References
- Aarthy, H., Panwar, U., & Singh, S. K. (2020). Structural dynamic studies on identification of EGCG analogues for the inhibition of Human Papillomavirus E7. Scientific Reports, 10(1), 1–24. https://doi.org/https://doi.org/10.1038/s41598-020-65446-7
- Abraham, M. J., Murtola, T., Schulz, R., Páll, S., Smith, J. C., Hess, B., & Lindahl, E. (2015). Gromacs: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX, 1–2, 19–25. https://doi.org/https://doi.org/10.1016/j.softx.2015.06.001
- Aminin, D., & Polonik, S. (2020). 1,4-naphthoquinones: Some biological properties and application. Chemical & Pharmaceutical Bulletin, 68(1), 46–57. https://doi.org/https://doi.org/10.1248/cpb.c19-00911
- 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), 450–453. https://doi.org/https://doi.org/10.1038/s41591-020-0820-9
- Araújo, I. A. C., de Paula, R. C., Alves, C. L., Faria, K. F., Oliveira, M. M. D., Mendes, G. G., Dias, E. M. F. A., Ribeiro, R. R., Oliveira, A. B. D., & Silva, S. M. D. (2019). Efficacy of lapachol on treatment of cutaneous and visceral leishmaniasis. Experimental Parasitology, 199, 67–73. https://doi.org/https://doi.org/10.1016/j.exppara.2019.02.013
- Bartlam, M., Yang, H., & Rao, Z. (2005). Structural insights into SARS coronavirus proteins. Current Opinion in Structural Biology, 15(6), 664–672. https://doi.org/https://doi.org/10.1016/j.sbi.2005.10.004
- Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., DiNola, A., & Haak, J. R. (1984). Molecular dynamics with coupling to an external bath. The Journal of Chemical Physics, 81(8), 3684–3690. https://doi.org/https://doi.org/10.1063/1.448118
- Bharadwaj, S., Azhar, E. I., Kamal, M. A., Bajrai, L. H., Dubey, A., Jha, K., Yadava, U., Kang, S. G. and Dwivedi, V. D. (2020). SARS-CoV-2 Mpro inhibitors: Identification of anti-SARS-CoV-2 Mpro compounds from FDA approved drugs. Journal of Biomolecular Structure and Dynamics, 1–16.
- Block, J. B., Serpick, A. A., Miller, W., & Wiernik, P. H. (1974). Early clinical studies with lapachol (NSC-11905). Cancer Chemotherapy Reports. Part 2, 4(4), 27–28.
- Buonaguro, L., Tagliamonte, M., Tornesello, M. L., & Buonaguro, F. M. (2020). SARS-CoV-2 RNA polymerase as target for antiviral therapy. Journal of Translational Medicine, 18(1), 185. https://doi.org/https://doi.org/10.1186/s12967-020-02355-3
- Chan, J. F.-W., Kok, K.-H., Zhu, Z., Chu, H., To, K. K.-W., Yuan, S., & Yuen, K.-Y. (2020). Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan. Emerging Microbes & Infections, 9(1), 221–236. https://doi.org/https://doi.org/10.1080/22221751.2020.1719902
- Chhikara, B. S., Rathi, B., Singh, J., & Poonam, F. N. U. (2020). Corona virus SARS-CoV-2 disease COVID-19: Infection, prevention and clinical advances of the prospective chemical drug therapeutics. Chemical Biology Letters, 7(1), 63–72.
- Costa, M., Feitosa, A., Oliveira, F., Cavalcanti, B., Da Silva, E., Dias, G., Sales, F., Sousa, B., Barroso-Neto, I., Pessoa, C., Caetano, E., Di Fiore, S., Fischer, R., Ladeira, L., & Freire, V. (2016). Controlled Release of Nor-β-lapachone by PLGA Microparticles: A Strategy for Improving Cytotoxicity against Prostate Cancer Cells. Molecules, 21(7), 873. https://doi.org/https://doi.org/10.3390/molecules21070873
- da Silva Júnior, E. N., Jardim, G. A. M., Jacob, C., Dhawa, U., Ackermann, L., & de Castro, S. L. (2019). Synthesis of quinones with highlighted biological applications: A critical update on the strategies towards bioactive compounds with emphasis on lapachones. European Journal of Medicinal Chemistry, 179, 863–915. https://doi.org/https://doi.org/10.1016/j.ejmech.2019.06.056
- de Sá, N. P., Cisalpino, P. S., Bertollo, C. M., Santos, P. C., Rosa, C. A., de Souza, D. D. G., Barbeira, P. J. S., Alves, T. M. D. A., Zani, C. L., & Johann, S. (2019). Thiosemicarbazone of lapachol acts on cell membrane in Paracoccidioides brasiliensis. Medical Mycology, 57(3), 332–339. https://doi.org/https://doi.org/10.1093/mmy/myy045
- Dias, D. A., Urban, S., & Roessner, U. (2012). A historical overview of natural products in drug discovery. Metabolites, 2(2), 303–336. https://doi.org/https://doi.org/10.3390/metabo2020303
- Doremalen, N. V., Bushmaker, T., Morris, D. H., Holbrook, M. G., Gamble, A., Williamson, B. N., Tamin, A., Harcourt, J. L., Thornburg, N. J., Gerber, S. I., & Lloyd-Smith, J. O. (2020). Aerosol and surface stability of SARS-CoV-2 as compared with SARS-CoV-1. New England Journal of Medicine, 382(16), 1564–1567.
- Egloff, M.-P., Ferron, F., Campanacci, V., Longhi, S., Rancurel, C., Dutartre, H., Snijder, E. J., Gorbalenya, A. E., Cambillau, C., & Canard, B. (2004). The severe acute respiratory syndrome-coronavirus replicative protein nsp9 is a single-stranded RNA-binding subunit unique in the RNA virus world. Proceedings of the National Academy of Sciences of the United States of America, 101(11), 3792–3796. https://doi.org/https://doi.org/10.1073/pnas.0307877101
- Essmann, U., Perera, L., Berkowitz, M. L., Darden, T., Lee, H., & Pedersen, L. G. (1995). A smooth particle mesh Ewald method. The Journal of Chemical Physics, 103(19), 8577–8593. https://doi.org/https://doi.org/10.1063/1.470117
- Flynn, R. L., & Zou, L. (2010). Oligonucleotide/oligosaccharide-binding fold proteins: A growing family of genome guardians. Critical Reviews in Biochemistry and Molecular Biology, 45(4), 266–275. https://doi.org/https://doi.org/10.3109/10409238.2010.488216
- Frieman, M., Yount, B., Agnihothram, S., Page, C., Donaldson, E., Roberts, A., Vogel, L., Woodruff, B., Scorpio, D., Subbarao, K., & Baric, R. S. (2012). Molecular determinants of severe acute respiratory syndrome coronavirus pathogenesis and virulence in young and aged mouse models of human disease. Journal of Virology, 86(2), 884–897. https://doi.org/https://doi.org/10.1128/JVI.05957-11
- Genheden, S., & Ryde, U. (2015). The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities. Expert Opinion on Drug Discovery, 10(5), 449–461. https://doi.org/https://doi.org/10.1517/17460441.2015.1032936
- 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. 30 abr. https://doi.org/https://doi.org/10.1038/s41586-020-2286-9
- Hsu, L. Y., Chia, P. Y., & Lim, J. F. (2020). The novel coronavirus (SARS-CoV-2) epidemic. Annals of the Academy of Medicine, Singapore, 49(3), 105–103. https://doi.org/https://doi.org/10.47102/annals-acadmedsg.202051
- Huang, B. (2009). MetaPocket: A meta approach to improve protein ligand binding site prediction. Omics : A Journal of Integrative Biology, 13(4), 325–330. https://doi.org/https://doi.org/10.1089/omi.2009.0045
- Hussain, H., & Green, I. R. (2017). Lapachol and lapachone analogs: A journey of two decades of patent research(1997-2016). Expert Opinion on Therapeutic Patents, 27(10), 1111–1121. https://doi.org/https://doi.org/10.1080/13543776.2017.1339792
- Jones, G., Willett, P., & Glen, R. C. (1995). Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation. Journal of Molecular Biology, 245(1), 43–53. https://doi.org/https://doi.org/10.1016/S0022-2836(95)80037-9
- Kim, D., Lee, J. Y., Yang, J. S., Kim, J. W., Kim, V. N., & Chang, H. (2020). The architecture of SARS-CoV-2 transcriptome. Cell, 181(4), 914-921.
- Kostal, J. (2016). Computational Chemistry in Predictive Toxicology: Status quo et quo vadis? In J. C. Fishbein & J. M. Heilman, (Eds.). Advances in molecular toxicology (Vol. 10, pp. 139–186). Elsevier. Chapter 4.
- Lai, C.-C., Liu, Y. H., Wang, C. Y., Wang, Y. H., Hsueh, S. C., Yen, M. Y., Ko, W. C., & Hsueh, P. R. (2020). Asymptomatic carrier state, acute respiratory disease, and pneumonia due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2): Facts and myths. Journal of Microbiology, Immunology, and Infection = Wei Mian Yu Gan Ran Za Zhi, 53(3), 404-412.
- Lai, M. M., & Stohlman, S. A. (1981). Comparative analysis of RNA genomes of mouse hepatitis viruses. Journal of Virology, 38(2), 661–670. https://doi.org/https://doi.org/10.1128/JVI.38.2.661-670.1981
- 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
- Littler, D. R., Gully, B. S., Colson, R. N., & Rossjohn, J. (2020). Crystal structure of the SARS-CoV-2 non-structural protein 9, Nsp9. Iscience, 23(7), 101258.
- Maréchal, Y. (2007). The hydrogen bond: Formation, thermodynamic properties, classification. In Y. Maréchal (Ed.), The hydrogen bond and the water molecule (pp. 3–24). Elsevier.
- Massova, I., & Kollman, P. A. (2000). Combined molecular mechanical and continuum solvent approach (MM-PBSA/GBSA) to predict ligand binding. Perspectives in Drug Discovery and Design, 18(1), 113–135. https://doi.org/https://doi.org/10.1023/A:1008763014207
- Miknis, Z. J., Donaldson, E. F., Umland, T. C., Rimmer, R. A., Baric, R. S., & Schultz, L. W. (2009). Severe acute respiratory syndrome coronavirus nsp9 dimerization is essential for efficient viral growth. Journal of Virology, 83(7), 3007–3018. https://doi.org/https://doi.org/10.1128/JVI.01505-08
- Nasiri, H. R., Madej, M. G., Panisch, R., Lafontaine, M., Bats, J. W., Lancaster, C. R. D., & Schwalbe, H. (2013). Design, Synthesis, and Biological Testing of Novel Naphthoquinones as Substrate-Based Inhibitors of the Quinol/Fumarate Reductase from Wolinella succinogenes. Journal of Medicinal Chemistry, 56(23), 9530–9541. https://doi.org/https://doi.org/10.1021/jm400978u
- Needleman, S. B., & Wunsch, C. D. (1970). A general method applicable to the search for similarities in the amino acid sequence of two proteins. Journal of Molecular Biology, 48(3), 443–453. https://doi.org/https://doi.org/10.1016/0022-2836(70)90057-4
- Oguntade, S., Ramharack, P., & Soliman, M. E. (2017). Characterizing the ligand-binding landscape of Zika NS3 helicase-promising lead compounds as potential inhibitors. Future Virology, 12(6), 261–273. https://doi.org/https://doi.org/10.2217/fvl-2017-0014
- Oliveira, K. M., Corrêa, R. S., Barbosa, M. I. F., Ellena, J., Cominetti, M. R., & Batista, A. A. (2017). Ruthenium (II)/triphenylphosphine complexes: An effective way to improve the cytotoxicity of lapachol. Polyhedron, 130, 108–114. https://doi.org/https://doi.org/10.1016/j.poly.2017.04.005
- Oliveira, M. F., Lemos, T. G., de Mattos, M. C., Segundo, T. A., Santiago, G. M. P., & Braz-Filho, R. (2002). New enamine derivatives of lapachol and biological activity. Anais da Academia Brasileira de Ciencias, 74(2), 211–221. https://doi.org/https://doi.org/10.1590/s0001-37652002000200004
- Parrinello, M., & Rahman, A. (1980). Crystal structure and pair potentials: A molecular-dynamics study. Physical Review Letters, 45(14), 1196–1199. https://doi.org/https://doi.org/10.1103/PhysRevLett.45.1196
- Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004). UCSF Chimera-a visualization system for exploratory research and analysis. Journal of Computational Chemistry, 25(13), 1605–1612. https://doi.org/https://doi.org/10.1002/jcc.20084 15264254
- Pinto, A. V., Pinto, M. d C., Lagrota, M. H., Wigg, M. D., & Aguiar, A. N. (1987). Antiviral activity of naphthoquinones. I. Lapachol derivatives against enteroviruses. Revista Latinoamericana de Microbiologia, 29(1), 15–20.
- Pires, D. E. V., Blundell, T. L., & Ascher, D. B. (2015). pkCSM: Predicting small-molecule pharmacokinetic and toxicity properties using graph-based signatures. Journal of Medicinal Chemistry, 58(9), 4066–4072. https://doi.org/https://doi.org/10.1021/acs.jmedchem.5b00104
- Ponnusamy, R., Moll, R., Weimar, T., Mesters, J. R., & Hilgenfeld, R. (2008). Variable oligomerization modes in coronavirus non-structural protein 9. Journal of Molecular Biology, 383(5), 1081–1096. https://doi.org/https://doi.org/10.1016/j.jmb.2008.07.071
- Robertson, M. P., Igel, H., Baertsch, R., Haussler, D., Ares, M., & Scott, W. G. (2004). The Structure of a rigorously conserved RNA element within the SARS virus genome. PLoS Biology, 3(1), e5. https://doi.org/https://doi.org/10.1371/journal.pbio.0030005
- Rout, J., Swain, B. C., & Tripathy, U. (2020). In silico investigation of spice molecules as potent inhibitor of SARS-CoV-2. Journal of Biomolecular Structure and Dynamics, 1–15. https://doi.org/https://doi.org/10.1080/07391102.2020.1819879
- Sacau, E. P., Estévez-Braun, A., Ravelo, A. G., Ferro, E. A., Tokuda, H., Mukainaka, T., & Nishino, H. (2003). Inhibitory effects of lapachol derivatives on epstein-barr virus activation. Bioorganic & Medicinal Chemistry, 11(4), 483–488. https://doi.org/https://doi.org/10.1016/S0968-0896(02)00542-4
- Santos, V. L. A., de Moraes, M. O., Pessoa, C., da Costa, M. P., Gonsalves, A. A., & Araújo, C. R. M. (2016). Cytotoxicity Activity of Semisynthetic Naphthoquinone-1-oximes against Cancer Cell Lines. Journal of Chemical and Pharmaceutical Research, 8(12), 202–206.
- Sutton, G., Fry, E., Carter, L., Sainsbury, S., Walter, T., Nettleship, J., Berrow, N., Owens, R., Gilbert, R., Davidson, A., Siddell, S., Poon, L. L. M., Diprose, J., Alderton, D., Walsh, M., Grimes, J. M., & Stuart, D. I. (2004). The nsp9 replicase protein of SARS-Coronavirus, structure and functional insights. Structure (London, England : 1993)), 12(2), 341–353. https://doi.org/https://doi.org/10.1016/j.str.2004.01.016
- WHO. (2021). Novel Coronavirus (2019-nCoV) situation reports. https://www.who.int/emergencies/diseases/novel-coronavirus-2019/situation-reports
- 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
- Yogo, Y., Hirano, N., Hino, S., Shibuta, H., & Matumoto, M. (1977). Polyadenylate in the virion RNA of mouse hepatitis virus. Journal of Biochemistry, 82(4), 1103–1108. https://doi.org/https://doi.org/10.1093/oxfordjournals.jbchem.a131782
- Zeng, Z., Deng, F., Shi, K., Ye, G., Wang, G., Fang, L., Xiao, S., Fu, Z., & Peng, G. (2018). Dimerization of coronavirus nsp9 with diverse modes enhances its nucleic acid binding affinity. Journal of Virology, 92(17), e00692-18. https://doi.org/https://doi.org/10.1128/JVI.00692-18
- Zhai, Y., Sun, F., Li, X., Pang, H., Xu, X., Bartlam, M., & Rao, Z. (2005). Insights into SARS-CoV transcription and replication from the structure of the nsp7-nsp8 hexadecamer. Nature Structural & Molecular Biology, 12(11), 980–986. https://doi.org/https://doi.org/10.1038/nsmb999
- Zhu, N., Zhang, D., Wang, W., Li, X., Yang, B., Song, J., Zhao, X., Huang, B., Shi, W., Lu, R., Niu, P., Zhan, F., Ma, X., Wang, D., Xu, W., Wu, G., Gao, G. F., & Tan, W. (2020). A novel coronavirus from patients with pneumonia in China, 2019. The New England Journal of Medicine, 382(8), 727–733. https://doi.org/https://doi.org/10.1056/NEJMoa2001017
- Zoete, V., Cuendet, M. A., Grosdidier, A., & Michielin, O. (2011). SwissParam: A fast force field generation tool for small organic molecules. Journal of Computational Chemistry, 32(11), 2359–2368. https://doi.org/https://doi.org/10.1002/jcc.21816