References
- Adinsoft, S. (2010). XLSTAT-software, version 10. Addinsoft.
- 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
- Ahmed, S., Mahtarin, R., Ahmed, S. S., Akter, S., Islam, M. S., Mamun, A., Al, Islam, R., Hossain, M. N., Ali, M. A., Sultana, M. U. C., Parves, M. D. R., Ullah, M. O., & Halim, M. A. (2020). Investigating the binding affinity, interaction, and structure-activity-relationship of 76 prescription antiviral drugs targeting RdRp and Mpro of SARS-CoV-2. Journal of Biomolecular Structure and Dynamics, 1–16. https://doi.org/https://doi.org/10.1080/07391102.2020.1796804
- Anderson, R. M., Heesterbeek, H., Klinkenberg, D., & Hollingsworth, T. D. (2020). How will country-based mitigation measures influence the course of the COVID-19 epidemic?. The Lancet, 395(10228), 931–934. https://doi.org/https://doi.org/10.1016/S0140-6736(20)30567-5
- Barrientos, A., & Concha, F. (1990). Phenomenological model of classification in conventional hydrocylones. In R. Baron (Ed.), Comminution (Vol. 819, Issue 1, pp. 287–305). Springer. https://doi.org/https://doi.org/10.1007/978-1-61779-465-0
- Cheng, F., Li, W., Zhou, Y., Shen, J., Wu, Z., Liu, G., Lee, P. W., & Tang, Y. (2012). admetSAR: A comprehensive source and free tool for assessment of chemical ADMET properties. Journal of Chemical Information and Modeling, 52(11), 3099–3105. https://doi.org/https://doi.org/10.1021/ci300367a
- De Jong, S. (1990). Multivariate calibration. H. Martens and T. Naes, Wiley. (1989). ISBN 0 471 90979 3. Price: £75.00, US$138.00. No. of pages: 504. Journal of Chemometrics, 4(6), 441–441. 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
- Friesner, R. A., Banks, J. L., Murphy, R. B., Halgren, T. A., Klicic, J. J., Mainz, D. T., Repasky, M. P., Knoll, E. H., Shelley, M., Perry, J. K., Shaw, D. E., Francis, P., & Shenkin, P. S. (2004). Glide: A new approach for rapid, accurate docking and scoring. 1. method and assessment of docking accuracy. Journal of Medicinal Chemistry, 47(7), 1739–1749. https://doi.org/https://doi.org/10.1021/jm0306430
- Gordon, D. E., Jang, G. M., Bouhaddou, M., Xu, J., Obernier, K., White, K. M., O’Meara, M. J., Rezelj, V. V., 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., … Krogan, N. J. (2020). A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature, 583(7816), 459–468. https://doi.org/https://doi.org/10.1038/s41586-020-2286-9
- 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, Hossain, M. N., Ali, M. A., & 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
- Jin, Z., Du, X., Xu, Y., Deng, Y., Liu, M., Zhao, Y., Zhang, B., Li, X., Zhang, L., Peng, C., Duan, Y., Yu, J., Wang, L., Yang, K., Liu, F., Jiang, R., Yang, X., You, T., Liu, X., … Yang, H. (2020). Structure of Mpro from COVID-19 virus and discovery of its inhibitors. Nature, 582(7811), 289–293. https://doi.org/https://doi.org/10.1038/s41586-020-2223-y
- Jin, Z., Zhao, Y., Sun, Y., Zhang, B., Wang, H., Wu, Y., Zhu, Y., Zhu, C., Hu, T., Du, X., Duan, Y., Yu, J., Yang, X., Yang, X., Yang, K., Liu, X., Guddat, L. W., Xiao, G., Zhang, L., … Rao, Z. (2020). Structural basis for the inhibition of SARS-CoV-2 main protease by antineoplastic drug carmofur. Nature Structural & Molecular Biology, 27(6), 529–532. https://doi.org/https://doi.org/10.1038/s41594-020-0440-6
- Johnson, D. S., Weerapana, E., & Cravatt, B. F. (2010). Strategies for discovering and derisking covalent, irreversible enzyme inhibitors. Future Medicinal Chemistry, 2(6), 949–964. https://doi.org/https://doi.org/10.4155/fmc.10.21
- Jones, G., Willett, P., Glen, R. C., Leach, A. R., & Taylor, R. (1997). Development and validation of a genetic algorithm for flexible docking. Journal of Molecular Biology, 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
- Kasmi, Y., Khataby, K., Souiri, A., & Ennaji, M. M. (2020). Coronaviridae: 100,000 years of emergence and reemergence. In Emerging and reemerging viral pathogens (pp. 127–149). Elsevier. https://doi.org/https://doi.org/10.1016/B978-0-12-819400-3.00007-7
- Kassambara, A., & Mundt, F. (2017). Package “factoextra” for R: Extract and visualize the results of multivariate data analyses. In R package version. Boston, MA, USA: Free Software Foundation, Inc.
- 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 and Modelling, 77, 386–398. https://doi.org/https://doi.org/10.1016/j.jmgm.2017.09.010
- Khetsuriani, N., Kazerouni, N. N., Erdman, D. D., Lu, X., Redd, S. C., Anderson, L. J., & Teague, W. G. (2007). Prevalence of viral respiratory tract infections in children with asthma. The Journal of Allergy and Clinical Immunology, 119(2), 314–321. https://doi.org/https://doi.org/10.1016/j.jaci.2006.08.041
- Krieger, E., Nielsen, J. E., Spronk, C. A. E. M., & Vriend, G. (2006). Fast empirical pKa prediction by Ewald summation. Journal of Molecular Graphics & Modelling, 25(4), 481–486. https://doi.org/https://doi.org/10.1016/j.jmgm.2006.02.009
- Krieger, E., & Vriend, G. (2015). New ways to boost molecular dynamics simulations. Journal of Computational Chemistry, 36(13), 996–1007. https://doi.org/https://doi.org/10.1002/jcc.23899
- Li, J., Abel, R., Zhu, K., Cao, Y., Zhao, S., & Friesner, R. A. (2011). The VSGB 2.0 model: A next generation energy model for high resolution protein structure modeling. Proteins, 79(10), 2794–2812. https://doi.org/https://doi.org/10.1002/prot.23106
- Liu, C., Zhou, Q., Li, Y., Garner, L. V., Watkins, S. P., Carter, L. J., Smoot, J., Gregg, A. C., Daniels, A. D., Jervey, S., & Albaiu, D. (2020). Research and development on therapeutic agents and vaccines for COVID-19 and related human coronavirus diseases. ACS Central Science, 6(3), 315–331. https://doi.org/https://doi.org/10.1021/acscentsci.0c00272
- Liu, X., & Wang, X.-J. (2020). Potential inhibitors against 2019-nCoV coronavirus M protease from clinically approved medicines. Journal of Genetics and Genomics = Yi Chuan Xue Bao, 47(2), 119–121. https://doi.org/https://doi.org/10.1016/j.jgg.2020.02.001
- Lyne, P. D., Lamb, M. L., & Saeh, J. C. (2006). Accurate prediction of the relative potencies of members of a series of kinase inhibitors using molecular docking and MM-GBSA scoring. Journal of Medicinal Chemistry, 49(16), 4805–4808. https://doi.org/https://doi.org/10.1021/jm060522a
- Mah, R., Thomas, J. R., & Shafer, C. M. (2014). Drug discovery considerations in the development of covalent inhibitors. Bioorganic & Medicinal Chemistry Letters, 24(1), 33–39. https://doi.org/https://doi.org/10.1016/j.bmcl.2013.10.003
- Morris, G. M., & Lim-Wilby, M. (2008). Molecular docking. Methods in Molecular Biology (Clifton, NJ), 443, 365–382. https://doi.org/https://doi.org/10.1007/978-1-59745-177-2_19
- Motohashi, H., & Inui, K. (2013). Organic cation transporter OCTs (SLC22) and MATEs (SLC47) in the human kidney. The AAPS Journal, 15(2), 581–588. https://doi.org/https://doi.org/10.1208/s12248-013-9465-7
- Mukhametov, A., & Raevsky, O. A. (2017). On the mechanism of substrate/non-substrate recognition by P-glycoprotein. Journal of Molecular Graphics and Modelling, 71, 227–232. https://doi.org/https://doi.org/10.1016/j.jmgm.2016.12.008
- Osman, E. E. A., Toogood, P. L., & Neamati, N. (2020). COVID-19: Living through another pandemic. ACS Infectious Diseases, 6(7), 1548–1552. https://doi.org/https://doi.org/10.1021/acsinfecdis.0c00224
- R Core Team. (2014). R: A language and environment for statistical computing. R Foundation for Statistical Computing. http://www.R-project.org/.
- Rahman, M. M., Saha, T., Islam, K. J., Suman, R. H., Biswas, S., Rahat, E. U., Hossen, M. R., Islam, R., Hossain, M. N., Mamun, A., Al, Khan, M., Ali, M. A., & Halim, M. A. (2020). Virtual screening, molecular dynamics and structure–activity relationship studies to identify potent approved drugs for Covid-19 treatment. Journal of Biomolecular Structure and Dynamics, 1–11. https://doi.org/https://doi.org/10.1080/07391102.2020.1794974
- RStudio Team. (2015). RStudio: Integrated development for R. RStudio, Inc. RStudio, Inc. http://www.rstudio.com/.
- Santos, M., & Moreira, R. (2007). Michael acceptors as cysteine protease inhibitors. Mini Reviews in Medicinal Chemistry, 7(10), 1040–1050. https://doi.org/https://doi.org/10.2174/138955707782110105
- Scarpino, A., Ferenczy, G. G., & Keserű, G. M. (2018). Comparative evaluation of covalent docking tools. Journal of Chemical Information and Modeling, 58(7), 1441–1458. https://doi.org/https://doi.org/10.1021/acs.jcim.8b00228
- Trott, O., & Olson, A. (2010). s. Journal of Computational Chemistry, 31(2), 455–461. https://doi.org/https://doi.org/10.1002/jcc.21334.AutoDock
- Velavan, T. P., & Meyer, C. G. (2020). The COVID-19 epidemic. Tropical Medicine & International Health: TM & IH, 25(3), 278–280. https://doi.org/https://doi.org/10.1111/tmi.13383
- Verma, S., Dixit, R., & Pandey, K. C. (2016). Cysteine proteases: Modes of activation and future prospects as pharmacological targets. Frontiers in Pharmacology, 7, 107–112. https://doi.org/https://doi.org/10.3389/fphar.2016.00107
- Wang, F., Chen, C., Tan, W., Yang, K., & Yang, H. (2016). Structure of main protease from human coronavirus NL63: Insights for wide spectrum anti-coronavirus drug design. Scientific Reports, 6, 22677–22612. https://doi.org/https://doi.org/10.1038/srep22677
- Watts, K. S., Dalal, P., Murphy, R. B., Sherman, W., Friesner, R. A., & Shelley, J. C. (2010). ConfGen: A conformational search method for efficient generation of bioactive conformers. Journal of Chemical Information and Modeling, 50(4), 534–546. https://doi.org/https://doi.org/10.1021/ci100015j
- 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
- Wu, F., Zhao, S., Yu, B., Chen, Y.-M., Wang, W., Song, Z.-G., Hu, Y., Tao, Z.-W., Tian, J.-H., Pei, Y.-Y., Yuan, M.-L., Zhang, Y.-L., Dai, F.-H., Liu, Y., Wang, Q.-M., Zheng, J.-J., Xu, L., Holmes, E. C., & Zhang, Y.-Z. (2020). A new coronavirus associated with human respiratory disease in China. Nature, 579(7798), 265–269. https://doi.org/https://doi.org/10.1038/s41586-020-2008-3
- 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., Lin, D., Sun, X., Curth, U., Drosten, C., Sauerhering, L., Becker, S., Rox, K., & Hilgenfeld, R. (2020). Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors. Science, 368(6489), 409–412. https://doi.org/https://doi.org/10.1126/science.abb3405
- Zheng, Y.-Y., Ma, Y.-T., Zhang, J.-Y., & Xie, X. (2020). COVID-19 and the cardiovascular system. Nature Reviews. Cardiology, 17(5), 259–260. https://doi.org/https://doi.org/10.1038/s41569-020-0360-5
- Zhu, K., Borrelli, K. W., Greenwood, J. R., Day, T., Abel, R., Farid, R. S., & Harder, E. (2014). Docking covalent inhibitors: A parameter free approach to pose prediction and scoring. Journal of Chemical Information and Modeling, 54(7), 1932–1940. https://doi.org/https://doi.org/10.1021/ci500118s