12,199
Views
124
CrossRef citations to date
0
Altmetric
Research Articles

In-silico approaches to detect inhibitors of the human severe acute respiratory syndrome coronavirus envelope protein ion channel

ORCID Icon, , , , & ORCID Icon
Pages 2617-2627 | Received 24 Mar 2020, Accepted 30 Mar 2020, Published online: 15 Apr 2020

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. doi:10.1016/j.softx.2015.06.001
  • Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990). Basic local alignment search tool. Journal of Molecular Biology, 215(3), 403–410. doi:10.1016/S0022-2836(05)80360-2
  • Ashour, H. M., Elkhatib, W. F., Rahman, M. M., & Elshabrawy, H. A. (2020). Insights into the recent 2019 novel coronavirus (SARS-CoV-2) in light of past human coronavirus outbreaks. Pathogens, 9(3), 186. doi:10.3390/pathogens9030186
  • Berger, O., Edholm, O., & Jähnig, F. (1997). Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure, and constant temperature. Biophysical Journal, 72(5), 2002–2013. doi:10.1016/S0006-3495(97)78845-3
  • Bertrand Teponno, R., Kusari, S., & Spiteller, M. (2016). Recent advances in research on lignans and neolignans. Natural Product Reports, 33(9), 1044–1092. doi:10.1039/C6NP00021E
  • Binkowski, T. A., Naghibzadeh, S., & Liang, J. (2003). CASTp: Computed atlas of surface topography of proteins. Nucleic Acids Research, 31(13), 3352–3355. doi:10.1093/nar/gkg512
  • Biovia, D. S. (2017). Discovery studio visualizer. San Diego, CA, USA.
  • Curtis, K. M., Yount, B., & Baric, R. S. (2002). Heterologous gene expression from transmissible gastroenteritis virus replicon particles. Journal of Virology, 76(3), 1422–1434. doi:10.1128/JVI.76.3.1422-1434.2002
  • Dhanda, S. K., Singla, D., Mondal, A. K., & Raghava, G. P. (2013). DrugMint: A webserver for predicting and designing of drug-like molecules. Biology Direct, 8(1), 28. doi:10.1186/1745-6150-8-28
  • Donde, R., Gupta, M. K., Gouda, G., Kumar, J., Vadde, R., Sahoo, K. K., Dash, S. K., & Behera, L. (2019). Computational characterization of structural and functional roles of DREB1A, DREB1B and DREB1C in enhancing cold tolerance in rice plant. Amino Acids, 51(5), 839–853. doi:10.1007/s00726-019-02727-0
  • Fischer, F., Stegen, C. F., Masters, P. S., & Samsonoff, W. A. (1998). Analysis of constructed E gene mutants of mouse hepatitis virus confirms a pivotal role for E protein in coronavirus assembly. Journal of Virology, 72(10), 7885–7894. doi:10.1128/JVI.72.10.7885-7894.1998
  • Gouda, G., Gupta, M. K., Donde, R., Kumar, J., Vadde, R., Mohapatra, T., & Behera, L. (2020). Computational approach towards understanding structural and functional role of cytokinin oxidase/dehydrogenase 2 (CKX2) in enhancing grain yield in rice plant. Journal of Biomolecular Structure and Dynamics, 38(4), 1158–1110. doi:10.1080/07391102.2019.1597771
  • Gupta, M. K., Donde, R., Gouda, G., Vadde, R., & Behera, L. (2019). De novo assembly and characterization of transcriptome towards understanding molecular mechanism associated with MYMIV-resistance in Vigna mungo - A computational study. BioRxiv, 844639. doi:10.1101/844639
  • Gupta, M. K., & Vadde, R. (2019a). In silico identification of natural product inhibitors for γ-secretase activating protein, a therapeutic target for Alzheimer’s disease. Journal of Cellular Biochemistry, 120(6), 10323–10336. doi:10.1002/jcb.28316
  • Gupta, M. K., & Vadde, R. (2020a). Insights into the structure-function relationship of both wild and mutant Zinc transporter ZnT8 in human: A computational structural biology approach. Journal of Biomolecular Structure & Dynamics, 38(1), 137-151.doi:doi:10.1080/07391102.2019.1567391
  • Gupta, M. K., & Vadde, R. (2020b). A computational structural biology study to understand the impact of mutation on structure–function relationship of inward-rectifier potassium ion channel Kir6.2 in human. Journal of Biomolecular Structure and Dynamics.. doi:doi:10.1080/07391102.2020.1733666
  • Gupta, M. K., Vadde, R., Donde, R., Gouda, G., Kumar, J., Nayak, S., Jena, M., & Behera, L. (2018). Insights into the structure–function relationship of brown plant hopper resistance protein, Bph14 of rice plant: A computational structural biology approach. Journal of Biomolecular Structure and Dynamics, 37(7), 1649–1617. doi:10.1080/07391102.2018.1462737
  • Gupta, M. K., Vadde, R., Gouda, G., Donde, R., Kumar, J., & Behera, L. (2019). Computational approach to understand molecular mechanism involved in BPH resistance in Bt- rice plant. Journal of Molecular Graphics and Modelling, 88, 209–220. doi:10.1016/j.jmgm.2019.01.018
  • Gupta, M. K., Vadde, R., & Sarojamma, V. (2020). Curcumin - A novel therapeutic agent in the prevention of colorectal cancer. Current Drug Metabolism, 20(12), 977–987. doi:10.2174/1389200220666191007153238
  • Ramphul, K., & Mejias, S. G. (2020). Coronavirus disease: A review of a new threat to public health. Cureus, 12(3), e7276. doi:doi:10.7759/cureus.7276.
  • Krijnse-Locker, J., Ericsson, M., Rottier, P. J., & Griffiths, G. (1994). Characterization of the budding compartment of mouse hepatitis virus: Evidence that transport from the RER to the Golgi complex requires only one vesicular transport step. The Journal of Cell Biology, 124(1), 55–70. doi:10.1083/jcb.124.1.55
  • Li, G., Fan, Y., Lai, Y., Han, T., Li, Z., Zhou, P., Pan, P., Wang, W., Hu, D., Liu, X., Zhang, Q., & Wu, J. (2020). Coronavirus infections and immune responses. Journal of Medical Virology, 92(4), 424–432. doi:10.1002/jmv.25685
  • Lin, Y.-C., Wang, C.-C., Chen, I.-S., Jheng, J.-L., Li, J.-H., & Tung, C.-W. (2013). TIPdb: A database of anticancer, antiplatelet, and antituberculosis phytochemicals from indigenous plants in Taiwan. The Scientific World Journal, 2013, 1–4. doi:10.1155/2013/736386
  • Mehrnejad, F., & Chaparzadeh, N. (2008). Structural and dynamical studies of humanin in water and TFE/water mixture: A molecular dynamics simulation. Journal of Biomolecular Structure and Dynamics, 26(2), 255–262. doi:10.1080/07391102.2008.10507241
  • 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. doi:10.1002/jcc.21256
  • Nieto-Torres, J. L., DeDiego, M. L., Verdiá-Báguena, C., Jimenez-Guardeño, J. M., Regla-Nava, J. A., Fernandez-Delgado, R., Castaño-Rodriguez, C., Alcaraz, A., Torres, J., Aguilella, V. M., & Enjuanes, L. (2014). Severe acute respiratory syndrome coronavirus envelope protein ion channel activity promotes virus fitness and pathogenesis. PLoS Pathogens, 10(5), e1004077. doi:10.1371/journal.ppat.1004077
  • Perlman, S., & Netland, J. (2009). Coronaviruses post-SARS: Update on replication and pathogenesis. Nature Reviews Microbiology, 7(6), 439–450. doi:10.1038/nrmicro2147
  • Pervushin, K., Tan, E., Parthasarathy, K., Lin, X., Jiang, F. L., Yu, D., Vararattanavech, A., Soong, T. W., Liu, D. X., & Torres, J. (2009). Structure and Inhibition of the SARS coronavirus envelope protein ion channel. PLoS Pathogens, 5(7), e1000511. doi:10.1371/journal.ppat.1000511
  • Rani, Y. G., & Lakshmi, B. S. (2019). Structural insight into the antagonistic action of diarylheptanoid on human estrogen receptor alpha. Journal of Biomolecular Structure and Dynamics, 37(5), 1189–1203. doi:10.1080/07391102.2018.1453378
  • Regla-Nava, J. A., Nieto-Torres, J. L., Jimenez-Guardeño, J. M., Fernandez-Delgado, R., Fett, C., Castaño-Rodríguez, C., Perlman, S., Enjuanes, L., & DeDiego, M. L. (2015). Severe acute respiratory syndrome coronaviruses with mutations in the E protein are attenuated and promising vaccine candidates. Journal of Virology, 89(7), 3870–3887. doi:10.1128/JVI.03566-14
  • Rota, P. A., Oberste, M. S., Monroe, S. S., Nix, W. A., Campagnoli, R., Icenogle, J. P., Peñaranda, S., Bankamp, B., Maher, K., Chen, M.-H., Tong, S., Tamin, A., Lowe, L., Frace, M., DeRisi, J. L., Chen, Q., Wang, D., Erdman, D. D., Peret, T. C. T., … Bellini, W. J. (2003). Characterization of a novel coronavirus associated with severe acute respiratory syndrome. Science, 300(5624), 1394–1399. doi:10.1126/science.1085952
  • Schoeman, D., & Fielding, B. C. (2019). Coronavirus envelope protein: Current knowledge. Virology Journal, 16(1), 69. doi:10.1186/s12985-019-1182-0
  • Schüttelkopf, A. W., & van Aalten, D. M. F. (2004). PRODRG: A tool for high-throughput crystallography of protein–ligand complexes. Acta Crystallographica Section D Biological Crystallography, 60(8), 1355–1363. doi:10.1107/S0907444904011679
  • Shang, W., Yang, Y., Rao, Y., & Rao, X. (2020). The outbreak of SARS-CoV-2 pneumonia calls for viral vaccines. NPJ Vaccines, 5(1), 1–3. doi:10.1038/s41541-020-0170-0
  • Tandon, G., Jaiswal, S., Iquebal, M. A., Kumar, S., Kaur, S., Rai, A., & Kumar, D. (2015). Evidence of salicylic acid pathway with EDS1 and PAD4 proteins by molecular dynamics simulation for grape improvement. Journal of Biomolecular Structure and Dynamics, 33(10), 2180–2191. doi:10.1080/07391102.2014.996187
  • Tooze, J., & Tooze, S. A. (1985). Infection of AtT20 murine pituitary tumour cells by mouse hepatitis virus strain A59: Virus budding is restricted to the Golgi region. European Journal of Cell Biology, 37, 203–212.
  • Torres, J., Maheswari, U., Parthasarathy, K., Ng, L., Liu, D. X., & Gong, X. (2007). Conductance and amantadine binding of a pore formed by a lysine-flanked transmembrane domain of SARS coronavirus envelope protein. Protein Science, 16(9), 2065–2071. doi:10.1110/ps.062730007
  • Venkatagopalan, P., Daskalova, S. M., Lopez, L. A., Dolezal, K. A., & Hogue, B. G. (2015). Coronavirus envelope (E) protein remains at the site of assembly. Virology, 478, 75–85. doi:10.1016/j.virol.2015.02.005
  • Verdiá-Báguena, C., Nieto-Torres, J. L., Alcaraz, A., Dediego, M. L., Enjuanes, L., & Aguilella, V. M. (2013). Analysis of SARS-CoV E protein ion channel activity by tuning the protein and lipid charge. Biochimica Et Biophysica Acta (Bba) - Biomembranes, 1828(9), 2026–2031. doi:10.1016/j.bbamem.2013.05.008
  • Verdiá-Báguena, C., Nieto-Torres, J. L., Alcaraz, A., DeDiego, M. L., Torres, J., Aguilella, V. M., & Enjuanes, L. (2012). Coronavirus E protein forms ion channels with functionally and structurally-involved membrane lipids. Virology, 432(2), 485–494. doi:10.1016/j.virol.2012.07.005
  • Westerbeck, J. W., & Machamer, C. E. (2019). The infectious bronchitis coronavirus envelope protein alters Golgi pH to protect the spike protein and promote the release of infectious virus. Journal of Virology, 93(11), e00015-19. doi:10.1128/JVI.00015-19
  • Wilson, L., McKinlay, C., Gage, P., & Ewart, G. (2004). SARS coronavirus E protein forms cation-selective ion channels. Virology, 330(1), 322–331. doi:10.1016/j.virol.2004.09.033
  • Wolf, M. G., Hoefling, M., Aponte-Santamaría, C., Grubmüller, H., & Groenhof, G. (2010). g_membed: Efficient insertion of a membrane protein into an equilibrated lipid bilayer with minimal perturbation. Journal of Computational Chemistry, 31(11), 2169–2174. doi:10.1002/jcc.21507

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.