COVID-19 In Silico Drug with Zingiber officinale Natural Product Compound Library Targeting the Mpro Protein

Authors

Renadya Maulani Wijaya, Department of Bioinformatics, School of Life Sciences, Indonesia International Institute for Life Sciences (i3L), Jakarta 13210, Indonesia
Muhammad Aldino Hafidzhah, Department of Bioinformatics, School of Life Sciences, Indonesia International Institute for Life Sciences (i3L), Jakarta 13210, Indonesia
Viol Dhea Kharisma, Computational Virology and Complexity Science Research Unit, Division of Molecular Biology and Genetics, Generasi Biologi Indonesia Foundation, Gresik 61171, Indonesia
Arif Nur Muhammad Ansori, Doctoral Program in Veterinary Science, Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya 60115, Indonesia
Arli Aditya Parikesit, Department of Bioinformatics, School of Life Sciences, Indonesia International Institute for Life Sciences (i3L), Jakarta 13210, IndonesiaFollow

Abstract

Coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has become a worldwide pandemic. Ginger (Zingiber officinale) is a rhizome, which is commonly used for culinary and medicinal purposes. In Indonesia, ginger is taken as traditional medicine by processing it into a drink known as jamu. The present study aimed to assess and evaluate the bioactive compounds in ginger that can be used in drug design for treating COVID-19. The crystal structure of the SARS-CoV-2 main protease (M^pro) was generated from a protein sequence database, i.e., Protein Data Bank, and the bioactive compounds in ginger were derived from the existing compounds library. M^pro is involved in polyprotein synthesis, including viral maturation and nonstructural protein gluing, making it a potential antiviral target. Furthermore, the bioactive compounds in ginger were analyzed using Lipinski’s rule of five to determine their drug-like molecular properties. Moreover, molecular docking analysis was conducted using the Python Prescription 0.8 (Virtual Screening Tool) software, and the interaction between SARS-CoV-2 M^pro and the bioactive compounds in ginger was extensively examined using the PyMOL software. Out all of the 16 bioactive compounds that were docked successfully, 4-gingerol, which has the lowest binding energy against SARS-CoV-2 M^pro, as per the virtual screening results, was proven to have the most potential as a viral inhibitor of SARS-CoV-2

Recommended Citation

Wijaya, Renadya Maulani; Hafidzhah, Muhammad Aldino; Kharisma, Viol Dhea; Ansori, Arif Nur Muhammad; and Parikesit, Arli Aditya (2021) "COVID-19 In Silico Drug with Zingiber officinale Natural Product Compound Library Targeting the Mpro Protein," Makara Journal of Science: Vol. 25: Iss. 3, Article 5.
DOI: 10.7454/mss.v25i3.1244
Available at: https://scholarhub.ui.ac.id/science/vol25/iss3/5