Potensi Pendekatan in Silico Sebagai Penghambat Aktivitas Protein Protease Utama SARS-CoV-2 dari Tiga Senyawa Tanaman Obat Jahe Merah

Cut Annisa Thahara, Rizarullah Rizarullah*, Ratih Ayu Atika, Abdul Wahab

Abstract


Corona Virus Disease (COVID-19) is a pneumonia outbreak that has been worldwide to date. This outbreak was caused by a Coronavirus originating from Hubei province that first occurred in Wuhan in December 2019. COVID-19 is caused by SARS-CoV-2. SARS-CoV-2 which causes corona has important proteins that are used to infect and replicate, one of which is the main protease protein (Mpro). Red ginger (Zingiber officinale var.Rubrum) is one of the spices that has properties to cure various diseases such as flu, cough and diarrhea. Ginger contains compounds that are antioxidants. The purpose of this study was to examine the potential biological activity of red ginger compounds, namely Gingerol 10, Shogaol 6, and Shogaol 8 as inhibitors of the main protease (MPro) protein activity of SARS-CoV-2. This research was conducted using the In Silico method and AutoDock Vina software was used for the tethering process. The results of gridbox optimization by redocking control ligands obtained RMSD results of 1,100 Å. The results of the tethering showed Gibbs free energy (ΔG) Test Ligand 1 (-5.5 kcal/mol), Test Ligand 2 (-6.0 kcal/mol), and Test Ligand 3 (-5.6 kcal/mol) which showed red ginger compounds have potential as inhibitor of the main protease (MPro) protein activity of SARS-CoV-2.

Keywords


Main Protease (MPro), Gingerol 10, Shogaol 6, dan Shogaol 8

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References


Al-Sehemi, A. G. et al. (2020) ‘Journal of Biomolecular Structure and Dynamics ISSN: (Print) (Online) Journal homepage: https://www.tandfonline.com/loi/tbsd20 Potential of NO donor furoxan as SARS-CoV-2 main protease (M pro ) inhibitors: in silico analysis Potential of NO donor furoxan as SARS-CoV-2 main protease (M pro ) inhibitors: in silico analysis’. doi: 10.1080/07391102.2020.1790038.

Angelina, M. et al. (2008) PENENTUAN LD 50 DAUN CINCO (Cyclea barbata Miers.) PADA MENCIT.

Asnawi, A. (2020) ‘TARGET KERJA OBAT ANTIVIRUS COVID-19: REVIEW DRUG TARGET OF ANTIVIRUS COVID-19: REVIEW’, Aiyi Asnawi Jurnal Farmagazine, VII(2). doi: 10.47653/farm.v7i2.172.

Beranda | Satgas Penanganan COVID-19 (no date). Available at: https://covid19.go.id/ (Accessed: 30 December 2020).

Coronavirus Update (Live): 82,403,833 Cases and 1,798,406 Deaths from COVID-19 Virus Pandemic - Worldometer (no date). Available at: https://www.worldometers.info/coronavirus/ (Accessed: 30 December 2020).

Cubuk, H. and Ozbil, M. (2020) ‘Comparison of Clinically Approved Molecules on SARS-CoV-2 Drug Target Proteins: A Molecular Docking Study’. doi: 10.26434/chemrxiv.12090828.

Drug Repurposing | BIOVIA Blog (no date). Available at: https://blogs.3ds.com/biovia/drug-repurposing/ (Accessed: 18 March 2021).

Du, X. et al. (2016) ‘Insights into protein–ligand interactions: Mechanisms, models, and methods’, International Journal of Molecular Sciences. MDPI AG. doi: 10.3390/ijms17020144.

Elbager, S. et al. (no date) ‘Identification of Potential Drug Targets and Prediction of the Potential Impact of High Risk Non Synonymous Single Nucleotide Polymorphism in SARS-CoV-2 3C like Proteinase (3CLpro): A Computational Approach’. doi: 10.26434/chemrxiv.12235181.v1.

Fakih, T. M. and Dewi, M. L. (2020) ‘IDENTIFIKASI PROTEASE UTAMA (Mpro) SEBAGAI MAKROMOLEKUL TARGET DALAM PENGEMBANGAN KANDIDAT INHIBITOR NOVEL CORONAVIRUS 2019 (SARS-CoV-2) SECARA IN SILICO’, Jurnal Ilmiah Farmasi Farmasyifa, 3(2), pp. 84–91. doi: 10.29313/jiff.v3i2.5913.

Itoh, Y. et al. (2019) ‘N+-C-H···O Hydrogen bonds in protein-ligand complexes’, Scientific Reports, 9(1), pp. 1–5. doi: 10.1038/s41598-018-36987-9.

Lipinski, C. A. (2004) ‘Lead- and drug-like compounds: The rule-of-five revolution’, Drug Discovery Today: Technologies. Drug Discov Today Technol, pp. 337–341. doi: 10.1016/j.ddtec.2004.11.007.

Mesecar, A. D. ; (2020) Full wwPDB X-ray Structure Validation Report i O Title : Structure of COVID-19 main protease bound to potent broad-spectrum non-covalent inhibitor X77. Available at: https://www.wwpdb.org/validation/2017/XrayValidationReportHelp (Accessed: 11 June 2021).

Ortiz, C. L. D. et al. (2019) ‘Potential Inhibitors of Galactofuranosyltransferase 2 (GlfT2): Molecular Docking, 3D-QSAR, and In Silico ADMETox Studies’, Scientific Reports, 9(1). doi: 10.1038/s41598-019-52764-8.

PubChem (no date). Available at: https://pubchem.ncbi.nlm.nih.gov/ (Accessed: 18 November 2021).

RCSB PDB - 6W63: Structure of COVID-19 main protease bound to potent broad-spectrum non-covalent inhibitor X77 (no date a).

Available at: https://www.rcsb.org/structure/6W63 (Accessed: 18 November 2021).

Rut, W. et al. (2020) ‘SARS-CoV-2 Mpro inhibitors and activity-based probes for patient-sample imaging’, Nature Chemical Biology. doi: 10.1038/s41589-020-00689-z.

Siswandono (2016) Kimia Medisinal 1. kedua. Surabaya: Airlangga University Press.

DOCKING KURKUMIN ENOL, BISDEMETOKSIKURKUMIN DAN ANALOGNYA SEBAGAI INHIBITOR ENZIM12-LIPOKSIGENASE, Jurnal Biofisika. Available at: https://journal.ipb.ac.id/index.php/biofisika/article/view/9354 (Accessed: 29 May 2021).

The Central Role of Enzymes as Biological Catalysts - The Cell - NCBI Bookshelf (no date). Available at: https://www.ncbi.nlm.nih.gov/books/NBK9921/ (Accessed: 21 April 2021).

Toksik, E. et al. (2021) KONSEP DASAR TOKSIKOLOGI INDUSTRI. Available at: www.fkm.ui.ac.id (Accessed: 12 June 2021).

Wlodawer, A. et al. (2008) ‘Protein crystallography for non-crystallographers, or how to get the best (but not more) from published macromolecular structures’, FEBS Journal. FEBS J, pp. 1–21. doi: 10.1111/j.1742-4658.2007.06178.x.

Xiao, W. et al. (2018) ‘Multi-Body Interactions in Molecular Docking Program Devised with Key Water Molecules in Protein Binding Sites’, Molecules, 23(9), p. 2321. doi: 10.3390/molecules23092321




DOI: https://doi.org/10.24815/jipi.v6i3.24914

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