Bioinformatics Approach for COVID-19 (Coronavirus) Disease Prevention Treatment and Drug Validation
Objectives: To determine the impact of Hydroxychloroquine on COVID special protease.
Methods: PyMOL software is used to find all possible residual rotameters and probabilities. AutoDock software is used to calculate and predict the interaction of molecules.
Results: Hydrochloroquine binds and is released through Protease 6y84 and 7buy and controls their actions in the body.
Conclusion: Drug designing and docking is helpful for the particular diseases. It helps us predict the intermolecular framework formed between a protein or a small molecule.
1.Ahmad S, Hafeez A, Siddqui SA, Ahmad M, Mishra S. A Review of COVID-19 (Coronavirus Disease-2019) Diagnosis, Treatments and Prevention. EJMO 2020;4:116–25.
2. Singhal T. A Review of Coronavirus Disease-2019 (COVID-19). Indian J Pediatr 2020;87:281–6.
3. Cascella M, Rajnik M, Cuomo A, et al. Features, Evaluation and Treatment Coronavirus (COVID-19) [Updated 2020 Apr 6]. In: StatPearls [Internet]. Treasure Island (FL): StatPearls Publishing; 2020 Jan-. Available from: https://www.ncbi.nlm.nih.gov/ books/NBK554776/
4. WorldMeters, https://www.worldometers.info/coronavirus/ (Accessed May 22, 2020).
5. Johns Hopkins University, COVID-19 Map FAQ, https://coronavirus.jhu.edu/map-faq (Accessed May 23, 2020).
6. WHO, Coronavirus disease 2019 (COVID-19) situation reports. https://www.who.int/emergencies/diseases/novel-coronavirus-2019/situation-reports (Accessed Feb 17, 2020).
7. Universal Community Health Center, Coronavirus COVID-19 Global Cases. https://www.uchcla.org/post/coronavirus-covid-19-global-cases (Accessed May 23, 2020).
8. DocPlayer.net. Pymol Tutorial. Go to This is the Protein Data Bank (PDB) - a database for protein structures. http://docplayer.net/34862614-Pymol-tutorial-go-to-this-is-the-proteindata-bank-pdb-a-database-for-protein-structures.html (Accessed May 23, 2020).
9. Epidemiology Working Group for NCIP Epidemic Response, Chinese Center for Disease Control and Prevention. Zhonghua Liu Xing Bing Xue Za Zhi = Zhonghua Liuxingbingxue Zazhi, vol. 41, no. 2, 2020, pp. 145-151.
10. Dong E, Du H, Gardner L. An interactive web-based dashboard to track COVID-19 in real time. Lancet Infect Dis 2020;20:533– 4.
11. Pirhadi S, Sunseri J, Koes DR. Open source molecular modeling. J Mol Graph Model 2016;69:127–43.
12. O'Boyle, N.M., Banck, M., James, C.A. et al. Open Babel: An open chemical toolbox. J Cheminform 3, 33 (2011). https:// doi.org/10.1186/1758-2946-3-33
13. Meng XY, Zhang HX, Mezei M, Cui M. Molecular docking: a powerful approach for structure-based drug discovery. Curr Comput Aided Drug Des 2011;7:146–57.
14. Forli S, Huey R, Pique ME, Sanner MF, Goodsell DS, Olson AJ. Computational protein-ligand docking and virtual drug screening with the AutoDock suite. Nat Protoc 2016;11:905– 19.
15. Meng XY, Zhang HX, Mezei M, Cui M. Molecular docking: a powerful approach for structure-based drug discovery. Curr Comput Aided Drug Des 2011;7:146–57.
16. Taoufik, A, Lamchouri, F., Senhaji, S., Toufik, H., (2019). Molecular docking, ADME/Tox prediction, and in vitro study of the cell growth inhibitory activity of five β-carboline alkaloids. Structural Chemistry. 30. 10.1007/s11224-019-01308-x.
17. Rizvi SM, Shakil S, Haneef M. A simple click by click protocol to perform docking: AutoDock 4.2 made easy for non-bioinformaticians. EXCLI J 2013;12:831–57.
18. O'Donoghue SI, Goodsell DS, Frangakis AS, Jossinet F, Laskowski RA, Nilges M, Saibil HR, Schafferhans A, Wade RC, Westhof E, Olson AJ. Visualization of macromolecular structures. Nat Methods 2010;7:S42–55.
19. Pettersen E.F, Toddard T.D, Huang C.C, UCSF Chimera—A Visualization System for Exploratory, Research and Analysis, Journal of Computational Chemistry 25;1606–12.
20. McCafferty C.L, Verbeke E.J.V, Structural Biology in the Multi-Omics Era. ACS Publications. https://pubs.acs.org/ doi/10.1021/acs.jcim.9b01164# (Accessed May 23, 2020).