Exploration of Anti-Diabetic Potential of Rubus ellipticus smith through Molecular Docking, Molecular Dynamics Simulation, and MMPBSA Calculation

Authors

  • P. Neupane Department of Chemistry, Amrit Campus, Tribhuvan University, Thamel, Kathmandu, Nepal
  • S. Dhital Department of Chemistry, Amrit Campus, Tribhuvan University, Thamel, Kathmandu, Nepal
  • N. Parajuli Department of Chemistry, Amrit Campus, Tribhuvan University, Thamel, Kathmandu, Nepal
  • T. Shrestha Department of Chemistry, Amrit Campus, Tribhuvan University, Thamel, Kathmandu, Nepal
  • S. Bharati Department of Chemistry, Amrit Campus, Tribhuvan University, Thamel, Kathmandu, Nepal
  • B. Maharjan Department of Chemistry, Amrit Campus, Tribhuvan University, Thamel, Kathmandu, Nepal
  • J. Adhikari Subin Bioinformatics and Cheminformatics Division, Scientific Research and Training Nepal P. Ltd., Kaushaltar, Bhaktapur, Nepal
  • R. L. S. Shrestha Department of Chemistry, Amrit Campus, Tribhuvan University, Thamel, Kathmandu, Nepal

DOI:

https://doi.org/10.3126/jnphyssoc.v9i2.62410

Keywords:

α-amylase, Computational, Binding affinity, Hyperclycemia

Abstract

Diabetes is a chronic metabolic disorder affecting a majority of the population worldwide. Hyperglycemia leading to diabetes mellitus could be managed through the inhibition of human pancreatic α-amylase enzyme. Phytochemicals are frequently reported to possess anti-diabetic activity through inhibition of normal functioning of α-amylase. This study aims to find potential α-amylase inhibitors from Rubus ellipticus Smith with molecular-level understanding using different computational tools. From the molecular docking calculations, rubuside F and rubuside D possessed good binding affinity of -10.0 kcal/mol and -9.9 kcal/mol, respectively better than the reference drugs (acarbose, miglitol, voglibose and metformin). Both the compounds showed good geometrical stability from molecular dynamics simulation accessed in terms of RMSD, hydrogen bond count, SASA, Rg and RMSF. Binding free energy changes of -27.92±4.15 kcal/mol and -28.75±4.15 kcal/mol, respectively for the two ligands indicated sustained thermodynamic spontaneity present in the adducts. The two phytochemicals could be proposed as potential inhibitors of human pancreatic α-amylase for the treatment of diabetes. Further, in vitro and in vivo experiments are recommended for the verification of computational insights in the course of drug design and discovery process.

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Author Biography

R. L. S. Shrestha, Department of Chemistry, Amrit Campus, Tribhuvan University, Thamel, Kathmandu, Nepal

Institute of Natural Resources Innovation, Kalimati, Kathmandu, Nepal

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Published

2023-12-31

How to Cite

Neupane, P., Dhital, S., Parajuli, N., Shrestha, T., Bharati, S., Maharjan, B., Adhikari Subin, J., & Shrestha, R. L. S. (2023). Exploration of Anti-Diabetic Potential of Rubus ellipticus smith through Molecular Docking, Molecular Dynamics Simulation, and MMPBSA Calculation. Journal of Nepal Physical Society, 9(2), 95–105. https://doi.org/10.3126/jnphyssoc.v9i2.62410

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