Allosteric modulation of conserved motifs and helices in 5HT_2BR: Advances drug discovery and therapeutic approach towards drug resistant epilepsy

Abstract

The 5HT_2BR, class-A GPCR is a new target, and its significance for seizure reduction in Dravet syndrome is just now gaining interest, suggesting its specific role in epileptic seizure management. Homology modeling of human 5HT_2BR (P41595), was performed using a template 4IB4, the modeled structure was cross-validated (stereo chemical hindrance, Ramachandran plot, enrichment analysis) to mimic a closer native structure. Virtual screening (8532 compounds), drug-likeliness, mutagenicity, and carcinogenicity profiling prioritized six compounds for molecular dynamics (500 ns), R_gyr, DCCM. The receptor’s C-alpha fluctuation upon bound agonist (6.91 Å), known antagonist (7.03 Å), and LAS 52115629 (5.83 Å) binding varies, leading to receptor stabilization. The residues C-alpha side-chain in active site strongly interacts (hydrogen bonds) with bound agonist (100% interaction: ASP135), known antagonist (95%:ASP135), and LAS 52115629 (100%:ASP135). The R_gyr for receptor-ligand complex, LAS 52115629 (25.68 Å), lies close to bound agonist-Ergotamine, and DCCM analysis also shows strong positive correlations for LAS 52115629 as compared to known drugs. LAS 52115629 is less likely to cause toxicity than known drugs. The structural parameters in the modeled receptor’s conserved motifs (DRY, PIF, NPY) were altered for receptor activation upon ligand-binding, which otherwise was in the in-activated state. The ligand (LAS 52115629)-binding further alters the helices-III, V, VI (G-protein bound), and VII, which form potential interacting sites with the receptor and are proven necessary for activating the receptor. Therefore, LAS 52115629 can act as a potential 5HT_2BR agonist, targeting drug-resistant epilepsy.

Communicated by Ramaswamy H. Sarma

Keywords:

• 5HT_2BR
• Conserved motifs
• G-Protein coupled receptor (GPCR)
• molecular dynamics simulations
• pharmaco-resistant epilepsy

Acknowledgments

Ms. Arushi Chauhan, one of the authors, wish to thank the Council of Scientific and Industrial Research (CSIR), New Delhi, India, for awarding a fellowship through the CSIR-UGC NET-SRF scheme (File no-09/141(0216)/2019-EMR-I).

Disclosure statement

No potential conflict of interest was reported by the authors.

Data and software availability

The X-RAY crystallized structure template of the 5HT_2BR chosen was PDB-ID (4IB4) (40) and modeled. Homology modeling was performed via open-source software SWISS-MODEL (35), validated by using SAVESv6.0 (36-39). The enrichment analysis, protein preparation, modeling, molecular docking simulations operations were performed on Maestro (release 2020-4), Schrödinger, LLC, New York, NY, and the USA. The ligand library was retrieved from Asinex database (https://www.asinex.com/gpcr). Pharmacokinetic study was performed through SwissADME (43) and structural activity relations were examined through VEGA (47), toxicity via ProTox-II (48). Molecular dynamics simulations were performed on Desmond Molecular DynamicAss System, D. E. Shaw Research, New York, NY, 2021 (49). Maestro-Desmond Interoperability Tools, Schrödinger, New York, NY, 2020 (release 2020-1). The data that support the findings of this study are available on request from the corresponding author. The data is not publicly available due to privacy or ethical restrictions.