In silico approach identified benzoylguanidines as SARS-CoV-2 main protease (M^pro) potential inhibitors

References

• 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/10.1016/j.softx.2015.06.001
   Google Scholar
• Albuquerque, S. O., Barros, T. G., Dias, L. R. S., Lima, C. H. d S., Azevedo, P. H., R., d A., Flores-Junior, L., A. P., dos Santos, E. G., Loponte, H. F., Pinheiro, S., Dias, W. B., Muri, E. M. F., & Todeschini, A. R. (2020). Biological evaluation and molecular modeling of peptidomimetic compounds as inhibitors for O-GlcNAc transferase (OGT). European Journal of Pharmaceutical Sciences: Official Journal of the European Federation for Pharmaceutical Sciences, 154, 105510. https://doi.org/10.1016/j.ejps.2020.105510
   PubMed Web of Science ®Google Scholar
• Arif, M. N. (2022). Catechin derivatives as inhibitor of COVID-19 main protease (Mpro): molecular docking studies unveil an opportunity against CORONA. Combinatorial Chemistry & High Throughput Screening, 25(1), 197–203. https://doi.org/10.2174/1871520620666201123101002
   PubMed Web of Science ®Google Scholar
• Báez-Santos, Y. M., St. John, S. E., & Mesecar, A. D. (2015). The SARS-coronavirus papain-like protease: Structure, function and inhibition by designed antiviral compounds. Antiviral Research, 115, 21–38. https://doi.org/10.1016/j.antiviral.2014.12.015
   PubMed Web of Science ®Google Scholar
• Beigel, J. H., Tomashek, K. M., Dodd, L. E., Mehta, A. K., Zingman, B. S., Kalil, A. C., Hohmann, E., Chu, H. Y., Luetkemeyer, A., Kline, S., Lopez de Castilla, D., Finberg, R. W., Dierberg, K., Tapson, V., Hsieh, L., Patterson, T. F., Paredes, R., Sweeney, D. A., Short, W. R., … Lane, H. C. (2020). Remdesivir for the treatment of Covid-19 — final report. New England Journal of Medicine, 383(19), 1813–1826. https://doi.org/10.1056/NEJMoa2007764
   PubMed Web of Science ®Google Scholar
• Benatti, F. R., Cavalcante, K. K. L., Orsato, A., & Perez, C. C. (2020). Synthesis of lapachol and 4-Hydroxyquinazoline derivatives as candidates for antimalarial activity. Orbital: The Electronic Journal of Chemistry, 12(4), 1−9. https://doi.org/10.17807/orbital.v12i4.1541
   Google Scholar
• Bepari, A. K., & Reza, H. M. (2021). Identification of a novel inhibitor of SARS-CoV-2 3CL-PRO through virtual screening and molecular dynamics simulation. PeerJ. 9, e11261. https://doi.org/10.7717/peerj.11261
   PubMed Web of Science ®Google Scholar
• Berendsen, H., J., C., van der Spoel, D., & van Drunen, R. (1995). GROMACS: A message-passing parallel molecular dynamics implementation. Computer Physics Communications, 91(1–3), 43–56. https://doi.org/10.1016/0010-4655(95)00042-E
   Web of Science ®Google Scholar
• Brito, T. O., Abreu, L. O., Gomes, K. M., Lourenço, M. C. S., Pereira, P. M. L., Yamada-Ogatta, S. F., de Fátima, Â., Tisher, C. A., Macedo, F., & Bispo, M. L. F. (2020). Benzoylthioureas: Design, synthesis and antimycobacterial evaluation. Medicinal Chemistry (Shariqah (United Arab Emirates)), 16(1), 93–103. https://doi.org/10.2174/1573406415666181208110753
   PubMed Web of Science ®Google Scholar
• Bussi, G., Donadio, D., & Parrinello, M. (2007). Canonical sampling through velocity rescaling. The Journal of Chemical Physics, 126(1), 014101. https://doi.org/10.1063/1.2408420
   PubMed Web of Science ®Google Scholar
• Camargo, P. G., Bortoleti, B. T., d S., Fabris, M., Gonçalves, M. D., Tomiotto-Pellissier, F., Costa, I. N., Conchon-Costa, I., Lima, C. H., d S., Pavanelli, W. R., Bispo, M. d L. F., & Macedo, Jr, F. (2022). Thiohydantoins as anti-leishmanial agents: n vitro biological evaluation and multi-target investigation by molecular docking studies. Journal of Biomolecular Structure and Dynamics, 40(7), 3213–3222. https://doi.org/10.1080/07391102.2020.1845979
   PubMed Web of Science ®Google Scholar
• Cihan-Üstündağ, G., Gürsoy, E., Naesens, L., Ulusoy-Güzeldemirci, N., & Çapan, G. (2016). Synthesis and antiviral properties of novel indole-based thiosemicarbazides and 4-thiazolidinones. Bioorganic & Medicinal Chemistry, 24(2), 240–246. https://doi.org/10.1016/j.bmc.2015.12.008
   PubMed Web of Science ®Google Scholar
• d., Souza, A. S., Pacheco, B. D. C., Pinheiro, S., Muri, E. M. F., Dias, L. R. S., Lima, C. H. S., Garrett, R., de Moraes, M. B. M., d., Souza, B. E. G., & Puzer, L. (2019). 3-Acyltetramic acids as a novel class of inhibitors for human kallikreins 5 and 7. Bioorganic & Medicinal Chemistry Letters, 29(9), 1094–1098. https://doi.org/10.1016/j.bmcl.2019.02.031
   PubMed Web of Science ®Google Scholar
• da Silva, T. U., Pougy, K. d C., Albuquerque, M. G., da Silva Lima, C. H., & Machado, S. d P. (2022). Development of parameters compatible with the CHARMM36 force field for [Fe 4 S 4] 2+ clusters and molecular dynamics simulations of adenosine-5’-phosphosulfate reductase in GROMACS 2019. Journal of Biomolecular Structure and Dynamics, 40(8), 3481–3491. https://doi.org/10.1080/07391102.2020.1847687
   PubMed Web of Science ®Google Scholar
• da Silva, T. U., Pougy, K. d C., Albuquerque, M. G., Lima, C. H., d S., & Machado, S. d P. (2022). Molecular dynamics simulations of aqueous systems of inhibitor candidates for adenosine-5′-phosphosufate reductase. Journal of Biomolecular Structure and Dynamics, Feb 1, 1–12. https://doi.org/10.1080/07391102.2022.2033137
   Google Scholar
• Daina, A., Michielin, O., & Zoete, V. (2017). SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Scientific Reports, 7(1), 42717. https://doi.org/10.1038/srep42717
   PubMed Web of Science ®Google Scholar
• Daneman, R., & Prat, A. (2015). The blood–brain barrier. Cold Spring Harbor Perspectives in Biology, 7(1), a020412. https://doi.org/10.1101/cshperspect.a020412
   PubMed Web of Science ®Google Scholar
• Darden, T., York, D., & Pedersen, L. (1993). Particle mesh Ewald: An N log (N) method for Ewald sums in large systems. The Journal of Chemical Physics, 98(12), 10089–10092. https://doi.org/10.1063/1.464397
   Web of Science ®Google Scholar
• de Carvalho, P. G. C., Ribeiro, J. M., Garbin, R. P. B., Nakazato, G., Yamada Ogatta, S. F., de Fátima, Â., de Lima Ferreira Bispo, M., & Macedo, F. (2019). Synthesis and antimicrobial activity of thiohydantoins obtained from L-amino acids. Letters in Drug Design & Discovery, 17(1), 94–102. https://doi.org/10.2174/1570180816666181212153011
   Web of Science ®Google Scholar
• DeLano, W. L. (2002). Pymol: An open-source molecular graphics tool. CCP4 Newsletter on Protein Crystallography, 40(1), 82–92.
   Google Scholar
• DeSimone, R., Currie, K., Mitchell, S., Darrow, J., & Pippin, D. (2004). Privileged structures: applications in drug discovery. Combinatorial Chemistry & High Throughput Screening, 7(5), 473–94494. https://doi.org/10.2174/1386207043328544
   PubMed Web of Science ®Google Scholar
• 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/10.1063/1.470117
   Web of Science ®Google Scholar
• Evans, D. A. (2014). History of the Harvard ChemDraw Project. Angewandte Chemie (International ed. in English), 53(42), 11140–11145. https://doi.org/10.1002/anie.201405820
   PubMed Web of Science ®Google Scholar
• FDA (2021a). FDA approves first treatment for COVID-19. https://www.fda.gov/news-events/press-announcements/fda-approves-first-treatment-covid-19
   Google Scholar
• FDA (2021b). Coronavirus (COVID-19) update: FDA authorizes first oral antiviral for treatment of COVID-19. https://www.fda.gov/news-events/press-announcements/coronavirus-covid-19-update-fda-authorizes-first-oral-antiviral-treatment-covid-19
   Google Scholar
• FDA (2021c). Fact sheet for healthcare providers: Emergency use authorization for Paxlovid. 12/22/2021. https://www.covid19oralrx.com/files/PP-PAX-USA-0007-EUA-Full-Prescribing-Info-HCP-Fact-Sheet-COVID-19-Oral-Antiviral-Combined.pdf
   Google Scholar
• Fu, L., Ye, F., Feng, Y., Yu, F., Wang, Q., Wu, Y., Zhao, C., Sun, H., Huang, B., Niu, P., Song, H., Shi, Y., Li, X., Tan, W., Qi, J., & Gao, G. F. (2020). Both Boceprevir and GC376 efficaciously inhibit SARS-CoV-2 by targeting its main protease. Nature Communications, 11(1), 4417. https://doi.org/10.1038/s41467-020-18233-x[PMC][32887884
   PubMed Web of Science ®Google Scholar
• Ghosh, R., Chakraborty, A., Biswas, A., & Chowdhuri, S. (2021). Evaluation of green tea polyphenols as novel corona virus (SARS CoV-2) main protease (Mpro) inhibitors – an in silico docking and molecular dynamics simulation study. Journal of Biomolecular Structure & Dynamics, 39(12), 4362–4374. https://doi.org/10.1080/07391102.2020.1779818
   PubMed Web of Science ®Google Scholar
• Ghosh, A. K., Williams, J. N., Ho, R. Y., Simpson, H. M., Hattori, S., Hayashi, H., Agniswamy, J., Wang, Y.-F., Weber, I. T., & Mitsuya, H. (2018). Design and synthesis of potent HIV-1 protease inhibitors containing bicyclic oxazolidinone scaffold as the P2 ligands: Structure–activity studies and biological and X-ray structural studies. Journal of Medicinal Chemistry, 61(21), 9722–9737. https://doi.org/10.1021/acs.jmedchem.8b01227
   PubMed Web of Science ®Google Scholar
• Gomes, D. E. B., da Silva, A. W., Lins, R. D., Pascutti, P. G., & A., S. (2009). HbMap2Grace. Software for mapping the hydrogen bond frequency. Laboratory for Molecular Modeling and Dynamics (LMDM); Rio de Janeiro, Brazil: 2009. version 1.0.
   Google Scholar
• Hagar, M., Ahmed, H. A., Aljohani, G., & Alhaddad, O. A. (2020). Investigation of some antiviral N-heterocycles as COVID 19 drug: Molecular docking and DFT calculations. International Journal of Molecular Sciences, 21(11), 3922. https://doi.org/10.3390/ijms21113922
   PubMed Web of Science ®Google Scholar
• Hage-Melim, L. I. d S., Federico, L. B., de Oliveira, N. K. S., Francisco, V. C. C., Correia, L. C., de Lima, H. B., Gomes, S. Q., Barcelos, M. P., Francischini, I. A. G., & da Silva, C. H. T. d P. (2020). Virtual screening, ADME/Tox predictions and the drug repurposing concept for future use of old drugs against the COVID-19. Life Sciences, 256, 117963. https://doi.org/10.1016/j.lfs.2020.117963
   PubMed Web of Science ®Google Scholar
• Harnden, M. R., Bailey, S., Boyd, M. R., Taylor, D. R., & Wright, N. D. (1978). Thiazolinone analogs of indolmycin with antiviral and antibacterial activity. Journal of Medicinal Chemistry, 21(1), 82–87. https://doi.org/10.1021/jm00199a015
   PubMed Web of Science ®Google Scholar
• 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
   Web of Science ®Google Scholar
• Hevener, K. E., Zhao, W., Ball, D. M., Babaoglu, K., Qi, J., White, S. W., & Lee, R. E. (2009). Validation of molecular docking programs for virtual screening against dihydropteroate synthase. Journal of Chemical Information and Modeling, 49(2), 444–460. https://doi.org/10.1021/ci800293n
   PubMed Web of Science ®Google Scholar
• Hishiki, T., Kato, F., Tajima, S., Toume, K., Umezaki, M., Takasaki, T., & Miura, T. (2017). Hirsutine, an indole alkaloid of uncaria rhynchophylla, inhibits late step in dengue virus lifecycle. Frontiers in Microbiology, 8, 1674. https://doi.org/10.3389/fmicb.2017.01674
   PubMed Web of Science ®Google Scholar
• Huang, J., & MacKerell, A. D. (2013). CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data. Journal of Computational Chemistry, 34(25), 2135–2145. https://doi.org/10.1002/jcc.23354
   PubMed Web of Science ®Google Scholar
• Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics, 14(1), 33–38. https://doi.org/10.1016/0263-7855(96)00018-5
   PubMedGoogle Scholar
• Hwu, J. R., Huang, W.-C., Lin, S.-Y., Tan, K.-T., Hu, Y.-C., Shieh, F.-K., Bachurin, S. O., Ustyugov, A., & Tsay, S.-C. (2019). Chikungunya virus inhibition by synthetic coumarin–guanosine conjugates. European Journal of Medicinal Chemistry, 166, 136–143. https://doi.org/10.1016/j.ejmech.2019.01.037
   PubMed Web of Science ®Google Scholar
• J. R. Yunta, M. (2017). It is important to compute intramolecular hydrogen bonding in drug design? American Journal of Modeling and Optimization, 5(1), 24–57. https://doi.org/10.12691/ajmo-5-1-3
   Google Scholar
• 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 SARS-CoV-2 and discovery of its inhibitors. Nature, 582(7811), 289–293. https://doi.org/10.1038/s41586-020-2223-y
   PubMed Web of Science ®Google Scholar
• Klein, K., & Zanger, U. M. (2013). Pharmacogenomics of cytochrome P450 3A4: Recent progress toward the “missing heritability” problem. Frontiers in Genetics, 4, 12. https://doi.org/10.3389/fgene.2013.00012
   PubMedGoogle Scholar
• Kokic, G., Hillen, H. S., Tegunov, D., Dienemann, C., Seitz, F., Schmitzova, J., Farnung, L., Siewert, A., Höbartner, C., & Cramer, P. (2021). Mechanism of SARS-CoV-2 polymerase stalling by remdesivir. Nature Communications, 12(1), 279. https://doi.org/10.1038/s41467-020-20542-0[PMC][33436624
   PubMed Web of Science ®Google Scholar
• Kontoyianni, M. (2017). Docking and virtual screening in drug discovery.Methods in Molecular Biology, 1647, 255–266. https://doi.org/10.1007/978-1-4939-7201-2_18
   Google Scholar
• Kumari, R., Kumar, R., & Lynn, A, Open Source Drug Discovery Consortium. (2014). g_mmpbsa —a GROMACS tool for high-throughput MM-PBSA calculations. Journal of Chemical Information and Modeling, 54(7), 1951–1962. https://doi.org/10.1021/ci500020m
   PubMed Web of Science ®Google Scholar
• Lee, J., Cheng, X., Swails, J. M., Yeom, M. S., Eastman, P. K., Lemkul, J. A., Wei, S., Buckner, J., Jeong, J. C., Qi, Y., Jo, S., Pande, V. S., Case, D. A., Brooks, C. L., MacKerell, A. D., Klauda, J. B., & Im, W. (2016). CHARMM-GUI input generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 additive force field. Journal of Chemical Theory and Computation, 12(1), 405–413. https://doi.org/10.1021/acs.jctc.5b00935
   PubMed Web of Science ®Google Scholar
• Lima, C., de Alencastro, R., Kaiser, C., de Souza, M., Rodrigues, C., & Albuquerque, M. (2015). Aqueous molecular dynamics simulations of the M. tuberculosis Enoyl-ACP Reductase-NADH system and its complex with a substrate mimic or diphenyl ethers inhibitors. International Journal of Molecular Sciences, 16(10), 23695–23722. https://doi.org/10.3390/ijms161023695
   PubMed Web of Science ®Google Scholar
• Lipinski, C. A., Lombardo, F., Dominy, B. W., & Feeney, P. J. (1997). Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Advanced Drug Delivery Reviews, 23(1-3), 3–25. https://doi.org/10.1016/S0169-409X(96)00423-1
   Web of Science ®Google Scholar
• Lipinski, C. A., Lombardo, F., Dominy, B. W., & Feeney, P. J. (2001). Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings 1PII of original article: S0169-409X(96)00423-1. The article was originally published in Advanced Drug Delivery Reviews 23 (1997). Advanced Drug Delivery Reviews, 46(1–3), 3–26. https://doi.org/10.1016/S0169-409X(00)00129-0
   PubMed Web of Science ®Google Scholar
• Lokhande, K. B., Doiphode, S., Vyas, R., & Swamy, K. V. (2021). Molecular docking and simulation studies on SARS-CoV-2 M pro reveals Mitoxantrone, Leucovorin, Birinapant, and Dynasore as potent drugs against COVID-19. Journal of Biomolecular Structure & Dynamics, 39(18), 7294–7305. https://doi.org/10.1080/07391102.2020.1805019
   PubMed Web of Science ®Google Scholar
• Maia, E. H. B., Assis, L. C., de Oliveira, T. A., da Silva, A. M., & Taranto, A. G. (2020). Structure-based virtual screening: From classical to artificial intelligence. Frontiers in Chemistry, 8, 343. https://doi.org/10.3389/fchem.2020.00343
   PubMed Web of Science ®Google Scholar
• Mengist, H. M., Dilnessa, T., & Jin, T. (2021). Structural basis of potential inhibitors targeting SARS-CoV-2 main protease. Frontiers in Chemistry, 9, 622898. https://doi.org/10.3389/fchem.2021.622898
   PubMed Web of Science ®Google Scholar
• Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., & Olson, A. J. (2009). AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of Computational Chemistry, 30(16), 2785–2791. https://doi.org/10.1002/jcc.21256
   PubMed Web of Science ®Google Scholar
• Musella, S., di Sarno, V., Ciaglia, T., Sala, M., Spensiero, A., Scala, M. C., Ostacolo, C., Andrei, G., Balzarini, J., Snoeck, R., Novellino, E., Campiglia, P., Bertamino, A., & Gomez-Monterrey, I. M. (2016). Identification of an indol-based derivative as potent and selective varicella zoster virus (VZV) inhibitor. European Journal of Medicinal Chemistry, 124, 773–781. https://doi.org/10.1016/j.ejmech.2016.09.014
   PubMed Web of Science ®Google Scholar
• O'Boyle, N. M., Banck, M., James, C. A., Morley, C., Vandermeersch, T., & Hutchison, G. R. (2011). Open Babel: An open chemical toolbox. Journal of Cheminformatics, 3(1), 33. https://doi.org/10.1186/1758-2946-3-33
   PubMed Web of Science ®Google Scholar
• O'Donovan, D. H., Kelly, B., Diez-Cecilia, E., Kitson, M., & Rozas, I. (2013). A structural study of N,N′-bis-aryl-N′′-acylguanidines. New Journal of Chemistry, 37(8), 2408. https://doi.org/10.1039/c3nj00285c
   Web of Science ®Google Scholar
• Ohashi, R., Watanabe, R., Esaki, T., Taniguchi, T., Torimoto-Katori, N., Watanabe, T., Ogasawara, Y., Takahashi, T., Tsukimoto, M., & Mizuguchi, K. (2019). Development of Simplified in vitro P-glycoprotein substrate assay and in silico prediction models to evaluate transport potential of P-glycoprotein. Molecular Pharmaceutics, 16(5), 1851–1863. https://doi.org/10.1021/acs.molpharmaceut.8b01143
   PubMed Web of Science ®Google Scholar
• Owen, D. R., Allerton, C. M. N., Anderson, A. S., Aschenbrenner, L., Avery, M., Berritt, S., Boras, B., Cardin, R. D., Carlo, A., Coffman, K. J., Dantonio, A., Di, L., Eng, H., Ferre, R., Gajiwala, K. S., Gibson, S. A., Greasley, S. E., Hurst, B. L., Kadar, E. P., … Zhu, Y. (2021). An oral SARS-CoV-2 M pro inhibitor clinical candidate for the treatment of COVID-19. Science (New York, N.Y.), 374(6575), 1586–1593. https://doi.org/10.1126/science.abl4784
   PubMed Web of Science ®Google Scholar
• Parrinello, M., & Rahman, A. (1981). Polymorphic transitions in single crystals: A new molecular dynamics method. Journal of Applied Physics, 52(12), 7182–7190. https://doi.org/10.1063/1.328693
   Web of Science ®Google Scholar
• Pehlivan, E., Naesens, L., & Ulusoy Güzeldemirci, N. (2018). Synthesis and antiviral activity evaluation of new 4-thiazolidinones bearing an imidazo[2,1-b]thiazole moiety. Marmara Pharmaceutical Journal, 22(2), 237–248. https://doi.org/10.12991/mpj.2018.61
   Google Scholar
• Pereira, P. M. L., Camargo, P. G., Fernandes, B. T., Flores-Junior, L. A. P., Dias, L. R. S., Lima, C. H. S., Pinge-Filho, P., Lioni, L. M. Y., Yamada-Ogatta, S. F., Bispo, M. L. F., & Macedo, F. (2021). In vitro evaluation of antitrypanosomal activity and molecular docking of benzoylthioureas. Parasitology International, 80, 102225. https://doi.org/10.1016/j.parint.2020.102225
   PubMed Web of Science ®Google Scholar
• Pilau, M. R., Alves, S. H., Weiblen, R., Arenhart, S., Cueto, A. P., & Lovato, L. T. (2011). Antiviral activity of the Lippia graveolens (Mexican oregano) essential oil and its main compound carvacrol against human and animal viruses. Brazilian Journal of Microbiology: [Publication of the Brazilian Society for Microbiology], 42(4), 1616–1624. https://doi.org/10.1590/S1517-83822011000400049
   PubMed Web of Science ®Google Scholar
• Sanna, G., Madeddu, S., Giliberti, G., Piras, S., Struga, M., Wrzosek, M., Kubiak-Tomaszewska, G., Koziol, A., Savchenko, O., Lis, T., Stefanska, J., Tomaszewski, P., Skrzycki, M., & Szulczyk, D. (2018). Synthesis and Biological Evaluation of Novel Indole-Derived Thioureas. Molecules, 23(10), 2554. https://doi.org/10.3390/molecules23102554
   PubMed Web of Science ®Google Scholar
• Santiago-Silva, K. M. d., Bortoleti, B. T. d S., Brito, T. d O., Costa, I. C., Lima, C. H. d S., Macedo, F., Miranda-Sapla, M. M., Pavanelli, W. R., & Bispo, M. d L. F. (2021). Exploring the antileishmanial activity of N1, N2 -disubstituted-benzoylguanidines: synthesis and molecular modeling studies. Journal of Biomolecular Structure and Dynamics, Aug 6, 1–16. https://doi.org/10.1080/07391102.2021.1959403
   Google Scholar
• Schaefer, G. O., Leland, R. J., & Emanuel, E. J. (2021). Making vaccines available to other countries before offering domestic booster vaccinations. JAMA, 326(10), 903–904. https://doi.org/10.1001/jama.2021.13226
   PubMed Web of Science ®Google Scholar
• Sharma, P., Joshi, T., Mathpal, S., Joshi, T., Pundir, H., Chandra, S., & Tamta, S. (2022). Identification of natural inhibitors against Mpro of SARS-CoV-2 by molecular docking, molecular dynamics simulation, and MM/PBSA methods. Journal of Biomolecular Structure & Dynamics, 40(6), 2757–2768. https://doi.org/10.1080/07391102.2020.1842806
   PubMed Web of Science ®Google Scholar
• Stoddard, S. V., Stoddard, S. D., Oelkers, B. K., Fitts, K., Whalum, K., Whalum, K., Hemphill, A. D., Manikonda, J., Martinez, L. M., Riley, E. G., Roof, C. M., Sarwar, N., Thomas, D. M., Ulmer, E., Wallace, F. E., Pandey, P., & Roy, S. (2020). Optimization rules for SARS-CoV-2 Mpro antivirals: ensemble docking and exploration of the Coronavirus protease active site. Viruses, 12(9), 942. https://doi.org/10.3390/v12090942
   PubMed Web of Science ®Google Scholar
• Tijsma, A., Thibaut, H. J., Franco, D., Dallmeier, K., & Neyts, J. (2016). Hydantoin: The mechanism of its in vitro anti-enterovirus activity revisited. Antiviral Research, 133, 106–109. https://doi.org/10.1016/j.antiviral.2016.07.023
   PubMed Web of Science ®Google Scholar
• Trott, O., & Olson, A. J. (2009). 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/10.1002/jcc.21334
   Google Scholar
• Turner, P. J. (2005). XMGRACE, Version 5.1.19. Center for Coastal and Land-Margin Research, Oregon Graduate Institute of Science and Technology.
   Google Scholar
• Uelisson da Silva, T., Tomaz da Silva, E., de Carvalho Pougy, K., Henrique da Silva Lima, C., & de Paula Machado, S. (2022). Molecular modeling of indazole-3-carboxylic acid and its metal complexes (Zn, Ni, Co, Fe and Mn) as NO synthase inhibitors: DFT calculations, docking studies and molecular dynamics simulations. Inorganic Chemistry Communications, 135, 109120. https://doi.org/10.1016/j.inoche.2021.109120
   Web of Science ®Google Scholar
• Vanommeslaeghe, K., Hatcher, E., Acharya, C., Kundu, S., Zhong, S., Shim, J., Darian, E., Guvench, O., Lopes, P., Vorobyov, I., & Mackerell, A. D. (2009). CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields. Journal of Computational Chemistry, 31(4), 671-90. https://doi.org/10.1002/jcc.21367
   Google Scholar
• Veber, D. F., Johnson, S. R., Cheng, H.-Y., Smith, B. R., Ward, K. W., & Kopple, K. D. (2002). Molecular properties that influence the oral bioavailability of drug candidates. Journal of Medicinal Chemistry, 45(12), 2615–2623. http://www.ncbi.nlm.nih.gov/pubmed/12036371
   PubMed Web of Science ®Google Scholar
• Wasukan, N., Kuno, M., & Maniratanachote, R. (2019). Molecular docking as a promising predictive model for silver nanoparticle-mediated inhibition of cytochrome P450 enzymes. Journal of Chemical Information and Modeling, 59(12), 5126–5134. https://doi.org/10.1021/acs.jcim.9b00572
   PubMed Web of Science ®Google Scholar
• World Health Organization. (2022a). WHO Coronavirus (COVID-19) Dashboard. https://covid19.who.int/
   Google Scholar
• World Health Organization. (2022b). Therapeutics and COVID-19: living guideline. https://app.magicapp.org/#/guideline/nBkO1E
   Google Scholar
• Xiong, G., Wu, Z., Yi, J., Fu, L., Yang, Z., Hsieh, C., Yin, M., Zeng, X., Wu, C., Lu, A., Chen, X., Hou, T., & Cao, D. (2021). ADMETlab 2.0: An integrated online platform for accurate and comprehensive predictions of ADMET properties. Nucleic Acids Research, 49(W1), W5–W14. https://doi.org/10.1093/nar/gkab255
   PubMed Web of Science ®Google Scholar
• Xu, C., Xin, Y., Chen, M., Ba, M., Guo, Q., Zhu, C., Guo, Y., & Shi, J. (2020). Discovery, synthesis, and optimization of an N-alkoxy indolylacetamide against HIV-1 carrying NNRTI-resistant mutations from the Isatis indigotica root. European Journal of Medicinal Chemistry, 189, 112071. https://doi.org/10.1016/j.ejmech.2020.112071
   PubMed Web of Science ®Google Scholar
• Yu, W., Wu, X., Zhao, Y., Chen, C., Yang, Z., Zhang, X., Ren, J., Wang, Y., Wu, C., Li, C., Chen, R., Wang, X., Zheng, W., Liao, H., & Yuan, X. (2021). Computational Simulation of HIV Protease Inhibitors to the Main Protease (Mpro) of SARS-CoV-2: Implications for COVID-19 Drugs Design. Molecules, 26(23), 7385. https://doi.org/10.3390/molecules26237385
   PubMed Web of Science ®Google Scholar
• 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 (New York, N.Y.), 368(6489), 409–412. https://doi.org/10.1126/science.abb3405
   PubMed Web of Science ®Google Scholar