New Insights on N-Methyl-D-Aspartate (NMDA) Receptor Under Combinatorial Molecular Docking and MD Simulation Studies Using Natural Bioactive Compounds Against Neurodegenerative Diseases

Ayushi Poddar; Anupriya; Priyangulta Beck; Harsimran Kaur Hora; Nisha Rani Soreng; Swati Shalika; Mukesh Nitin

doi:10.55544/jrasb.3.2.34

Authors

Ayushi Poddar Department of Tech. Biosciences, Digianalix, South Samaj Street, Tharpakhna, Ranchi, Jharkhand, INDIA. | Department of Biotechnology, Gossner College, Ranchi, Jharkhand, INDIA.
Anupriya Department of Tech. Biosciences, Digianalix, South Samaj Street, Tharpakhna, Ranchi, Jharkhand, INDIA. | Department of Biotechnology, Gossner College, Ranchi, Jharkhand, INDIA.
Priyangulta Beck Department of Tech. Biosciences, Digianalix, South Samaj Street, Tharpakhna, Ranchi, Jharkhand, INDIA.
Harsimran Kaur Hora Department of Tech. Biosciences, Digianalix, South Samaj Street, Tharpakhna, Ranchi, Jharkhand, INDIA.
Nisha Rani Soreng Department of Biotechnology, Gossner College, Ranchi, Jharkhand, INDIA.
Swati Shalika Department of Biotechnology, Marwari College, Ranchi, Jharkhand, INDIA.
Mukesh Nitin Department of Tech. Biosciences, Digianalix, South Samaj Street, Tharpakhna, Ranchi, Jharkhand, INDIA.

DOI:

https://doi.org/10.55544/jrasb.3.2.34

Keywords:

neurodegenerative diseases, NMDA receptor, natural bioactive compounds, in silico docking, molecular dynamics simulations, beta-carotene, catechins

Abstract

Neurodegenerative diseases pose a significant challenge, and novel therapeutic strategies are urgently needed. N-methyl-D-aspartate (NMDA) receptor is reported to play a critical role in the central nervous system and has emerged as a potential target for drug discovery. This study explored the potential scope of natural bioactive compounds as ligands for the NMDA receptor using current advances of docking studies with molecular dynamic (MD) simulations. An extensive virtual screening of 500 natural compounds were executed based on wide scientific literature and bibliography search. Docking simulations identified promising candidates with favorable binding affinities, with the top compounds - DL-Alanosine, and Zeinoxanthin (PubChem CIDs 153353 and 5281234) exhibiting exceptionally high docking scores of -6.6 and -6.4, against NMDA respectively. Further, MD simulations suggested the stability of the top-scoring compounds in complex with the NMDA receptor. These findings will provide a new insights to researchers and scientists on proceeding with new alternatives on the investigation of natural bioactive compounds as therapeutic lead candidates for targeting various receptors like NMDA in neurodegenerative diseases. However, in vitro and in vivo studies are warranted to validate these results and elucidate the underlying mechanisms of action.

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