References
- Aanouz, I., Belhassan, A., El Khatabi, K., Lakhlifi, T., El Idrissi, M., & Bouachrine, M. (2020). Moroccan Medicinal plants as inhibitors of COVID-19: Computational investigations. Journal of Biomolecular Structure & Dynamics, 1–12. https://doi.org/https://doi.org/10.1080/07391102.2020.1758790
- Ahmed, S., Islam, N., Shahinozzaman, M., Fakayode, S. O., Afrin, N., & Halim, M. A. (2020). Virtual screening, molecular dynamics, density functional theory and quantitative structure activity relationship studies to design peroxisome proliferator-activated receptor-γ agonists as anti-diabetic drugs. Journal of Biomolecular Structure and Dynamics, 1–15. https://doi.org/https://doi.org/10.1080/07391102.2020.1714482
- Andersen, K. G., Rambaut, A., Lipkin, W. I., Holmes, E. C., & Garry, R. F. (2020). The proximal origin of SARS-CoV-2. Nature Medicine, 26(4), 450–452. https://doi.org/https://doi.org/10.1038/s41591-020-0820-9
- Ashburn, T. T., & Thor, K. B. (2004, August). Drug repositioning: Identifying and developing new uses for existing drugs. Nature Reviews. Drug Discovery, 3(8), 673–683. . Nature Publishing Group. https://doi.org/https://doi.org/10.1038/nrd1468
- Barrows, N. J., Campos, R. K., Powell, S. T., Prasanth, K. R., Schott-Lerner, G., Soto-Acosta, R., Galarza-Muñoz, G., McGrath, E. L., Urrabaz-Garza, R., Gao, J., Wu, P., Menon, R., Saade, G., Fernandez-Salas, I., Rossi, S. L., Vasilakis, N., Routh, A., Bradrick, S. S., & Garcia-Blanco, M. A. (2016). A Screen of FDA-Approved Drugs for Inhibitors of Zika Virus Infection. Cell Host & Microbe, 20(2), 259–270. https://doi.org/https://doi.org/10.1016/j.chom.2016.07.004
- Bertoni, M., Kiefer, F., Biasini, M., Bordoli, L., & Schwede, T. (2017). Modeling protein quaternary structure of homo- and hetero-oligomers beyond binary interactions by homology. Scientific Reports, 7(1), 10480. https://doi.org/https://doi.org/10.1038/s41598-017-09654-8
- Bikadi, Z., & Hazai, E. (2009). Application of the PM6 semi-empirical method to modeling proteins enhances docking accuracy of AutoDock. Journal of Cheminformatics, 1(1), 15. https://doi.org/https://doi.org/10.1186/1758-2946-1-15
- Boopathi, S., Poma, A. B., & Kolandaivel, P. (2020). Novel 2019 Coronavirus Structure, Mechanism of Action, Antiviral drug promises and rule out against its treatment. Journal of Biomolecular Structure & Dynamics, 1–14. https://doi.org/https://doi.org/10.1080/07391102.2020.1758788
- Burley, S. K., Berman, H. M., Bhikadiya, C., Bi, C., Chen, L., Di Costanzo, L., Christie, C., Dalenberg, K., Duarte, J. M., Dutta, S., Feng, Z., Ghosh, S., Goodsell, D. S., Green, R. K., Guranovic, V., Guzenko, D., Hudson, B. P., Kalro, T., Liang, Y., … Zardecki, C. (2019). RCSB Protein Data Bank: Biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy. Nucleic Acids Res, 47(D1), D464–D474. https://doi.org/https://doi.org/10.1093/nar/gky1004
- Ciliberto, G., & Cardone, L. (2020). Boosting the arsenal against COVID-19 through computational drug repurposing. Drug Discovery Today, 25(6), 946–948. https://doi.org/https://doi.org/10.1016/j.drudis.2020.04.005
- Cui, J., Li, F., & Shi, Z. L. (2019). Origin and evolution of pathogenic coronaviruses. Nature Reviews. Microbiology, 17(3), 181–192. https://doi.org/https://doi.org/10.1038/s41579-018-0118-9
- De Jong, S. (1990). Multivariate calibration, H. Martens and T. Naes, Wiley, New York, 1989. Journal of Chemometrics, 4(6), 441–441. ISBN 0 471 90979 3. Price: £75.00, US$138.00. No. of pages: 504. https://doi.org/https://doi.org/10.1002/cem.1180040607
- Dickson, C. J., Madej, B. D., Skjevik, Å. A., Betz, R. M., Teigen, K., Gould, I. R., & Walker, R. C. (2014). Lipid14: The amber lipid force field. Journal of Chemical Theory and Computation, 10(2), 865–879. https://doi.org/https://doi.org/10.1021/ct4010307
- Elmezayen, A. D., Al-Obaidi, A., Şahin, A. T., & Yelekçi, K. (2020). Drug repurposing for coronavirus (COVID-19): In silico screening of known drugs against coronavirus 3CL hydrolase and protease enzymes. Journal of Biomolecular Structure and Dynamics, 1–12. https://doi.org/https://doi.org/10.1080/07391102.2020.1758791
- Frisch, M. J., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., Scalmani, G., Barone, V., Petersson, G. A., Nakatsuji, H., Li, X., Caricato, M., Marenich, A. V., Bloino, J., Janesko, B. G., Gomperts, R., Mennucci, B., Hratchian, H. P., Ortiz, J. V., & Fox, D. J. (2009). Gaussian 09, Revision D.01. Wallingford CT: Gaussian, Inc.
- Gao, Y., Yan, L., Huang, Y., Liu, F., Zhao, Y., Cao, L., Wang, T., Sun, Q., Ming, Z., Zhang, L., Ge, J., Zheng, L., Zhang, Y., Wang, H., Zhu, Y., Zhu, C., Hu, T., Hua, T., Zhang, B., … Rao, Z. (2020). Structure of the RNA-dependent RNA polymerase from COVID-19 virus. Science (New York, N.Y.). 368(6492), 779–782. https://doi.org/https://doi.org/10.1126/science.abb7498
- Gilson, M. K., & Honig, B. (1988). Calculation of the total electrostatic energy of a macromolecular system: solvation energies, binding energies, and conformational analysis. Proteins, 4(1), 7–18. Reprint, (061/4), https://doi.org/https://doi.org/10.1002/prot.340040104
- Gordon, D. E., Jang, G. M., Bouhaddou, M., Xu, J., Obernier, K., O’Meara, M. J., Guo, J. Z., Swaney, D. L., Tummino, T. A., Hüttenhain, R., Kaake, R. M., Richards, A. L., Tutuncuoglu, B., Foussard, H., Batra, J., Haas, K., Modak, M., Kim, M., Haas, P., & Krogan, N. J. (2020). A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing. Nature, 583, 459–468. https://doi.org/10.1038/s41586-020-2286-9
- Guex, N., & Peitsch, M. C. (1997). SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling. Electrophoresis, 18(15), 2714–2723. https://doi.org/https://doi.org/10.1002/elps.1150181505
- Harrison, C. (2020). Coronavirus puts drug repurposing on the fast track. Nature Biotechnology, 38(4), 379–381. https://doi.org/https://doi.org/10.1038/d41587-020-00003-1
- Hicks, C., & Gulick, R. M. (2009). Raltegravir: The first HIV Type 1 Integrase Inhibitor. Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America, 48(7), 931–939. https://doi.org/https://doi.org/10.1086/597290
- Hilgenfeld, R. (2014). From SARS to MERS: Crystallographic studies on coronaviral proteases enable antiviral drug design. The FEBS Journal, 281(18), 4085–4096. https://doi.org/https://doi.org/10.1111/febs.12936
- Hodos, R. A., Kidd, B. A., Shameer, K., Readhead, B. P., & Dudley, J. T. (2016). In silico methods for drug repurposing and pharmacology. Wiley Interdisciplinary Reviews. Systems Biology and Medicine, 8(3), 186–210. https://doi.org/https://doi.org/10.1002/wsbm.1337
- Hosseini, F. S., Amanlou, M. (2020). Simeprevir, potential candidate to repurpose for coronavirus infection: Virtual screening and molecular docking study. Preprints 2020, 2020020438. https://doi.org/https://doi.org/10.20944/Preprints202002.0438.V1, (February), 0–2.
- Hu, F., Jiang, J., & Yin, P. (2020). Prediction of potential commercially inhibitors against SARS-CoV-2 by multi-task deep model, 1–8.
- Hussain, S., Pan, J., Chen, Y., Yang, Y., Xu, J., Peng, Y., Wu, Y., Li, Z., Zhu, Y., Tien, P., & Guo, D. (2005). Identification of novel subgenomic RNAs and noncanonical transcription initiation signals of severe acute respiratory syndrome coronavirus. Journal of Virology, 79(9), 5288–5295. https://doi.org/https://doi.org/10.1128/JVI.79.9.5288-5295.2005
- Islam, M. J., Khan, A. M., Parves, M. R., Hossain, M. N., & Halim, M. A. (2019). Prediction of Deleterious Non-synonymous SNPs of Human STK11 Gene by Combining Algorithms, Molecular Docking, and Molecular Dynamics Simulation. Scientific Reports, 9(1), 16426. https://doi.org/https://doi.org/10.1038/s41598-019-52308-0
- Islam, R., Parves, R., Paul, A. S., Uddin, N., Rahman, M. S., Mamun, A., Al, … Halim, M. A. (2020). A Molecular Modeling Approach to Identify Effective Antiviral Phytochemicals against the Main Protease of SARS-CoV-2. Journal of Biomolecular Structure and Dynamics, 1–20. https://doi.org/https://doi.org/10.1080/07391102.2020.1761883
- Johansen, L. M., DeWald, L. E., Shoemaker, C. J., Hoffstrom, B. G., Lear-Rooney, C. M., Stossel, A., Nelson, E., Delos, S. E., Simmons, J. A., Grenier, J. M., Pierce, L. T., Pajouhesh, H., Lehár, J., Hensley, L. E., Glass, P. J., White, J. M., & Olinger, G. G. (2015). A screen of approved drugs and molecular probes identifies therapeutics with anti-Ebola virus activity. Sci Transl Med, 7(290), 290ra89https://doi.org/https://doi.org/10.1126/scitranslmed.aaa5597
- Jones, G., Willett, P., Glen, R. C., Leach, A. R., & Taylor, R. (1997). Development and validation of a genetic algorithm for flexible docking. J. Mol. Biol, 267(3), 727–748. https://doi.org/https://doi.org/10.1006/jmbi.1996.0897
- Junaid, M., Islam, N., Hossain, M. K., Ullah, M. O., & Halim, M. A. (2019). Metal based donepezil analogues designed to inhibit human acetylcholinesterase for Alzheimer’s disease. Plos One, 14(2), e0211935. https://doi.org/https://doi.org/10.1371/journal.pone.0211935
- Khan, R. J., Jha, R. K., Amera, G., Jain, M., Singh, E., Pathak, A., Singh, R. P., Muthukumaran, J., & Singh, A. K. (2020). Targeting SARS-CoV-2: A Systematic Drug Repurposing Approach to Identify Promising Inhibitors Against 3C-like Proteinase and 2’-O-RiboseMethyltransferase. Journal of Biomolecular Structure & Dynamics, 1–40. https://doi.org/https://doi.org/10.1080/07391102.2020.1753577
- Khan, A. M., Shawon, J., & Halim, M. A. (2017). Multiple receptor conformers based molecular docking study of fluorine enhanced ethionamide with mycobacterium enoyl ACP reductase (InhA). Journal of Molecular Graphics & Modelling, 77, 386–398. https://doi.org/https://doi.org/10.1016/j.jmgm.2017.09.010
- Khan, S. A., Zia, K., Ashraf, S., Uddin, R., & Ul-Haq, Z. (2020). Identification of chymotrypsin-like protease inhibitors of SARS-CoV-2 via integrated computational approach. Journal of Biomolecular Structure and Dynamics, 1–10. https://doi.org/https://doi.org/10.1080/07391102.2020.1751298
- Kollman, P. A., Massova, I., Reyes, C., Kuhn, B., Huo, S., Chong, L., Lee, M., Lee, T., Duan, Y., Wang, W., Donini, O., Cieplak, P., Srinivasan, J., Case, D. A., & Cheatham, T. E. (2000). Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models. Accounts of Chemical Research, 33(12), 889–897. https://doi.org/https://doi.org/10.1021/ar000033j
- Krieger, E., Darden, T., Nabuurs, S. B., Finkelstein, A., & Vriend, G. (2004). Making optimal use of empirical energy functions: Force-field parameterization in crystal space. Proteins, 57(4), 678–683. https://doi.org/https://doi.org/10.1002/prot.20251
- Li, H., Wang, Y. M., Xu, J. Y., & Cao, B. (2020). [Potential antiviral therapeutics for 2019 Novel Coronavirus]. Zhonghua Jie he he hu xi za Zhi = Zhonghua Jiehe he Huxi Zazhi = Chinese Journal of Tuberculosis and Respiratory Diseases, 43(0), E002https://doi.org/https://doi.org/10.3760/cma.j.issn.1001-0939.2020.0002
- Li, Y., Zhang, J., Wang, N., Li, H., Shi, Y., Guo, G., Liu K., Zeng H., Zou, Q. (2020). Therapeutic Drugs Targeting 2019-nCoV Main Protease by High-Throughput Screening. BioRxiv, 2020.01.28.922922. https://doi.org/https://doi.org/10.1101/2020.01.28.922922
- Mathias, A. A., German, P., Murray, B. P., Wei, L., Jain, A., West, S., Warren, D., Hui, J., & Kearney, B. P. (2010). Pharmacokinetics and Pharmacodynamics of GS-9350: A Novel Pharmacokinetic Enhancer Without Anti-HIV Activity. Clin. Pharmacol. Ther, 87(3), 322–329. https://doi.org/https://doi.org/10.1038/clpt.2009.228
- Muralidharan, N., Sakthivel, R., Velmurugan, D., & Gromiha, M. M. (2020). Computational studies of drug repurposing and synergism of lopinavir, oseltamivir and ritonavir binding with SARS-CoV-2 protease against COVID-19. Journal of Biomolecular Structure and Dynamics, 1–6. https://doi.org/https://doi.org/10.1080/07391102.2020.1752802
- Neves, B. J., Braga, R. C., Melo-Filho, C. C., Moreira-Filho, J. T., Muratov, E. N., & Andrade, C. H. (2018). QSAR-based virtual screening: Advances and applications in drug discovery. Frontiers in Pharmacology, 9(NOV), 1275. https://doi.org/https://doi.org/10.3389/fphar.2018.01275
- Pant, S., Singh, M., Ravichandiran, V., Murty, U. S. N., & Srivastava, H. K. (2020). Peptide-like and small-molecule inhibitors against Covid-19. Journal of Biomolecular Structure & Dynamics, 1–15. https://doi.org/https://doi.org/10.1080/07391102.2020.1757510
- R Core Team (2014). R Core Team (2014). R: A language and environment for statistical computing. R Foundation for Statistical Computing. URL http://www.R-Project.Org/.
- Razzaghi-Asl, N., Mirzayi, S., Mahnam, K., & Sepehri, S. (2018). Identification of COX-2 inhibitors via structure-based virtual screening and molecular dynamics simulation. J. Mol. Graph. Model, 83, 138–152. https://doi.org/https://doi.org/10.1016/j.jmgm.2018.05.010
- Remmert, M., Biegert, A., Hauser, A., & Söding, J. (2011). HHblits: Lightning-fast iterative protein sequence searching by HMM-HMM alignment. Nature Methods, 9(2), 173–175. https://doi.org/https://doi.org/10.1038/nmeth.1818
- Romano, M., Ruggiero, A., Squeglia, F., Maga, G., & Berisio, R. (2020). A Structural View of SARS-CoV-2 RNA Replication Machinery: RNA Synthesis, Proofreading and Final Capping. Cells, 9(5), 1267. https://doi.org/https://doi.org/10.3390/cells9051267
- Rstudio Team (2019). RStudio: Integrated development for R. RStudio, Inc., Boston MA. RStudio. https://doi.org/https://doi.org/10.1007/978-3-642-20966-6
- Sarma, P., Sekhar, N., Prajapat, M., Avti, P., Kaur, H., Kumar, S., … Medhi, B. (2020). In-silico homology assisted identification of inhibitor of RNA binding against 2019-nCoV N-protein (N terminal domain). Journal of Biomolecular Structure & Dynamics, 1–11. https://doi.org/https://doi.org/10.1080/07391102.2020.1753580
- Shahinozzaman, M., Ishii, T., Ahmed, S., Halim, M. A., & Tawata, S. (2019). A computational approach to explore and identify potential herbal inhibitors for the p21-activated kinase 1 (PAK1). . Journal of Biomolecular Structure and Dynamics, 1–13. https://doi.org/https://doi.org/10.1080/07391102.2019.1659855
- Sun, W., Sanderson, P. E., & Zheng, W. (2016, July). Drug combination therapy increases successful drug repositioning. Drug Discovery Today, 21(7), 1189–1195. https://doi.org/https://doi.org/10.1016/j.drudis.2016.05.015
- Talwani, R., Heil, E. L., Gilliam, B. L., & Temesgen, Z. (2013). Simeprevir: A macrocyclic hcv protease inhibitor. Drugs of Today (Barcelona, Spain : 1998), 49(12), 769. December). https://doi.org/https://doi.org/10.1358/dot.2013.49.12.2067249
- Trott, O., & Olson, A. J. (2010). AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry, 31(2), 455–461. https://doi.org/https://doi.org/10.1002/jcc.21334
- Waterhouse, A., Bertoni, M., Bienert, S., Studer, G., Tauriello, G., Gumienny, R., Heer, F. T., de Beer, T. A. P., Rempfer, C., Bordoli, L., Lepore, R., & Schwede, T. (2018). SWISS-MODEL: Homology modelling of protein structures and complexes. Nucleic Acids Research, 46(W1), W296–W303. https://doi.org/https://doi.org/10.1093/nar/gky427
- Wickham, H. (2009). ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag. https://doi.org/https://doi.org/10.1007/978-0-387-98141-3
- Wold, S., Esbensen, K., & Geladi, P. (1987). Principal component analysis. Chemometrics and Intelligent Laboratory Systems, 2(1-3), 37–52. https://doi.org/https://doi.org/10.1016/0169-7439(87)80084-9
- Wong, S. K., Li, W., Moore, M. J., Choe, H., & Farzan, M. (2004). A 193-Amino Acid Fragment of the SARS Coronavirus S Protein Efficiently Binds Angiotensin-converting Enzyme 2. The Journal of Biological Chemistry, 279(5), 3197–3201. https://doi.org/https://doi.org/10.1074/jbc.C300520200
- Woo, P. C. Y., Huang, Y., Lau, S. K. P., & Yuen, K. Y. (2010). Coronavirus genomics and bioinformatics analysis. Viruses, 2(8), 1804–1820. MDPI AG. https://doi.org/https://doi.org/10.3390/v2081803
- XLSTAT | Statistical Software for Excel. (2017). XLSTAT | Statistical Software for Excel. Retrieved April 26, 2020, from https://www.xlstat.com/en/
- Xu, J., Shi, P.-Y., Li, H., & Zhou, J. (2020). Broad Spectrum Antiviral Agent Niclosamide and Its Therapeutic Potential. ACS Infectious Diseases, 6(5), 909–915. https://doi.org/https://doi.org/10.1021/acsinfecdis.0c00052
- Zhang, L., Zhou, R. (2020). Binding mechanism of remdesivir to SARS-CoV-2 RNA dependent RNA polymerase. Preprints, (2020030267). https://doi.org/https://doi.org/10.20944/preprints202003.0267.v1
- Zhou, Y., Hou, Y., Shen, J., Huang, Y., Martin, W., & Cheng, F. (2020). Network-based drug repurposing for novel coronavirus 2019-nCoV/SARS-CoV-2. Cell Discovery, 6(1), 14–18. https://doi.org/https://doi.org/10.1038/s41421-020-0153-3