References
- Amaral, J. L., Santos, S. J. M., Souza, P. F. N., de Morais, P. A., Maia, F. F., Carvalho, H. F., & Freire, V. N. (2020). Quantum biochemistry in cancer immunotherapy: New insights about CTLA-4/ipilimumab and design of ipilimumab-derived peptides with high potential in cancer treatment. Molecular Immunology, 127, 203–211. https://doi.org/https://doi.org/10.1016/j.molimm.2020.09.013
- 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
- Burrell, C. J., Howard, C. R., & Murphy, F. A. (2017). Chapter 13 – Coronaviruses. In Fenner and White’s Medical Virology, 5th ed, pp. 437–446. Elsevier. https://doi.org/https://doi.org/10.1016/B978-0-12-375156-0.00031-X.
- 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), 445–460. https://doi.org/https://doi.org/10.3390/v12040445
- Campos, D. M. O., Bezerra, K. S., Esmaile, S. C., Fulco, U. L., Albuquerque, E. L., & Oliveira, J. I. N. (2020). Intermolecular interactions of cn-716 and acyl-KR-aldehyde dipeptide inhibitors against Zika virus. Physical Chemistry Chemical Physics: PCCP, 22(27), 15683–15695. https://doi.org/https://doi.org/10.1039/d0cp02254c
- Choudhary, S., Malik, Y. S., & Tomar, S. (2020). Identification of SARS-CoV-2 cell entry inhibitors by drug repurposing using in silico structure-based virtual screening approach. Frontiers in Immunology, 11, 1664. https://doi.org/https://doi.org/10.3389/fimmu.2020.01664
- de Oliveira, O. V., Rocha, G. B., Paluch, A. S., & Costa, L. T. (2020). Repurposing approved drugs as inhibitors of SARS-CoV-2 S-protein from molecular modeling and virtual screening. Journal of Biomolecular Structure and Dynamics, 15, 1–10. https://doi.org/https://doi.org/10.1080/07391102.2020.1772885.
- Delley, B. (2000). From molecules to solids with the DMol3 approach. Journal of Chemical Physics, 113(18), 7756–7764. https://doi.org/https://doi.org/10.1063/1.1316015
- Diamond, M. S., & Pierson, T. C. (2020). The challenges of vaccine development against a new virus during a pandemic. Cell Host & Microbe, 27(5), 699–703. https://doi.org/https://doi.org/10.1016/j.chom.2020.04.021
- Elfiky, A. A. (2020). Ribavirin, Remdesivir, Sofosbuvir, Galidesivir, and Tenofovir against SARS-CoV-2 RNA dependent RNA polymerase (RdRp): A molecular docking study. Life Sciences, 253, 117592. https://doi.org/https://doi.org/10.1016/j.lfs.2020.117592
- Hoffmann, M., Kleine-Weber, H., Schroeder, S., Krüger, N., Herrler, T., Erichsen, S., Schiergens, T. S., Herrler, G., Wu, N. H., Nitsche, A., Müller, M. A., Drosten, C., & Pöhlmann, S. (2020). SARS-CoV-2 cell entry depends on ACE2 and TMPRSS2 and is blocked by a clinically proven protease inhibitor. Cell, 181(2), 271–280.e8. https://doi.org/https://doi.org/10.1016/j.cell.2020.02.052
- Korber, B., Fischer, W. M., Gnanakaran, S., Yoon, H., Theiler, J., Abfalterer, W., Hengartner, N., Giorgi, E. E., Bhattacharya, T., Foley, B., Hastie, K. M., Parker, M. D., Partridge, D. G., Evans, C. M., Freeman, T. M., de Silva, T. I., McDanal, C., Perez, L. G., Tang, H., … Montefiori, D. C, Sheffield COVID-19 Genomics Group (2020). Tracking changes in SARS-CoV-2 spike: Evidence that D614G increases infectivity of the COVID-19 virus. Cell, 182(4), 812–827. https://doi.org/https://doi.org/10.1016/j.cell.2020.06.043
- Laskowski, R. A., & Swindells, M. B. (2011). LigPlot+: Multiple ligand-protein interaction diagrams for drug discovery. Journal of Chemical Information and Modeling, 51(10), 2778–2786. https://doi.org/https://doi.org/10.1021/ci200227u
- Li, H., Liu, L., Zhang, D., Xu, J., Dai, H., Tang, N., Su, X., & Cao, B. (2020). SARS-CoV-2 and viral sepsis: Observations and hypotheses. Lancet (London, England), 395(10235), 1517–1520. https://doi.org/https://doi.org/10.1016/S0140-6736(20)30920-X
- Li, Q., Guan, X., Wu, P., Wang, X., Zhou, L., Tong, Y., Ren, R., Leung, K. S. M., Lau, E. H. Y., Wong, J. Y., Xing, X., Xiang, N., Wu, Y., Li, C., Chen, Q., Li, D., Liu, T., Zhao, J., Liu, M. … Feng, Z. (2020). Early transmission dynamics in Wuhan, China, of novel coronavirus-infected pneumonia. The New England Journal of Medicine, 382(13), 1199–1207. https://doi.org/https://doi.org/10.1056/NEJMoa2001316
- Meher, P. K., Sahu, T. K., & Rao, A. R. (2016). Prediction of donor splice sites using random forest with a new sequence encoding approach. BioData Mining, 9, 4. https://doi.org/https://doi.org/10.1186/s13040-016-0086-4
- Moal, I. H., & Bates, P. A. (2010). SwarmDock and the use of normal modes in protein-protein docking. International Journal of Molecular Sciences, 11(10), 3623–3648. https://doi.org/https://doi.org/10.3390/ijms11103623
- Morais, P. A., Maia, F. F., Solis-Calero, C., Caetano, E. W. S., Freire, V. N., & Carvalho, H. F. (2020). The urokinase plasminogen activator binding to its receptor: A quantum biochemistry description within an in/homogeneous dielectric function framework with application to uPA-uPAR peptide inhibitors. Physical Chemistry Chemical Physics, 22(6), 3570–3583. https://doi.org/https://doi.org/10.1039/C9CP06530J
- Moreira, R. A., Chwastyk, M., Baker, J. L., Guzman, H. V., & Poma, A. B. (2020). Quantitative determination of mechanical stability in the novel coronavirus spike protein. Nanoscale, 12(31), 16409–16413. https://doi.org/https://doi.org/10.1039/d0nr03969a
- Peiris, J. S. M. (2012). Coronaviruses. In Medical Microbiology, 18th ed, pp. 587–593. Elsevier. https://doi.org/https://doi.org/10.1016/B978-0-7020-4089-4.00072-X.
- Qiao, B., & Olvera de la Cruz, M. (2020). Enhanced binding of SARS-CoV-2 spike protein to receptor by distal polybasic cleavage sites. ACS Nano, 14(8), 10616–10623. https://doi.org/https://doi.org/10.1021/acsnano.0c04798
- Ramírez-Aportela, E., López-Blanco, J. R., & Chacón, P. (2016). FRODOCK 2.0: Fast protein-protein docking server. Bioinformatics (Oxford, England), 32(15), 2386–2388. https://doi.org/https://doi.org/10.1093/bioinformatics/btw141
- Robertson, M. J., Tirado-Rives, J., & Jorgensen, W. L. (2015). Improved peptide and protein torsional energetics with the OPLSAA force field. Journal of Chemical Theory and Computation, 11(7), 3499–3509. https://doi.org/https://doi.org/10.1021/acs.jctc.5b00356
- Shen, Y., Maupetit, J., Derreumaux, P., & Tufféry, P. (2014). Improved PEP-FOLD approach for peptide and miniprotein structure prediction. Journal of Chemical Theory and Computation, 10(10), 4745–4758. https://doi.org/https://doi.org/10.1021/ct500592m
- Song, Z., Xu, Y., Bao, L., Zhang, L., Yu, P., Qu, Y., Zhu, H., Zhao, W., Han, Y., & Qin, C. (2019). From SARS to MERS, thrusting coronaviruses into the spotlight. Viruses, 11(1), 59. https://doi.org/https://doi.org/10.3390/v11010059
- Souza, P. F. N., Lopes, F. E. S., Amaral, J. L., Freitas, C. D. T., & Oliveira, J. T. A. (2020). A molecular docking study revealed that synthetic peptides induced conformational changes in the structure of SARS-CoV-2 spike glycoprotein, disrupting the interaction with human ACE2 receptor. International Journal of Biological Macromolecules, 164, 66–76. https://doi.org/https://doi.org/10.1016/j.ijbiomac.2020.07.174
- Souza, P. F. N., Marques, L. S. M., Oliveira, J. T. A., Lima, P. G., Dias, L. P., Neto, N. A. S., Lopes, F. E. S., Sousa, J. S., Silva, A. F. B., Caneiro, R. F., Lopes, J. L. S., Ramos, M. V., & Freitas, C. D. T. (2020). Synthetic antimicrobial peptides: From choice of the best sequences to action mechanisms. Biochimie, 175, 132–145. https://doi.org/https://doi.org/10.1016/j.biochi.2020.05.016
- Tay, M. Z., Poh, C. M., Rénia, L., MacAry, P. A., & Ng, L. F. P. (2020). The trinity of COVID-19: Immunity, inflammation and intervention. Nature Reviews Immunology, 20(6), 363–374. https://doi.org/https://doi.org/10.1038/s41577-020-0311-8
- Thakur, N., Qureshi, A., & Kumar, M. (2012). AVPpred: Collection and prediction of highly effective antiviral peptides. Nucleic Acids Research, 40(Web Server issue), W199–W204. https://doi.org/https://doi.org/10.1093/nar/gks450
- Walls, A. C., Park, Y.-J., Tortorici, M. A., Wall, A., McGuire, A. T., & Veesler, D. (2020). Structure, function, and antigenicity of the SARS-CoV-2 spike glycoprotein. Cell, 181(2), 281–292.e6. https://doi.org/https://doi.org/10.1016/j.cell.2020.02.058
- Wrapp, D., Wang, N., Corbett, K. S., Goldsmith, J. A., Hsieh, C. L., Abiona, O., Graham, B. S., & McLellan, J. S. (2020). Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. Science (New York, NY), 367(6483), 1260–1263. https://doi.org/https://doi.org/10.1126/science.abb2507
- Wu, C., Liu, Y., Yang, Y., Zhang, P., Zhong, W., Wang, Y., Wang, Q., Xu, Y., Li, M., Li, X., Zheng, M., Chen, L., & Li, H. (2020). Analysis of therapeutic targets for SARS-CoV-2 and discovery of potential drugs by computational methods. Acta Pharmaceutica Sinica. B, 10(5), 766–788. https://doi.org/https://doi.org/10.1016/j.apsb.2020.02.008
- Yan, R., Zhang, Y., Li, Y., Xia, L., Guo, Y., & Zhou, Q. (2020). Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2. Science (New York, NY), 367(6485), 1444–1448. https://doi.org/https://doi.org/10.1126/science.abb2762
- Yuan, Y., Cao, D., Zhang, Y., Ma, J., Qi, J., Wang, Q., Lu, G., Wu, Y., Yan, J., Shi, Y., Zhang, X., & Gao, G. F. (2017). Cryo-EM structures of MERS-CoV and SARS-CoV spike glycoproteins reveal the dynamic receptor binding domains. Nature Communications, 8, 15092. https://doi.org/https://doi.org/10.1038/ncomms15092
- Zhang, Y., Xu, J., Jia, R., Yi, C., Gu, W., Liu, P., Dong, X., Zhou, H., Shang, B., Cheng, S., Sun, X., Ye, J., Li, X., Zhang, J., Ling, Z., Ma, L., Wu, B., Zeng, M., Zhou, W., & Sun, B. (2020). Protective humoral immunity in SARS-CoV-2 infected pediatric patients. Cellular & Molecular Immunology, 17(7), 768–770. https://doi.org/https://doi.org/10.1038/s41423-020-0438-3
- Zhang, D. W., & Zhang, J. Z. H. (2003). Molecular fractionation with conjugate caps for full quantum mechanical calculation of protein-molecule interaction energy. Journal of Chemical Physics, 119(7), 3599–3605. https://doi.org/https://doi.org/10.1063/1.1591727
- Zhou, P., Yang, X. L., Wang, X. G., Hu, B., Zhang, L., Zhang, W., Si, H. R., Zhu, Y., Li, B., Huang, C. L., Chen, H. D., Chen, J., Luo, Y., Guo, H., Jiang, R. D., Liu, M. Q., Chen, Y., Shen, X. R., Wang, X. … Shi, Z.-L. (2020). A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature, 579(7798), 270–273. https://doi.org/https://doi.org/10.1038/s41586-020-2012-7