MOLECULAR DOCKING OF CYMBOPOGON NARDUS (L.) RENDLE COMPOUNDS AS A PROTEASE INHIBITOR OF SARS-COV-2

Authors

  • FAJRI RIFALDI Faculty of Pharmacy, Universitas Pancasila, South Jakarta, DKI Jakarta, 12640, Indonesia
  • ESTI MUMPUNI Faculty of Pharmacy, Universitas Pancasila, South Jakarta, DKI Jakarta, 12640, Indonesia
  • SHIRLY KUMALA Faculty of Pharmacy, Universitas Pancasila, South Jakarta, DKI Jakarta, 12640, Indonesia
  • NOVI YANTIH Faculty of Pharmacy, Universitas Pancasila, South Jakarta, DKI Jakarta, 12640, Indonesia
  • DESI NADYA AULENA Faculty of Pharmacy, Universitas Pancasila, South Jakarta, DKI Jakarta, 12640, Indonesia
  • SAFIRA NAFISA Faculty of Pharmacy, Universitas Pancasila, South Jakarta, DKI Jakarta, 12640, Indonesia

DOI:

https://doi.org/10.22159/ijap.2022.v14s3.24

Keywords:

SARS-CoV-2, Main protease, Cymbopogon nardus, Molecular docking

Abstract

Objective: The study aimed to obtain active compounds from Cymbopogon nardus as candidates for protease inhibitor of SARS-CoV-2 virus by assessing the ligand-binding affinity in the binding pocket of SARS-CoV-2 main protease protein.

Methods: Molecular docking as a protease inhibitor of SARS-CoV-2 was carried using computational software Molegro Virtual Docker (MVD); computational docking was carried using receptors with Protein Data Bank (PDB) were also used to compare the affinity strength of the test compounds against the protease receptor (code of 5R81). The compounds of Cymbopogon nardus were optimized before docking using ChemDraw and minimized energy using Chem3D. Visualization of the docking result by using Discovery Studio and pkCSM was utilized to perform a pharmacokinetic and toxicological analysis (ADMET).

Results: The result showed geranyl acetate, elemol, citronellal, and citronellyl acetate compounds from Cymbopogon nardus has a rerank score more negative than native ligand from 5R81 receptor as a protease inhibitor of SARS-CoV-2.

Conclusion: Cymbopogon nardus can be developed as an antivirus with the mechanism of a protease inhibitor of SARS-CoV-2 candidates after further experimental tests.

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References

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Published

28-06-2022

How to Cite

RIFALDI, F., MUMPUNI, E., KUMALA, S., YANTIH, N., AULENA, D. N., & NAFISA, S. (2022). MOLECULAR DOCKING OF CYMBOPOGON NARDUS (L.) RENDLE COMPOUNDS AS A PROTEASE INHIBITOR OF SARS-COV-2. International Journal of Applied Pharmaceutics, 14(3), 112–115. https://doi.org/10.22159/ijap.2022.v14s3.24

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