ABSTRACT
Purpose: A recent outbreak of a type of coronavirus—SARS-CoV-2 has caused over 200,000 deaths and limited drugs are available. SARS-CoV-2 shows similarity with SARS-CoV. Previous studies have proven that RH121 and indigo are effective in inhibiting 3CLpro from SARS-CoV, but no research has been done to test the two inhibitors on 3CLpro from SARS-CoV-2. This study investigates if RH121 and indigo are still effective in inhibiting 3CLpro from SARS-CoV-2, and compares the two inhibitors in terms of their inhibitory efficiency. Method: For the cell-free assay, substrate Thr-Ser-Ala-Val-Leu-Gln-pNA will be used, and pNA will be released. The absorbance of pNA will be measured using a microplate reader. The cell-based assay will use vero cell lines, vector, plasmid pcDNA3.1-3CLpro-S-Luc, luciferin, and luminometer. The luciferase activity will be tested by Luciferase Reporter Assay System. Possible results: There are seven possible results: (1) RH121 failed to inhibit 3CLpro from SARS-CoV2, but Indigo successfully inhibits 3CLpro from SARS-CoV2. (2) Indigo failed to inhibit 3CLpro from SARS-CoV2, but RH121 successfully inhibits 3CLpro from SARS-CoV-2. (3) Both Indigo and RH121 failed to inhibit 3CLpro from SARS-CoV-2. (4) Indigo has a higher IC50 value than RH121 in cell-based assay, but has a lesser IC50 value than RH121 in cell-free assay. (5) RH121 has a higher IC50 value than Indigo in cell-based assay, but has a lesser IC50 value than Indigo in cell-free assay. (6) Indigo has a higher IC50 value than RH121 in both cell-based assay and cell-free assay. (7) RH121 has a higher IC50 value than Indigo in both cell-based assay and cell-free assay. Conclusion: The result of this study would provide valuable information regarding which inhibitor best inhibits the 3CLpro of SARS-CoV-2 for future trials. Further studies should be done regarding the bioavailability of the two inhibitors and their competitive/uncompetitive nature. The ED50 and TD50 of the two inhibitors should also be investigated in future trials to obtain the therapeutic index and the therapeutic window of RH121 and indigo.
- Ali, I., & Alharbi, O. M. L. (2020). COVID-19: Disease, management, treatment, and social impact. Science of The Total Environment, 728, 138861. doi:https://doi.org/10.1016/j.scitotenv.2020.138861.Google ScholarCross Ref
- Tahir ul Qamar, M., Alqahtani, S. M., Alamri, M. A., & Chen, L.-L. (2020). Structural basis of SARS-CoV-2 3CLpro and anti-COVID-19 drug discovery from medicinal plants. Journal of Pharmaceutical Analysis. doi:https://doi.org/10.1016/j.jpha.2020.03.009.Google ScholarCross Ref
- Coronavirus disease-covid-19-situation report. (2020).Google Scholar
- Singhal, T. (2020). A Review of Coronavirus Disease-2019 (COVID-19). Indian journal of pediatrics, 87(4), 281-286. doi:10.1007/s12098-020-03263-6.Google ScholarCross Ref
- Prajapat, M., Sarma, P., Shekhar, N., Avti, P., Sinha, S., Kaur, H., Medhi, B. (2020). Drug targets for corona virus: A systematic review. Indian journal of pharmacology, 52(1), 56-65. doi:10.4103/ijp.IJP_115_20.Google ScholarCross Ref
- Lin, C. W., Tsai, F. J., Tsai, C. H., Lai, C. C., Wan, L., Ho, T. Y., Chao, P. D. (2005). Anti-SARS coronavirus 3C-like protease effects of Isatis indigotica root and plant-derived phenolic compounds. Antiviral Res, 68(1), 36-42. doi:10.1016/j.antiviral.2005.07.002.Google ScholarCross Ref
- Fang, S. G., Shen, H., Wang, J., Tay, F. P. L., & Liu, D. X. (2008). Proteolytic processing of polyproteins 1a and 1ab between non-structural proteins 10 and 11/12 of Coronavirus infectious bronchitis virus is dispensable for viral replication in cultured cells. Virology, 379(2), 175-180. doi:https://doi.org/10.1016/j.virol.2008.06.038.Google ScholarCross Ref
- Fuzimoto, A. D., & Isidoro, C. (2020). The antiviral and the coronavirus-host protein pathways inhibiting properties of herbs and natural compounds - Additional weapons in the fight against the COVID-19 pandemic? Journal of Traditional and Complementary Medicine. doi:https://doi.org/10.1016/j.jtcme.2020.05.003.Google ScholarCross Ref
- Li, C., Teng, X., Qi, Y., Tang, B., Shi, H., Ma, X., & Lai, L. (2016). Conformational Flexibility of a Short Loop near the Active Site of the SARS-3CLpro is Essential to Maintain Catalytic Activity. Scientific Reports, 6(1), 20918. doi:10.1038/srep20918.Google ScholarCross Ref
- Luo, W., Su, X., Gong, S., Qin, Y., Liu, W., Li, J.,. Xu, Q. (2009). Anti-SARS coronavirus 3C-like protease effects of Rheum palmatum L. extracts. Biosci Trends, 3(4), 124-126.Google Scholar
- Roth, R. I., & Levin, J. (1989). Amplification of chromogenic staining of proteases within electrophoretic gels. Journal of Biochemical and Biophysical Methods, 19(2), 129-141. doi:https://doi.org/10.1016/0165-022X(89)90021-3.Google ScholarCross Ref
- Eun, H.-M. (1996). 1 - Enzymes and Nucleic Acids: General Principles. In H.-M. Eun (Ed.), Enzymology Primer for Recombinant DNA Technology (pp. 1-108). San Diego: Academic Press.Google Scholar
- Delaune, K. P., & Alsayouri, K. (2020). Physiology, Noncompetitive Inhibitor. In StatPearls. Treasure Island (FL).Google Scholar
- Jakubowski, H. (2019). Noncompetitive and Mixed inhibition. Retrieved from https://bio.libretexts.org/Bookshelves/Biochemistry/Book%3A_Biochemistry_Online_(Jakubowski)/06%3A_TRANSPORT_AND_KINETICS/6C%3A_Enzyme_Inhibition/C4%3A_Noncompetitive_and_Mixed_Inhibition.Google Scholar
- Aldred, E. M., Buck, C., & Vall, K. (2009). Chapter 19 - Pharmacodynamics: How drugs elicit a physiological effect. In E. M. Aldred, C. Buck, & K. Vall (Eds.), Pharmacology (pp. 137-143). Edinburgh: Churchill Livingstone.Google Scholar
- Palmer, T., & Bonner, P. L. (2011). 8 - Enzyme Inhibition. In T. Palmer & P. L. Bonner (Eds.), Enzymes (Second Edition) (pp. 126-152): Woodhead Publishing.Google ScholarCross Ref
- Chen, L.-R., Wang, Y.-C., Lin, Y. W., Chou, S.-Y., Chen, S.-F., Liu, L. T., Juang, S.-H. (2005). Synthesis and evaluation of isatin derivatives as effective SARS coronavirus 3CL protease inhibitors. Bioorganic & Medicinal Chemistry Letters, 15(12), 3058-3062. doi:https://doi.org/10.1016/j.bmcl.2005.04.027Google ScholarCross Ref
- PubChem Database. Retrieved from: https://pubchem.ncbi.nlm.nih.gov/bioassay/1344314.Google Scholar
- Dimethyl Sulfoxide - High Purity Solvents. Retrieved from: https://www.sigmaaldrich.com/chemistry/solvents/dimethyl-sulfoxide-center.html.Google Scholar
- Nidetzky, B., Fürlinger, M., Haltrich, D., & Kulbe, K. D. (1998). Stability and stabilization of glucose-fructose oxidoreductase from Zymomonas mobilis against irreversible inactivation during substrate turnover in biochemical reactors. In A. Ballesteros, F. J. Plou, J. L. Iborra, & P. J. Halling (Eds.), Progress in Biotechnology (Vol. 15, pp. 19-26): Elsevier.Google ScholarCross Ref
- Swinney, D. C. (2011). Chapter 18 - Molecular Mechanism of Action (MMoA) in Drug Discovery. In J. E. Macor (Ed.), Annual Reports in Medicinal Chemistry (Vol. 46, pp. 301-317): Academic Press.Google Scholar
- Ammerman, N. C., Beier-Sexton, M., & Azad, A. F. (2008). Growth and maintenance of Vero cell lines. Current protocols in microbiology, Appendix 4, Appendix-4E. doi:10.1002/9780471729259.mca04es11.Google ScholarCross Ref
- Khan, F. (August 26, 2013). The Luciferase Reporter Assay: How it works. Retrieved from https://bitesizebio.com/10774/the-luciferase-reporter-assay-how-it-works/.Google Scholar
- Anderson, W. Beer's Law Lab Explained: Absorbance vs. Concentration. Retrieved from https://schoolworkhelper.net/beers-law-lab-explained-absorbance-vs-concentration/.Google Scholar
- Seed area. Retrieved from http://www.seedarea.com/wholesale-/498-isatis-indigotica-100g-approx-1400-seeds.html.Google Scholar
- Wikipedia. Retrieved from https://en.wikipedia.org/wiki/Rheum_palmatumGoogle Scholar
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