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1.
International Journal of Applied Pharmaceutics ; 14(Special Issue 3):112-115, 2022.
Article in English | EMBASE | ID: covidwho-1939570

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.

2.
Journal of Experimental Biology and Agricultural Sciences ; 9(Suppl. 2):S208-S214, 2021.
Article in English | CAB Abstracts | ID: covidwho-1818854

ABSTRACT

Diseases caused by the coronavirus have become an important concern in early 2020. The coronavirus is a new type of virus that is included in the SARS-CoV-2 group. One of the possible mechanisms of SARS-CoV-2 inhibition involves protease receptors inhibition. This research was aimed to in silico screening of Ziziphus spina-christi (L.) Desf., and Strychnos ligustrine active ingredients as the main protease inhibitors of SARS-CoV-2 by assessing the ligand-binding affinity in the binding pocket of SARS-CoV-2 main protease protein. The molecular docking method is generally used to predict the inhibitory site and bonds formation. In the current study, some generally used antiviral compounds from the PDB (Protein Data Bank) were also used to compare the affinity strength of the test compound against the protease receptor (code of 5R7Y). The inhibitory activity against the main protease receptor proven by the ChemPLP score is more negative than the receptor's native ligand and the comparison compounds. Jubanine B, a compound of Z. spina-christi has the most robust inhibition activity on the SARS-CoV-2 protease receptor. Results of this study can be concluded that this can be used to develop as a candidate for traditional medicine against SARS-CoV-2 but still it required some more in vitro and in vivo studies.

3.
Journal of Experimental Biology and Agricultural Sciences ; 8(Suppl. 1):S202-S209, 2020.
Article in English | CAB Abstracts | ID: covidwho-1328328

ABSTRACT

The emerging coronavirus, Covid-19, has become a worldwide pandemic. The existence of the Covid-19 virus pandemic in the world demands the need to identify and characterize new drug candidates to address the health problem caused by the Covid-19 virus. This study aims to find candidate compounds from strychnine bush (Strychnos lucida), pineapple (Ananas comosus), and ginger (Zingiber officinale) acting as the Mpro receptor inhibitor on Covid-19 virus based on docking modeling. The docking process is carried out using a protein with the pdb code 6LU7, a crystal main protein protease (Mpro) of the Covid-19 which binds to the N3 molecule as an inhibitor based on computational tests. The docking process is conducted using N3 comparison, favipiravir, active metabolite remdesivir, and hydroxychloroquine. The docking result shows that the compounds, ananas 26, zingiberenol, and zingiberol have lower docking energy compared to native ligand (N3), favipiravir, active metabolite remdesivir, and hydroxychloroquine. Ananas 26 compound has the most hydrogen bonds with the Mpro active amino acid residue of the Covid-19 virus, namely: HIS163, ASN142, ASP187, TYR54, and HIS41. This makes Ananas 26 more stable in binding pocket enzymes and more effective in inhibiting enzyme performance than other compounds and positive controls. Potential candidate compounds as SARS-CoV-2 Main Protease inhibitors, ananas 26 from pineapple and zingiberenol as well as zingiberol from ginger, can then undergo potential inhibitor tests by in vitro and in vivo methods on SARS-CoV-2.

4.
Journal of Experimental Biology and Agricultural Sciences ; 8(Special Issue 1):S202-S209, 2020.
Article in English | Scopus | ID: covidwho-994752

ABSTRACT

The emerging coronavirus, Covid-19, has become a worldwide pandemic. The existence of the Covid-19 virus pandemic in the world demands the need to identify and characterize new drug candidates to address the health problem caused by the Covid-19 virus. This study aims to find candidate compounds from strychnine bush (Strychnos lucida), pineapple (Ananas comosus), and ginger (Zingiber officinale) acting as the Mpro receptor inhibitor on Covid-19 virus based on docking modeling. The docking process is carried out using a protein with the pdb code 6LU7, a crystal main protein protease (Mpro) of the Covid-19 which binds to the N3 molecule as an inhibitor based on computational tests. The docking process is conducted using N3 comparison, favipiravir, active metabolite remdesivir, and hydroxychloroquine. The docking result shows that the compounds, ananas 26, zingiberenol, and zingiberol have lower docking energy compared to native ligand (N3), favipiravir, active metabolite remdesivir, and hydroxychloroquine. Ananas 26 compound has the most hydrogen bonds with the Mpro active amino acid residue of the Covid-19 virus, namely: HIS163, ASN142, ASP187, TYR54, and HIS41. This makes Ananas 26 more stable in binding pocket enzymes and more effective in inhibiting enzyme performance than other compounds and positive controls. Potential candidate compounds as SARS-CoV-2 Main Protease inhibitors, ananas 26 from pineapple and zingiberenol as well as zingiberol from ginger, can then undergo potential inhibitor tests by in vitro and in vivo methods on SARS-CoV-2. © 2020, Editorial board of Journal of Experimental Biology and Agricultural Sciences. All rights reserved.

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