro (release 2020-4), Schrödinger, LLC, New York, NY, and the USA. Molecular dynamics simulations were performed on Desmond Molecular Dynamics System, D. E. Shaw Research, New York, NY, 2021. Maestro-Desmond Interoperability Tools, Schrödinger, New York, NY, 2021 (release 2021-3). The data supporting this study’s findings are available on request from the corresponding author. The data are not publicly available due to privacy or ethical restrictions.