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.
ABSTRACT
Recently, the world is facing outbreaks of severe acute respiratory syndrome coronavirus 2 or SARS-CoV-2 and the number of infected patients is increasing every day. Researchers are doing their best to find the most effective treatment to tackle this deathly virus. Several approaches had been proposed to be tested in the lab for efficacy but none of them are qualified to be used as the treatment of the COVID-19. Therefore, this study aimed to design a vaccine based on epitope, which was obtained from the nucleocapsid phosphoprotein (N protein). 38 samples of SARS-CoV-2 isolates were retrieved from the GISAID Database and NCBI GenBank. These samples were used to check the evolutionary relationship of the SARS-CoV-2 and determine whether these nucleocapsid proteins are well-conserved with less or even no mutations occur at all, and whether there was any evolutionary relationship between the recent coronavirus with the previous coronavirus by conducting the phylogenetic analysis. Then, it is desirable to see the molecular interaction between the human BCR/FAB receptor with the predicted peptides through the molecular docking process. All of the peptides were generated by the IEDB analysis tools and have already been tested for antigenicity, so the one that was being docked is the peptide that has antigen properties. Based on the analysis that had been done, the PEP1 was recommended as an epitope-based peptide vaccine candidate to deal with the SARS-CoV-2 outbreaks. Copyright © 2020 THE AUTHOR(S).