In silico analysis of marine natural product from sponge (Clathria Sp.) for their activity as inhibitor of SARS-CoV-2 Main Protease

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
• Afendi, F. M., Okada, T., Yamazaki, M., Hirai-Morita, A., Nakamura, Y., Nakamura, K., Ikeda, S., Takahashi, H., Altaf-Ul-Amin, M., Darusman, L. K., Saito, K., & Kanaya, S. (2012). KNApSAcK family databases: Integrated metabolite-plant species databases for multifaceted plant research. Plant & Cell Physiology, 53(2), e1. https://doi.org/10.1093/pcp/pcr165
   PubMed Web of Science ®Google Scholar
• Bell, E. W., & Zhang, Y. (2019). DockRMSD: An open-source tool for atom mapping and RMSD calculation of symmetric molecules through graph isomorphism. Journal of Cheminformatics, 11(1), 40. https://doi.org/10.1186/s13321-019-0362-7
   PubMed Web of Science ®Google Scholar
• Driggin, E., Madhavan, M. V., Bikdeli, B., Chuich, T., Laracy, J., Biondi-Zoccai, G., Brown, T. S., Der Nigoghossian, C., Zidar, D. A., Haythe, J., Brodie, D., Beckman, J. A., Kirtane, A. J., Stone, G. W., Krumholz, H. M., & Parikh, S. A. (2020). Cardiovascular considerations for patients, health care workers, and health systems during the COVID-19 pandemic. Journal of the American College of Cardiology, 75(18), 2352–2371. https://doi.org/10.1016/j.jacc.2020.03.031
   PubMed Web of Science ®Google Scholar
• Enmozhi, S. K., Raja, K., Sebastine, I., & Joseph, J. (2020). Andrographolide as a potential inhibitor of SARS-CoV-2 main protease: An in silico approach. Journal of Biomolecular Structure & Dynamics, 1–10. https://doi.org/10.1080/07391102.2020.1760136
   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
• 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/10.1517/17460441.2015.1032936
   PubMed Web of Science ®Google Scholar
• Jaspars, M., De Pascale, D., Andersen, J. H., Reyes, F., Crawford, A. D., & Ianora, A. (2016). The marine biodiscovery pipeline and ocean medicines of tomorrow. Journal of the Marine Biological Association of the United Kingdom, 96(1), 151–158. https://doi.org/10.1017/S0025315415002106
   Web of Science ®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. https://doi.org/10.1038/s41586-020-2223-y
   Web of Science ®Google Scholar
• Khaerunnisa, S, Kurniawan, H., Awaluddin, R., & Suhartati, S. (2020). Potential inhibitor of COVID-19 main protease (M pro) from several medicinal plant compounds by molecular docking study. Preprints, 1–14. https://doi.org/10.20944/preprints202003.0226.v1
   Google Scholar
• Lamm, G. (2003). The Poisson–Boltzmann equation. Reviews in Computational Chemistry, 19, 147–365. https://doi.org/10.1002/0471466638.ch4
   Web of Science ®Google Scholar
• Lolok, N., Sumiwi, S. A., Muhtadi, A., Susilawati, Y., Hendriani, R., Syah, D., Ramadhan, F., Levita, J., & Sahidin, I. (2021). Molecular docking and molecular dynamics studies of bioactive compounds contained in noni fruit (Morinda citrifolia L.) against human pancreatic α-amylase. Journal of Biomolecular Structure and Dynamics, 1–8. https://doi.org/10.1080/07391102.2021.1894981
   Google Scholar
• Mark, P., & Nilsson, L. (2001). Structure and dynamics of the TIP3P, SPC, and SPC/E water models at 298 K. The Journal of Physical Chemistry A, 105(43), 9954–9960. https://doi.org/10.1021/jp003020w
   Web of Science ®Google Scholar
• Mirza, M. U., & Froeyen, M. (2020). Structural elucidation of SARS-CoV-2 vital proteins: Computational methods reveal potential drug candidates against main protease, Nsp12 polymerase and Nsp13 helicase. Journal of Pharmaceutical Analysis, 10(4), 320–328. https://doi.org/10.1016/j.jpha.2020.04.008
   Google Scholar
• Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., & Olson, A. J. (2010). AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of Computational Chemistry, 30(16), 2785–2791. https://doi.org/10.1002/jcc.21256.AutoDock4
   Google Scholar
• Nakamura, K., Shimura, N., Otabe, Y., Hirai-Morita, A., Nakamura, Y., Ono, N., Ul-Amin, M. A., & Kanaya, S. (2013). KNApSAcK-3D: A three-dimensional structure database of plant metabolites. Plant & Cell Physiology, 54(2), e4. https://doi.org/10.1093/pcp/pcs186
   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, 33. https://doi.org/10.1186/1758-2946-3-33
   PubMed Web of Science ®Google Scholar
• Ogidigo, J. O., Iwuchukwu, E. A., Ibeji, C. U., Okpalefe, O., & Soliman, M. E. S. (2020). Natural phyto, compounds as possible noncovalent inhibitors against SARS-CoV2 protease: Computational approach. Journal of Biomolecular Structure and Dynamics, 1–18. https://doi.org/10.1080/07391102.2020.1837681
   Google Scholar
• Products, M. N. (2011). 2011 Future Med Chemi eribulin Marine natural products.pdf. pp. 1475–1489.
   Google Scholar
• Ramadhan, D. S. F., Fakih, T. M., & Arfan, A. (2020). Activity prediction of bioactive compounds contained in Etlingera elatior against the SARS-CoV-2 main protease: An in silico approach. Borneo Journal of Pharmacy, 3(4), 235–242. https://doi.org/10.33084/bjop.v3i4.1634
   Google Scholar
• Reiner, Ž., Hatamipour, M., Banach, M., Pirro, M., Al-Rasadi, K., Jamialahmadi, T., Radenkovic, D., Montecucco, F., & Sahebkar, A. (2020). Statins and the COVID-19 main protease: In silico evidence on direct interaction. Archives of Medical Science, 16(3), 490–496. https://doi.org/10.5114/aoms.2020.94655
   PubMed Web of Science ®Google Scholar
• Rudi, A., Yosief, T., Loya, S., Hizi, A., Schleyer, M., & Kashman, Y. (2001). Clathsterol, a novel anti-HIV-1 RT sulfated sterol from the sponge Clathria species. Journal of Natural Products, 64(11), 1451–1453. https://doi.org/10.1021/np010121s
   PubMed Web of Science ®Google Scholar
• Sahidin, I., Sadarun, B., Aslan, L. O. M., Wahyuni, Malaka, M. H., & Fristiohady, A. (2019). Structural relationship among steroids from Sulawesi Tenggara’s sponge Clathria sp. and their radical scavenger activity. IOP Conference Series: Earth and Environmental Science, 370(1), 012027. https://doi.org/10.1088/1755-1315/370/1/012027
   Google Scholar
• Sinha, S. K., et al. (2020). An in-silico evaluation of different Saikosaponins for their potency against SARS-CoV-2 using NSP15 and fusion spike glycoprotein as targets. Journal of Biomolecular Structure & Dynamics, 1–13. https://doi.org/10.1080/07391102.2020.1762741
   Google Scholar
• Sousa da Silva, A. W., & Vranken, W. F. (2012). ACPYPE - AnteChamber PYthon Parser interfacE. BMC Research Notes, 5(1), 367. https://doi.org/10.1186/1756-0500-5-367
   PubMedGoogle Scholar
• World Health Organization. 2020. WHO Director-General's Remarks at the Media Briefing on 2019-nCoV on 11 February 2020. https://www.who.int/dg/speeches/detail/who-director-general-s-remarks-at-the-mediabriefing-on-2019-ncov-on-11-february-2020
   Google Scholar
• Xu, X., Chen, P., Wang, J., Feng, J., Zhou, H., Li, X., Zhong, W., & Hao, P. (2020). Evolution of the novel coronavirus from the ongoing Wuhan outbreak and modeling of its spike protein for risk of human transmission. Science China Life Sciences, 63(3), 457–460. https://doi.org/10.1007/s11427-020-1637-5
   PubMed Web of Science ®Google Scholar