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Research Article

Identification and characterization of domain-specific inhibitors of DENV NS3 and NS5 proteins by in silico screening methods

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Received 15 Jul 2023, Accepted 26 Jan 2024, Published online: 09 Feb 2024

References

  • Balmaseda, A., Hammond, S. N., Pérez, L., Tellez, Y., Saborío, S. I., Mercado, J. C., Cuadra, R., Rocha, J., Pérez, M. A., Silva, S., Rocha, C., & Harris, E. (2006). Serotype-specific differnces in clinical manifestations of dengue. The American Journal of Tropical Medicine and Hygiene, 74(3), 449–456. https://doi.org/10.4269/ajtmh.2006.74.449
  • Banerjee, P., Eckert, A. O., Schrey, A. K., & Preissner, R. (2018). ProTox-II: A webserver for the prediction of toxicity of chemicals. Nucleic Acids Research, 46(W1), W257–W263. https://doi.org/10.1093/nar/gky318
  • 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/10.1063/1.448118
  • Bhatt, S., Gething, P. W., Brady, O. J., Messina, J. P., Farlow, A. W., Moyes, C. L., Drake, J. M., Brownstein, J. S., Hoen, A. G., Sankoh, O., Myers, M. F., George, D. B., Jaenisch, T., Wint, G. R. W., Simmons, C. P., Scott, T. W., Farrar, J. J., & Hay, S. I. (2013). The global distribution and burden of dengue. Nature, 496(7446), 504–507. https://doi.org/10.1038/nature12060
  • Brady, O. J., Gething, P. W., Bhatt, S., Messina, J. P., Brownstein, J. S., Hoen, A. G., Moyes, C. L., Farlow, A. W., Scott, T. W., & Hay, S. I. (2012). Refining the global spatial limits of dengue virus transmission by evidence-based consensus. PLoS Neglected Tropical Diseases, 6(8), e1760. https://doi.org/10.1371/journal.pntd.0001760
  • Brecher, M., Chen, H., Liu, B., Banavali, N. K., Jones, S. A., Zhang, J., Li, Z., Kramer, L. D., & Li, H. (2015). Novel broad spectrum inhibitors targeting the flavivirus methyltransferase. PLoS One, 10(6), e0130062. https://doi.org/10.1371/journal.pone.0130062
  • Cologna, R., Armstrong, P. M., & Rico-Hesse, R. (2005). Selection for virulent dengue viruses occurs in humans and mosquitoes. Journal of Virology, 79(2), 853–859. https://doi.org/10.1128/JVI.79.2.853-859.2005
  • DeLano, W. L. (2002). The PyMOL Molecular Graphics System. San Carlos: Delano Scientific.
  • Dong, H., Chang, D. C., Xie, X., Toh, Y. X., Chung, K. Y., Zou, G., Lescar, J., Lim, S. P., & Shi, P. Y. (2010). Biochemical and genetic characterization of dengue virus methyltransferase. Virology, 405(2), 568–578. https://doi.org/10.1016/j.virol.2010.06.039
  • Dwivedi, V. D., Tripathi, I. P., Tripathi, R. C., Bharadwaj, S., & Mishra, S. K. (2017). Genomics, proteomics and evolution of dengue virus. Briefings in Functional Genomics, 16(4), elw040–227. https://doi.org/10.1093/bfgp/elw040
  • Egloff, M.-P., Benarroch, D., Selisko, B., Romette, J.-L., & Canard, B. (2002). An RNA cap (nucleoside-2'-O-)-methyltransferase in the flavivirus RNA polymerase NS5: Crystal structure and functional characterization. The EMBO Journal, 21(11), 2757–2768. https://doi.org/10.1093/emboj/21.11.2757
  • Gadaleta, D., Vuković, K., Toma, C., Lavado, G. J., Karmaus, A. L., Mansouri, K., Kleinstreuer, N. C., Benfenati, E., & Roncaglioni, A. (2019). SAR and QSAR modeling of a large collection of LD50 rat acute oral toxicity data. Journal of Cheminformatics, 11(1), 58. https://doi.org/10.1186/s13321-019-0383-2
  • Gopala Reddy, S. B., Chin, W.-X., & Shivananju, N. S. (2018). Dengue virus NS2 and NS4: Minor proteins, mammoth roles. Biochemical Pharmacology, 154, 54–63. https://doi.org/10.1016/j.bcp.2018.04.008
  • Grant, B. J., Rodrigues, A. P. C., ElSawy, K. M., McCammon, J. A., & Caves, L. S. D. (2006). Bio3d: An R package for the comparative analysis of protein structures. Bioinformatics (Oxford, England), 22(21), 2695–2696. https://doi.org/10.1093/bioinformatics/btl461
  • Guedes, I.A., Pereira, F.S.S., and Dardenne, L.E. (2018). Empirical Scoring Functions for Structure-Based Virtual Screening: Applications, Critical Aspects, and Challenges, Front. Pharmacol, 9.
  • Halstead, S. B. (2018). Safety issues from a Phase 3 clinical trial of a live-attenuated chimeric yellow fever tetravalent dengue vaccine. Human Vaccines & Immunotherapeutics, 14(9), 2158–2162. https://doi.org/10.1080/21645515.2018.1445448
  • Heilman, J. M., De Wolff, J., Beards, G. M., & Basden, B. J. (2014). Dengue fever: A Wikipedia clinical review. Open Medicine: A Peer-Reviewed, Independent, Open-Access Journal, 8(4), e105-115–e115.
  • 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
  • Kapoor, M., Zhang, L., Ramachandra, M., Kusukawa, J., Ebner, K.E., and Padmanabhan, R. (1995). Association between NS3 and NS5 Proteins of Dengue Virus Type 2 in the Putative RNA Replicase Is Linked to Differential Phosphorylation of NS5. J. Biol. Chem., 270(32), 19100–19106.
  • Kroschewski, H., Siew, P. L., Butcher, R. E., Thai, L. Y., Lescar, J., Wright, P. J., Vasudevan, S. G., & Davidson, A. D. (2008). Mutagenesis of the dengue virus type 2 NS5 methyltransferase domain. The Journal of Biological Chemistry, 283(28), 19410–19421. https://doi.org/10.1074/jbc.M800613200
  • 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/10.1021/ci200227u
  • Lindorff-Larsen, K., Piana, S., Palmo, K., Maragakis, P., Klepeis, J. L., Dror, R. O., & Shaw, D. E. (2010). Improved side-chain torsion potentials for the Amber ff99SB protein force field. Proteins: Structure, Function, and Bioinformatics, 78(8), 1950–1958. https://doi.org/10.1002/prot.22711
  • Luo, D., Xu, T., Watson, R. P., Scherer-Becker, D., Sampath, A., Jahnke, W., Yeong, S. S., Wang, C. H., Lim, S. P., Strongin, A., Vasudevan, S. G., & Lescar, J. (2008). Insights into RNA unwinding and ATP hydrolysis by the flavivirus NS3 protein. The EMBO Journal, 27(23), 3209–3219. https://doi.org/10.1038/emboj.2008.232
  • Murthy, H. M. K., Clum, S., & Padmanabhan, R. (1999). Dengue virus NS3 serine protease. Crystal structure and insights into interaction of the active site with substrates by molecular modeling and structural analysis of mutational effects. The Journal of Biological Chemistry, 274(9), 5573–5580. https://doi.org/10.1074/jbc.274.9.5573
  • Murugesan, A., & Manoharan, M. (2020). Emerging and reemerging viral pathogens (pp. 281–359). Elsevier.
  • Olivier, S., Maria, A. M., Francois, D., & Bruno, O. V. (2006). Receptor-Based Computational Screening of Compound Databases: The Main Docking-Scoring Engines. Current Protein and Peptide Science, 7, 369–393.
  • Ponder, J. W., & Case, D. A. (2003). Force fields for protein simulations. Advances in Protein Chemistry, 66, 27–85. https://doi.org/10.1016/s0065-3233(03)66002-x
  • Rarey, M., Kramer, B., Lengauer, T., & Klebe, G. (1996). A fast flexible docking method using an incremental construction algorithm. Journal of Molecular Biology, 261(3), 470–489. https://doi.org/10.1006/jmbi.1996.0477
  • 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
  • Swarbrick, C. M. D., Basavannacharya, C., Chan, K. W. K., Chan, S.-A., Singh, D., Wei, N., Phoo, W. W., Luo, D., Lescar, J., & Vasudevan, S. G. (2017). NS3 helicase from dengue virus specifically recognizes viral RNA sequence to ensure optimal replication. Nucleic Acids Research, 45(22), 12904–12920. https://doi.org/10.1093/nar/gkx1127
  • Trainor, G. L. (2007). The importance of plasma protein binding in drug discovery. Expert Opinion on Drug Discovery, 2(1), 51–64. https://doi.org/10.1517/17460441.2.1.51
  • Turner, P. J. (2005). Center for coastal and land-margin research. Oregon Graduate Institute of Science and Technology.
  • Vainio, M. J., & Johnson, M. S. (2007). Generating conformer ensembles using a multiobjective genetic algorithm. Journal of Chemical Information and Modeling, 47(6), 2462–2474. https://doi.org/10.1021/ci6005646
  • Valdés-Tresanco, M. S., Valdés-Tresanco, M. E., Valiente, P. A., & Moreno, E. (2021). gmx_MMPBSA: A new tool to perform end-state free energy calculations with GROMACS. Journal of Chemical Theory and Computation, 17(10), 6281–6291. https://doi.org/10.1021/acs.jctc.1c00645
  • Yap, T. L., Xu, T., Chen, Y.-L., Malet, H., Egloff, M.-P., Canard, B., Vasudevan, S. G., & Lescar, J. (2007). Crystal structure of the dengue virus RNA-dependent RNA polymerase catalytic domain at 1.85-angstrom resolution. Journal of Virology, 81(9), 4753–4765. https://doi.org/10.1128/JVI.02283-06

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