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Research Articles

Designing Self-Inhibitory fusion peptide analogous to viral spike protein against novel severe acute respiratory syndrome (SARS-CoV-2)

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Pages 11357-11372 | Received 14 Aug 2020, Accepted 15 Jul 2021, Published online: 11 Aug 2021

References

  • Adamczak, R., Porollo, A., & Meller, J. (2005). Combining prediction of secondary structure and solvent accessibility in proteins. Proteins, 59(3), 467–475. https://doi.org/10.1002/prot.20441
  • Aydin, H., Al-Khooly, D., & Lee, J. E. (2014). Influence of hydrophobic and electrostatic residues on SARS-coronavirus S2 protein stability: Insights into mechanisms of general viral fusion and inhibitor design. Protein Science : a Publication of the Protein Society, 23(5), 603–617. https://doi.org/10.1002/pro.2442
  • Badani, H., Garry, R. F., & Wimley, W. C. (2014). Peptide entry inhibitors of enveloped viruses: The importance of interfacial hydrophobicity. Biochimica et Biophysica Acta, 1838(9), 2180–2197. https://doi.org/10.1016/j.bbamem.2014.04.015
  • Basu, A., Antanasijevic, A., Wang, M., Li, B., Mills, D. M., Ames, J. A., Nash, P. J., Williams, J. D., Peet, N. P., Moir, D. T., Prichard, M. N., Keith, K. A., Barnard, D. L., Caffrey, M., Rong, L., & Bowlin, T. L. (2014) New small molecule entry inhibitors targeting hemagglutinin-mediated influenza a virus fusion. Journal of Virology, 88(3), 1447–1460.
  • Chen, K., Kurgan, L. A., & Ruan, J. (2007). Prediction of flexible/rigid regions from protein sequences using k-spaced amino acid pairs. BMC Structural Biology, 7(1), 25. https://doi.org/10.1186/1472-6807-7-25
  • Cheng, G., Montero, A., Gastaminza, P., Whitten-Bauer, C., Wieland, S. F., Isogawa, M., Fredericksen, B., Selvarajah, S., Gallay, P. A., Ghadiri, M. R., & Chisari, F. V. (2008). A virocidal amphipathic {alpha}-helical peptide that inhibits hepatitis C virus infection in vitro. Proceedings of the National Academy of Sciences of the United States of America, 105(8), 3088–3093. https://doi.org/10.1073/pnas.0712380105
  • Chew, S. K. (2007). SARS: How a global epidemic was stopped. Bulletin of the World Health Organization, 85(4), 324–324. https://doi.org/10.2471/BLT.07.032763
  • Chin, A., Chu, J., Perera, M., Hui, K., Yen, H.-L., Chan, M., Peiris, M., & Poon, L. (2020). Stability of SARS-CoV-2 in different environmental conditions. medRxiv.
  • Cooper, D. A., & Lange, J. M. (2004). Peptide inhibitors of virus-cell fusion: Enfuvirtide as a case study in clinical discovery and development. The Lancet. Infectious Diseases, 4(7), 426–436.
  • Costin, J. M., Jenwitheesuk, E., Lok, S.-M., Hunsperger, E., Conrads, K. A., Fontaine, K. A., Rees, C. R., Rossmann, M. G., Isern, S., Samudrala, R., & Michael, S. F. (2010). Structural optimization and de novo design of dengue virus entry inhibitory peptides. PLoS Neglected Tropical Diseases, 4(6), e721. https://doi.org/10.1371/journal.pntd.0000721
  • Fung, H. B., & Guo, Y. (2004). Enfuvirtide: A fusion inhibitor for the treatment of HIV infection. Clinical Therapeutics, 26(3), 352–378.
  • Gallaher, W. R., (2006). Detection of a fusion peptide sequence in the transmembrane protein of human immunodeficiency virus. Medicinal Research Reviews, 26(4), 414–433.
  • Gupta, S., Kapoor, P., Chaudhary, K., Gautam, A., Kumar, R., Raghava, G. P., & Open Source Drug Discovery Consortium. (2013). In silico approach for predicting toxicity of peptides and proteins. PloS One, 8(9), e73957. https://doi.org/10.1371/journal.pone.0073957
  • Hall, T., Biosciences, I., & Carlsbad, C. (2011). BioEdit: An important software for molecular biology. GERF Bulletin of Biosciences. 2(1), 60–61.
  • He, Y., Xiao, Y., Song, H., Liang, Q., Ju, D., Chen, X., Lu, H., Jing, W., Jiang, S., & Zhang, L. (2008). Design and evaluation of sifuvirtide, a novel HIV-1 fusion inhibitor. Journal of Biological Chemistry, 283(17), 11126.
  • HeeShin, W. (2014). Prediction of protein structure and interaction by GALAXY protein modeling programs. Biodesign, 2, 1–11.
  • Ho, T.-Y., Wu, S.-L., Chen, J.-C., Wei, Y.-C., Cheng, S.-E., Chang, Y.-H., Liu, H.-J., & Hsiang, C.-Y. (2006). Design and biological activities of novel inhibitory peptides for SARS-CoV spike protein and angiotensin-converting enzyme 2 interaction. Antiviral Research, 69(2), 70–76. https://doi.org/10.1016/j.antiviral.2005.10.005
  • Jones, J. C., Turpin, E. A., Bultmann, H., Brandt, C. R., & Schultz-Cherry, S. (2006). Inhibition of influenza virus infection by a novel antiviral peptide that targets viral attachment to cells. Journal of Virology, 80(24), 11960–11967. https://doi.org/10.1128/JVI.01678-06
  • Kliger, Y., Gallo, S. A., Peisajovich, S. G., Munoz-Barroso, I., Avkin, S., Blumenthal, R., & Shai, Y. (2001). Mode of action of an antiviral peptide from HIV-1. Inhibition at a post-lipid mixing stage. The Journal of Biological Chemistry, 276(2), 1391–1397. https://doi.org/10.1074/jbc.M004113200
  • Kumari, R., Kumar, R., & Lynn, A. (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
  • LaBonte, J., Lebbos, J., & Kirkpatrick, P. (2003). Enfuvirtide. Nature Reviews. Drug Discovery, 2(5), 345–346.
  • Lan, J., Ge, J., Yu, J., Shan, S., Zhou, H., Fan, S., Zhang, Q., Shi, X., Wang, Q., Zhang, L. (2020). Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor. Nature, 581, 215–220.
  • Letko, M., Marzi, A., & Munster, V. (2020). Functional assessment of cell entry and receptor usage for SARS-CoV-2 and other lineage B beta coronaviruses. Nature Microbiology, 5, 562–569.
  • Liu, S., Lu, H., Niu, J., Xu, Y., Wu, S., & Jiang, S. (2005). Different from the HIV fusion inhibitor C34, the anti-HIV drug Fuzeon (T-20) inhibits HIV-1 entry by targeting multiple sites in gp41 and gp120. Journal of Biological Chemistry, 280(12), 11259–11273.
  • Lu, L., Liu, Q., Zhu, Y., Chan, K.-H., Qin, L., Li, Y., Wang, Q., Chan, J. F.-W., Du, L., Yu, F., Ma, C., Ye, S., Yuen, K.-Y., Zhang, R., & Jiang, S. (2014). Structure-based discovery of Middle East respiratory syndrome coronavirus fusion inhibitor. Nature Communications, 5(1), 3067. https://doi.org/10.1038/ncomms4067
  • Maselko, M., Ward, C., & Pastey, M. (2011). A RhoA-derived peptide inhibits human immunodeficiency virus-1 entry in vitro. Current HIV Research, 9(1), 1–5. https://doi.org/10.2174/157016211794582605
  • Matthews, T., Salgo, M., Greenberg, M., Chung, J., DeMasi, R., Bolognesi, D., (2004). Enfuvirtide: The first therapy to inhibit the entry of HIV-1 into host CD4 lymphocytes. Nature Reviews. Drug Discovery, 3(3), 215–25.
  • Ortega, J. T., Serrano, M. L., Pujol, F. H., Rangel, H. R., (2020). Role of changes in SARS-CoV-2 spike protein in the interaction with the human ACE2 receptor: An in silico analysis. EXCLI Journal, 19(7807), 410–417.
  • Pang, Y.-P., Vummenthala, A., Mishra, R. K., Park, J. G., Wang, S., Davis, J., Millard, C. B., Schmidt, J. J., (2009). Potent new small-molecule inhibitor of botulinum neurotoxin serotype A endopeptidase developed by synthesis-based computer-aided molecular design. PloS One, 4(11), e7730–11134.
  • Pommié, C., Levadoux, S., Sabatier, R., Lefranc, G., & Lefranc, M. P. (2004). IMGT standardized criteria for statistical analysis of immunoglobulin V-REGION amino acid properties. Journal of Molecular Recognition : JMR, 17(1), 17–32. https://doi.org/10.1002/jmr.647
  • Prajapat, M., Sarma, P., Shekhar, N., Avti, P., Sinha, S., Kaur, H., Kumar, S., Bhattacharyya, A., Kumar, H., Bansal, S., & Medhi, B. (2020). Drug targets for corona virus: A systematic review. Indian Journal of Pharmacology, 52(1), 56–65.
  • Pruitt, K. D., Tatusova, T., & Maglott, D. R. (2005). NCBI Reference Sequence (RefSeq): A curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Research, 33(Database issue), D501–D504. https://doi.org/10.1093/nar/gki025
  • Sainz, B., Mossel, E. C., Gallaher, W. R., Wimley, W. C., Peters, C. J., Wilson, R. B., & Garry, R. F. (2006). Inhibition of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) infectivity by peptides analogous to the viral spike protein. Virus Research, 120(1-2), 146–155. https://doi.org/10.1016/j.virusres.2006.03.001
  • Shang, J., Ye, G., Shi, K., Wan, Y., Luo, C., Aihara, H., Geng, Q., Auerbach, A., & Li, F. (2020). Structural basis of receptor recognition by SARS-CoV-2. Nature, 581, 221–224.
  • Sigrist, C. J., Bridge, A., & Le Mercier, P. (2020). A potential role for integrins in host cell entry by SARS-CoV-2. Antiviral Research, 177, 104759. https://doi.org/10.1016/j.antiviral.2020.104759
  • Snider, C., Jayasinghe, S., Hristova, K., & White, S. H. (2009). MPEx: A tool for exploring membrane proteins. Protein Science : a Publication of the Protein Society, 18(12), 2624–2628. https://doi.org/10.1002/pro.256
  • Taguchi, F., (1995). The S2 subunit of the murine coronavirus spike protein is not involved in receptor binding. Journal of Virology, 69(11), 7260–7263.
  • Taguchi, F., & Shimazaki, Y. K. (2000). Functional analysis of an epitope in the S2 subunit of the murine coronavirus spike protein: Involvement in fusion activity. Journal of General Virology, 81(12), 2867–2871.
  • Thomas, C. J., Casquilho-Gray, H. E., York, J., DeCamp, D. L., Dai, D., Petrilli, E. B., Boger, D. L., Slayden, R. A., Amberg, S. M., Sprang, S. R., Nunberg, J. H., (2011). A specific interaction of small molecule entry inhibitors with the envelope glycoprotein complex of the Junín hemorrhagic fever arenavirus. The Journal of Biological Chemistry, 286(8), 6192–6200.
  • van Doremalen, N., Bushmaker, T., Morris, D. H., Holbrook, M. G., Gamble, A., Williamson, B. N., Tamin, A., Harcourt, J. L., Thornburg, N. J., Gerber, S. I., Lloyd-Smith, J. O., de Wit, E., Munster, V. J., (2020). Aerosol and Surface Stability of SARS-CoV-2 as Compared with SARS-CoV-1. New England Journal of Medicine, 382(16), 1564–1567.
  • Walls, A. C., Park, Y.-J., Tortorici, M. A., Wall, A., McGuire, A. T., & Veesler, D. (2020). Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein. Cell, 181(2), 281–292.e6. https://doi.org/10.1016/j.cell.2020.02.058
  • White, S. H., & Wimley, W. C. (1999). Membrane protein folding and stability: Physical principles. Annual Review of Biophysics and Biomolecular Structure, 28(1), 319–365. https://doi.org/10.1146/annurev.biophys.28.1.319
  • Wild, C., Greenwell, T., & Matthews, T. (1993). A synthetic peptide from HIV-1 gp41 is a potent inhibitor of virus-mediated cell-cell fusion. AIDS Research and Human Retroviruses, 9(11), 1051–1053.
  • Wild, C., Oas, T., McDanal, C., Bolognesi, D., & Matthews, T. (1992). A synthetic peptide inhibitor of human immunodeficiency virus replication: Correlation between solution structure and viral inhibition. Proceedings of the National Academy of Sciences of the United States of America, 89(21), 10537–10541.
  • Wimley, W. C., & White, S. H. (1996). Experimentally determined hydrophobicity scale for proteins at membrane interfaces. Nature Structural Biology, 3(10), 842–848. https://doi.org/10.1038/nsb1096-842
  • Wu, C., Liu, Y., Yang, Y., Zhang, P., Zhong, W., Wang, Y., Wang, Q., Xu, Y., Li, M., Li, X., Zheng, M., Chen, L., & Li, H. (2020). Analysis of therapeutic targets for SARS-CoV-2 and discovery of potential drugs by computational methods. Acta Pharmaceutica Sinica. B, 10(5), 766–788. https://doi.org/10.1016/j.apsb.2020.02.008
  • Xia, S., Liu, Q., Wang, Q., Sun, Z., Su, S., Du, L., Ying, T., Lu, L., & Jiang, S. Middle East respiratory syndrome coronavirus (MERS-CoV) entry inhibitors targeting spike protein. Virus Research, (2014). 194, 200–210.
  • Xia, S., Liu, M., Wang, C., Xu, W., Lan, Q., Feng, S., Qi, F., Bao, L., Du, L., Liu, S., Qin, C., Sun, F., Shi, Z., Zhu, Y., Jiang, S., & Lu, L. (2020). Inhibition of SARS-CoV-2 (previously 2019-nCoV) infection by a highly potent pan-coronavirus fusion inhibitor targeting its spike protein that harbors a high capacity to mediate membrane fusion. Cell Research, 30(4), 343–355. https://doi.org/10.1038/s41422-020-0305-x
  • Xia, S., Yan, L., Xu, W., Agrawal, A. S., Algaissi, A., Tseng, C.-T K., Wang, Q., Du, L., Tan, W., Wilson, I. A., Jiang, S., Yang, B., & Lu, L. (2019). A pan-coronavirus fusion inhibitor targeting the HR1 domain of human coronavirus spike. Science Advances, 5(4), eaav4580. https://doi.org/10.1126/sciadv.aav4580
  • Xu, Y., Rahman, N. A., Othman, R., Hu, P., & Huang, M. (2012). Computational identification of self-inhibitory peptides from envelope proteins. Proteins, 80(9), 2154–2168. https://doi.org/10.1002/prot.24105
  • Yeung, K. S., Yamanaka, G. A., & Meanwell, N. A. (2006). Severe acute respiratory syndrome coronavirus entry into host cells: Opportunities for therapeutic intervention. Medicinal Research Reviews, 26(4), 414.
  • Yi, A. H., Fochtman, B. C., Rizzo, C. R., & Jacobs, A. (2016). Inhibition of HIV entry by targeting the envelope transmembrane subunit gp41. Current HIV Research, 14(3), 283–294. https://doi.org/10.2174/1570162x14999160224103908
  • Zhang, R., Li, Y., Zhang, A. L., Wang, Y., Molina, M. J. (2020). Identifying airborne transmission as the dominant route for the spread of COVID-19. Proceedings of the National Academy of Sciences
  • Zhou, P., Yang, X.-L., Wang, X.-G., Hu, B., Zhang, L., Zhang, W., Si, H.-R., Zhu, Y., Li, B., Huang, C.-L., Chen, H.-D., Chen, J., Luo, Y., Guo, H., Jiang, R.-D., Liu, M.-Q., Chen, Y., Shen, X.-R., Wang, X., … Shi, Z.-L. (2020). A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature, 579(7798), 270–273. https://doi.org/10.1038/s41586-020-2012-7

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