Computational investigation of phytochemicals from Withania somnifera (Indian ginseng/ashwagandha) as plausible inhibitors of GluN2B-containing NMDA receptors

Abstract

N-Methyl-d-aspartate receptor (NMDAR)-mediated excitotoxicity has been implicated in multi-neurodegenerative diseases. Owing to dearth of efficacy and adverse effects of NMDA receptor antagonists, search for herbal remedies acting like salutary agents is a dynamic expanse of investigation to contest neurodegenerative disease. Withania somnifera (W. somnifera) has been used since antiquity as a nerve tonic and nootropic agents in Ayurveda, an old Indian system of medicine. In the present study, we have explored phytochemicals from Ayurvedic herb W. somnifera as an inhibitor of NMDA receptor-mediated excitotoxicity through allosteric reticence of the GluN1-GluN2B encompassing NMDARs by dint of molecular docking and dynamics studies. Thus, steering and constraining GluN1-GluN2B may be effective in the management of neurodegenerative diseases including Alzheimer’s disease. Out of the curtained phytochemicals, chlorogenic acid revealed significant docking scores of –8.856 and –8.645 kcal/mol and free binding energies of –49.84 and –50.67 kcal/mol in Chain AB and Chain CD of NMDARs, respectively. Chlorogenic acid in AB chain forms four hydrogen bonding with Glu110, Arg115, Leu135 and Asp136 amino acid residues and five hydrogen bond with Glu106, Ala107, Ile133, Ile335and Arg155 amino acid residues of CD chain. To further validate the interaction of top scored molecule chlorogenic acid, molecular dynamics study of 100 ns was carried out. It indicated that the protein–ligand complex was stable throughout the simulation period, and minimal backbone fluctuations have ensued in the system. In silico pharmacokinetic predictions of the screened phytochemicals were within the defined range described for human use.

Communicated by Ramaswamy H. Sarma

Keywords:

• NMDA
• GluN2B
• Withania somnifera
• docking
• MMGBSA
• molecular dynamic simulation
• Alzheimer’s disease

Disclosure statement

There are no conflicts to declare.