A simulation-based approach to target Zika virus RNA-dependent RNA polymerase with marine compounds for antiviral development

References

• Alandijany, T. A., El-Daly, M. M., Tolah, A. M., Bajrai, L. H., Khateb, A. M., Alsaady, I. M., Altwaim, S. A., Dubey, A., Dwivedi, V. D., & Azhar, E. I. (2023). Investigating the mechanism of action of anti-dengue compounds as potential binders of zika virus RNA-dependent RNA polymerase. Viruses, 15(7), 1501. https://doi.org/10.3390/v15071501
   PubMed Web of Science ®Google Scholar
• Aziz, A., Suleman, M., Shah, A., Ullah, A., Rashid, F., Khan, S., Iqbal, A., Luo, S., Xie, L., & Xie, Z. (2023). Comparative mutational analysis of the zika virus genome from different geographical locations and its effect on the efficacy of zika virus-specific neutralizing antibodies. Frontiers in Microbiology, 14, 1098323. https://doi.org/10.3389/fmicb.2023.1098323
   PubMed Web of Science ®Google Scholar
• 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. Journal of Chemical Physics, 81(8), 3684–3690. https://doi.org/10.1063/1.448118
   Web of Science ®Google Scholar
• Bowers, K. J., Chow, E., Xu, H., Dror, R. O., Eastwood, M. P., Gregersen, B. A., Klepeis, J. L., Kolossvary, I., Moraes, M. A., & Sacerdoti, F. D. (2006). Scalable algorithms for molecular dynamics simulations on commodity clusters [Paper presentation]. Proceedings of the Proceedings of the 2006 ACM/IEEE Conference on Supercomputing (pp. 84-es). Association for Computing Machinery: New York, NY, USA.
   Google Scholar
• Brasil, P., Calvet, G. A., Siqueira, A. M., Wakimoto, M., de Sequeira, P. C., Nobre, A., Quintana, M. D S. B., Mendonça, M. C. L. D., Lupi, O., de Souza, R. V., Romero, C., Zogbi, H., Bressan, C. D S., Alves, S. S., Lourenço-de-Oliveira, R., Nogueira, R. M. R., Carvalho, M. S., de Filippis, A. M. B., & Jaenisch, T. (2016). Zika virus outbreak in Rio de Janeiro, Brazil: Clinical characterization, epidemiological and virological aspects. PLoS Neglected Tropical Diseases, 10(4), e0004636. https://doi.org/10.1371/journal.pntd.0004636
   PubMed Web of Science ®Google Scholar
• Bullard-Feibelman, K. M., Govero, J., Zhu, Z., Salazar, V., Veselinovic, M., Diamond, M. S., & Geiss, B. J. (2017). The FDA-approved drug sofosbuvir inhibits zika virus infection. Antiviral Research, 137, 134–140. https://doi.org/10.1016/j.antiviral.2016.11.023
   PubMed Web of Science ®Google Scholar
• Cao-Lormeau, V.-M., Blake, A., Mons, S., Lastère, S., Roche, C., Vanhomwegen, J., Dub, T., Baudouin, L., Teissier, A., Larre, P., Vial, A.-L., Decam, C., Choumet, V., Halstead, S. K., Willison, H. J., Musset, L., Manuguerra, J.-C., Despres, P., Fournier, E., … Ghawché, F. (2016). Guillain-Barré syndrome outbreak associated with zika virus infection in French polynesia: A case-control study. Lancet (London, England), 387(10027), 1531–1539. https://doi.org/10.1016/S0140-6736(16)00562-6
   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. Journal of Chemical Physics, 98(12), 10089–10092. https://doi.org/10.1063/1.464397
   Web of Science ®Google Scholar
• Debbab, A., Aly, A. H., Lin, W. H., & Proksch, P. (2010). Bioactive compounds from marine bacteria and fungi. Microbial Biotechnology, 3(5), 544–563. https://doi.org/10.1111/j.1751-7915.2010.00179.x
   PubMed Web of Science ®Google Scholar
• Eberhardt, J., Santos-Martins, D., Tillack, A. F., & Forli, S. (2021). AutoDock Vina 1.2. 0: New docking methods, expanded force field, and python bindings. Journal of Chemical Information and Modeling, 61(8), 3891–3898. https://doi.org/10.1021/acs.jcim.1c00203
   PubMed Web of Science ®Google Scholar
• Gattan, H. S., Mahmoud Alawi, M., Bajrai, L. H., Alandijany, T. A., Alsaady, I. M., El-Daly, M. M., Dwivedi, V. D., & Azhar, E. I. (2023). A multifaceted computational approach to understanding the MERS-CoV main protease and brown algae compounds’ interaction. Marine Drugs, 21(12), 626. https://doi.org/10.3390/md21120626
   PubMed Web of Science ®Google Scholar
• Gharbi-Ayachi, A., Santhanakrishnan, S., Wong, Y. H., Chan, K. W. K., Tan, S. T., Bates, R. W., Vasudevan, S. G., El Sahili, A., & Lescar, J. (2020). Non-nucleoside inhibitors of zika virus RNA-dependent RNA polymerase. Journal of Virology, 94(21), e00794-20. https://doi.org/10.1128/JVI.00794-20
   PubMed Web of Science ®Google Scholar
• Godoy, A. S., Lima, G. M. A., Oliveira, K. I. Z., Torres, N. U., Maluf, F. V., Guido, R. V. C., & Oliva, G. (2017). Crystal structure of zika virus NS5 RNA-dependent RNA polymerase. Nature Communications, 8(1), 14764. https://doi.org/10.1038/ncomms14764
   PubMedGoogle Scholar
• Goh, V. S. L., Mok, C.-K., & Chu, J. J. H. (2020). Antiviral natural products for arbovirus infections. Molecules (Basel, Switzerland), 25(12), 2796. https://doi.org/10.3390/molecules25122796
   PubMed Web of Science ®Google Scholar
• GROMACS. Gmx Sham GROMACS 2023.3 Documentation.
   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
• Hess, B., Kutzner, C., Van Der Spoel, D., & Lindahl, E. (2008). GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. Journal of Chemical Theory and Computation, 4(3), 435–447. https://doi.org/10.1021/ct700301q
   PubMed Web of Science ®Google Scholar
• Hunter, J. D. (2007). Matplotlib: A 2D graphics environment. Computing in Science & Engineering, 9(3), 90–95. https://doi.org/10.1109/MCSE.2007.55
   Web of Science ®Google Scholar
• Imran, M., Alotaibi, N. M., Thabet, H. K., Alruwaili, J. A., Eltaib, L., Alshehri, A., Kamal, M., & Abida. (2024). Investigation of natural compounds as methyltransferase inhibitors against dengue virus: An in silico approach. Journal of Biomolecular Structure & dynamics, 1–16. Ahead of Print. https://doi.org/10.1080/07391102.2024.2309647
   PubMedGoogle Scholar
• Khongwichit, S., Chuchaona, W., Vongpunsawad, S., & Poovorawan, Y. (2023). Molecular epidemiology, clinical analysis, and genetic characterization of zika virus infections in Thailand (2020–2023). Scientific Reports, 13(1), 21030. https://doi.org/10.1038/s41598-023-48508-4
   PubMedGoogle Scholar
• Kumar, S., El-Kafrawy, S. A., Bharadwaj, S., Maitra, S. S., Alandijany, T. A., Faizo, A. A., Khateb, A. M., Dwivedi, V. D., & Azhar, E. I. (2022). Discovery of bispecific lead compounds from azadirachta indica against ZIKA NS2B-NS3 protease and NS5 RNA dependent RNA polymerase using molecular simulations. Molecules (Basel, Switzerland), 27(8), 2562. https://doi.org/10.3390/molecules27082562
   PubMed Web of Science ®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
• Labbé, C. M., Rey, J., Lagorce, D., Vavruša, M., Becot, J., Sperandio, O., Villoutreix, B. O., Tufféry, P., & Miteva, M. A. (2015). MTiOpenScreen: A web server for structure-based virtual screening. Nucleic Acids Research, 43(W1), W448–W454. https://doi.org/10.1093/nar/gkv306
   PubMed Web of Science ®Google Scholar
• Lyu, C., Chen, T., Qiang, B., Liu, N., Wang, H., Zhang, L., & Liu, Z. (2021). CMNPD: A comprehensive marine natural products database towards facilitating drug discovery from the ocean. Nucleic Acids Research, 49(D1), D509–D515. https://doi.org/10.1093/nar/gkaa763
   PubMed Web of Science ®Google Scholar
• Mishra, P. C., Alanazi, A. M., Panda, S. P., Alam, A., Dubey, A., Jha, S. K., & Kamal, M. A. (2023). Computational exploration of zika virus RNA-dependent RNA polymerase inhibitors: A promising antiviral drug discovery approach. Journal of Biomolecular Structure & Dynamics, 1–12. Ahead of Print. https://doi.org/10.1080/07391102.2023.2292794
   Web of Science ®Google Scholar
• Mlakar, J., Korva, M., Tul, N., Popović, M., Poljšak-Prijatelj, M., Mraz, J., Kolenc, M., Resman Rus, K., Vesnaver Vipotnik, T., Fabjan Vodušek, V., Vizjak, A., Pižem, J., Petrovec, M., & Avšič Županc, T. (2016). Zika virus associated with microcephaly. New England Journal of Medicine, 374(10), 951–958. https://doi.org/10.1056/NEJMoa1600651
   PubMed Web of Science ®Google Scholar
• Musso, D., & Gubler, D. J. (2016). Zika virus. Clinical Microbiology Reviews, 29(3), 487–524. https://doi.org/10.1128/CMR.00072-15
   PubMed Web of Science ®Google Scholar
• Paissoni, C., Spiliotopoulos, D., Musco, G., & Spitaleri, A. (2015). GMXPBSA 2.1: A GROMACS tool to perform MM/PBSA and computational alanine scanning. Computer Physics Communications. 186, 105–107. https://doi.org/10.1016/j.cpc.2014.09.010
   Google Scholar
• 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/10.1002/jcc.20084
   PubMed Web of Science ®Google Scholar
• Schrödinger Release Maestro. (2021). Schrödinger.
   Google Scholar
• Shukla, D., Alanazi, A. M., Panda, S. P., Dwivedi, V. D., & Kamal, M. A. (2023). Unveiling the antiviral potential of plant compounds from the Meliaceae family against the Zika virus through QSAR modeling and MD simulation analysis. Journal of Biomolecular Structure & Dynamics, 1–16. Ahead of Print. https://doi.org/10.1080/07391102.2023.2259498
   Web of Science ®Google Scholar
• Tan, L. T. (2023). Impact of marine chemical ecology research on the discovery and development of new pharmaceuticals. Marine Drugs, 21(3), 174. https://doi.org/10.3390/md21030174
   PubMed Web of Science ®Google Scholar
• Trott, O., & Olson, A. J. (2010). 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
   PubMed Web of Science ®Google Scholar
• Vanommeslaeghe, K., Raman, E. P., & MacKerell, A. D. (2012). Automation of the CHARMM general force field (CGenFF) II: Assignment of bonded parameters and partial atomic charges. Journal of Chemical Information and Modeling, 52(12), 3155–3168. https://doi.org/10.1021/ci3003649
   PubMed Web of Science ®Google Scholar
• Wang, A., Thurmond, S., Islas, L., Hui, K., & Hai, R. (2017). Zika virus genome biology and molecular pathogenesis. Emerging Microbes & Infections, 6(3), e13. https://doi.org/10.1038/emi.2016.141
   PubMedGoogle Scholar
• Wang, L., Zhou, R., Liu, Y., Guo, S., Yi, D., Zhao, J., Li, Q., Zhang, Y., Liang, C., Wang, J., Shan, G., & Cen, S. (2024). A cell-based assay to discover inhibitors of zika virus RNA-dependent RNA polymerase. Virology, 589, 109939. https://doi.org/10.1016/j.virol.2023.109939
   PubMed Web of Science ®Google Scholar
• Wang, Z., Qader, M., Wang, Y., Kong, F., Wang, Q., & Wang, C. (2023). Progress in the discovery of new bioactive substances from deep-sea associated fungi during 2020-2022. Frontiers in Marine Science, 10, 1232891. https://doi.org/10.3389/fmars.2023.1232891
   Web of Science ®Google Scholar
• Wikan, N., & Smith, D. R. (2016). Zika virus: History of a newly emerging arbovirus. Lancet. Infectious Diseases, 16(7), e119–e126. https://doi.org/10.1016/S1473-3099(16)30010-X
   PubMed Web of Science ®Google Scholar
• Yuan, J., Yu, J., Huang, Y., He, Z., Luo, J., Wu, Y., Zheng, Y., Wu, J., Zhu, X., Wang, H., & Li, M. (2020). Antibiotic fidaxomicin is an RdRp inhibitor as a potential new therapeutic agent against zika virus. BMC Medicine, 18(1), 204. https://doi.org/10.1186/s12916-020-01663-1
   PubMed Web of Science ®Google Scholar