References
- Bagchi, A. (2020). Unusual nature of long non-coding RNAs coding for ‘unusual peptides’. Gene, 729, 144298. https://doi.org/10.1016/j.gene.2019
- Berendsen, H. J. C., Grigera, J. R., & Straatsma, T. P. (1987). The missing term in effective pair potentials. The Journal of Physical Chemistry, 91(24), 6269–6271. https://doi.org/10.1021/j100308a038
- Biswas, S., Roy, R., Biswas, R., & Bagchi, A. (2020). Structural analysis of the effects of mutations in Ubl domain of Parkin leading to Parkinson’s disease. Gene, 726, 144186. https://doi.org/10.1016/j.gene.2019
- Bodiwala, H. S., Sabde, S., Mitra, D., Bhutani, K. K., & Singh, I. P. (2011). Synthesis of 9-substituted derivatives of berberine as anti-HIV agents. European Journal of Medicinal Chemistry, 46(4), 1045-1049. https://doi.org/10.1016/j.ejmech.2011.01.016
- Calligari, P., Bobone, S., Ricci, G., & Bocedi, A. (2020). Molecular investigation of SARS-CoV-2 proteins and their interactions with antiviral drugs. Viruses, 12(4), 445. https://doi.org/10.3390/v12040445
- Cava, C., Bertoli, G., & Castiglioni, I. (2020). Silico discovery of candidate drugs against Covid-19. Viruses, 12(4), 404. https://doi.org/10.3390/v12040404
- Chen Cao, Y., Xin Deng, Q., & Xue Dai, S. (2020). Remdesivir for severe acute respiratory syndrome coronavirus 2 causing COVID-19: An evaluation of the evidence. Travel Medicine and Infectious Disease, 35, 101647. https://doi.org/10.1016/j.tmaid.2020.101647
- Chen, Y. W., Yiu, C. B., & Wong, K. Y. (2020). Prediction of the SARS-CoV-2 (2019-nCoV) 3C-like protease (3CL pro) structure: Virtual screening reveals velpatasvir, ledipasvir, and other drug repurposing candidates. Version 2. F1000Research, 9, 129. https://doi.org/10.12688/f1000research.22457.2
- Cosconati, S., Forli, S., Perryman, A. L., Harris, R., Goodsell, D. S., & Olson, A. J. (2010). Virtual screening with AutoDock: Theory and practice. Expert Opinion on Drug Discovery, 5(6), 597–607. https://doi.org/10.1517/17460441.2010.484460
- De Tommasi, N., De Simone, F., Pizza, C., Mahmood, N., Moore, P. S., Conti, C., Orsi, N., & Stein, M. L. (1992). Constituents of Eriobotrya japonica. A study of their antiviral properties. Journal of Natural Products, 55(8), 1067–1073. https://doi.org/10.1021/np50086a006
- Eisenberg, D., Lüthy, R., & Bowie, J. U. (1997). VERIFY3D: Assessment of protein models with three-dimensional profiles. Methods in Enzymology, 277, 396–406. https://doi.org/10.1016/S0076-6879(97)77022-8
- Elfiky, A. A. (2020). Anti-HCV, nucleotide inhibitors, repurposing against COVID-19. Life Sciences, 248, 117477. https://doi.org/10.1016/j.lfs.2020.117477 Epub 2020 Feb 28.
- Fung, S. Y., Yuen, K. S., Ye, Z. W., Chan, C. P., & Jin, D. Y. (2020). A tug-of-war between severe acute respiratory syndrome coronavirus 2 and host antiviral defence: Lessons from other pathogenic viruses. Emerging Microbes and Infections, 9, 558-570. https://doi.org/10.1080/22221751.2020.1736644.
- Gasteiger, E., Gattiker, A., Hoogland, C., Ivanyi, I., Appel, R. D., & Bairoch, A. (2003). ExPASy: The proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Research, 31, 3784–3788. https://doi.org/10.1093/nar/gkg563
- Gaulton, A., Hersey, A., Nowotka, M., Bento, A. P., Chambers, J., Mendez, D., Mutowo, P., Atkinson, F., Bellis, L. J., Cibrián-Uhalte, E., Davies, M., Dedman, N., Karlsson, A., Magariños, M. P., Overington, J. P., Papadatos, G., Smit, I., & Leach, A. R. (2017). The ChEMBL database in 2017. Nucleic Acids Research, 45(D1), D945–D954. https://doi.org/10.1093/nar/gkw1074
- Hess, B., Bekker, H., Berendsen, H. J. C., & Fraaije, J. G. E. M. (1997). LINCS: A linear constraint solver for molecular simulations. Journal of Computational Chemistry, 18(12), 1463–1472. https://doi.org/10.1002/(SICI)1096-987X(199709)18:12 < 1463::AID-JCC4 > 3.0.CO;2-H
- Ibrahim, I. M., Abdelmalek, D. H., Elshahat, M. E., & Elfiky, A. A. (2020). COVID-19 spike-host cell receptor GRP78 binding site prediction. The Journal of Infection, 80(5), 554–562. https://doi.org/10.1016/j.jinf.2020.02.026
- Jiménez-Alberto, A., Ribas-Aparicio, R. M., Aparicio-Ozores, G., & Castelán-Vega, J. A. (2020). Virtual screening of approved drugs as potential SARS-CoV-2 main protease inhibitors. Computational Biology and Chemistry, 88, 107325. https://doi.org/10.1016/j.compbiolchem.2020.107325
- Kamitani, W., Huang, C., Narayanan, K., Lokugamage, K. G., & Makino, S. (2009). A two-pronged strategy to suppress host protein synthesis by SARS coronavirus Nsp1 protein. Nature Structural & Molecular Biology, 16, 1134–1140. https://doi.org/10.1038/nsmb.1680
- Kelley, L. A., Mezulis, S., Yates, C. M., Wass, M. N., & Sternberg, M. J. E. (2015). The Phyre2 web portal for protein modeling, prediction and analysis. Nature Protocols, 10, 845-858. https://doi.org/10.1038/nprot.2015.053
- Laskowski, R. A., MacArthur, M. W., Moss, D. S., & Thornton, J. M. (1993). PROCHECK: A program to check the stereochemical quality of protein structures. Journal of Applied Crystallography, 26(2), 283–291. https://doi.org/10.1107/S0021889892009944
- Liang, J., Pitsillou, E., Karagiannis, C., Darmawan, K. K., Ng, K., Hung, A., & Karagiannis, T. C. (2020). Interaction of the prototypical α-ketoamide inhibitor with the SARS-CoV-2 main protease active site in silico: Molecular dynamic simulations highlight the stability of the ligand-protein complex. Computational Biology and Chemistry, 87, 107292. https://doi.org/10.1016/j.compbiolchem.2020.107292
- Mohamed, S. F., Flefel, E. M., Amr, A. E. G. E., & Abd El-Shafy, D. N. (2010). Anti-HSV-1 activity and mechanism of action of some new synthesized substituted pyrimidine, thiopyrimidine and thiazolopyrimidine derivatives. European Journal of Medicinal Chemistry, 45, 1494-1501. https://doi.org/10.1016/j.ejmech.2009.12.057
- Narayanan, K., Huang, C., Lokugamage, K., Kamitani, W., Ikegami, T., Tseng, C.-T K., & Makino, S. (2008). Severe acute respiratory syndrome coronavirus nsp1 suppresses host gene expression, including that of type I interferon, in infected cells. Journal of Virology, 82(9), 4471–4479. https://doi.org/10.1128/JVI.02472-07
- Osorio, A. A., Munoz, A., Torres-Romero, D., Bedoya, L. M., Perestelo, N. R., Jimenez, I. A., Alcami, J., & Bazzocchi, I. L. (2012). Olean-18-ene triterpenoids from Celastraceae species inhibit HIV replication targeting NF-kB and Sp1 dependent transcription. European Journal of Medicinal Chemistry, 43(38), no–no. https://doi.org/10.1016/j.ejmech.2012.03.035
- Sagui, C., & Darden, T. A. (1999). Molecular dynamics simulations of biomolecules: Long-range electrostatic effects. Annual Review of Biophysics and Biomolecular Structure, 28(1), 155–179. https://doi.org/10.1146/annurev.biophys
- Sahin, A. R. (2020). 2019 Novel Coronavirus (COVID-19) outbreak: A review of the current literature. Eurasian Journal of Medicine and Oncology, 4, 1-7. https://doi.org/10.14744/ejmo.2020.12220
- Shiryaev, S. A., Cheltsov, A. V., Gawlik, K., Ratnikov, B. I., & Strongin, A. Y. (2011). Virtual ligand screening of the national cancer institute (NCI) compound library leads to the allosteric inhibitory scaffolds of the West Nile virus NS3 proteinase. Assay and Drug Development Technologies, 9, 69-78. https://doi.org/10.1089/adt.2010.0309
- Tilocca, B., Soggiu, A., Sanguinetti, M., Musella, V., Britti, D., Bonizzi, L., Urbani, A., & Roncada, P. (2020). Comparative computational analysis of SARS-CoV-2 nucleocapsid protein epitopes in taxonomically related coronaviruses. Microbes and Infection, 22, 188–194. https://doi.org/10.1016/j.micinf.2020.04.002
- Van Der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., & Berendsen, H. J. C. (2005). GROMACS: Fast, flexible, and free. Journal of Computational Chemistry, 26(16), 1701–1718. https://doi.org/10.1002/jcc.20291
- Wiederstein, M., & Sippl, M. J. (2007). ProSA-web: Interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Research, 35(Web Server issue), W407-10. https://doi.org/10.1093/nar/gkm290
- Wu, C. (2020). Analysis of therapeutic targets for SARS-CoV-2 and discovery of potential drugs by computational methods. Acta Pharmaceutica Sinica B, 10, 766-788. https://doi.org/10.1016/j.apsb.2020.02.008
- Yeo, H., Li, Y., Fu, L., Zhu, J.-L., Gullen, E. A., Dutschman, G. E., Lee, Y., Chung, R., Huang, E.-S., Austin, D. J., & Cheng, Y.-C. (2005). Synthesis and antiviral activity of helioxanthin analogues. Journal of Medicinal Chemistry, 48(2), 534–546. https://doi.org/10.1021/jm034265a
- Yu, F., Wang, Q., Zhang, Z., Peng, Y., Qiu, Y., Shi, Y., Zheng, Y., Xiao, S., Wang, H., Huang, X., Zhu, L., Chen, K., Zhao, C., Zhang, C., Yu, M., Sun, D., Zhang, L., & Zhou, D. (2013). Development of oleanane-type triterpenes as a new class of HCV entry inhibitors. Journal of Medicinal Chemistry, 56(11), 4300–4319. https://doi.org/10.1021/jm301910a