151
Views
13
CrossRef citations to date
0
Altmetric
Research Article

HHV-5 epitope: A potential vaccine candidate with high antigenicity and large coverage

, , , , , & show all
Pages 2098-2109 | Received 22 Dec 2017, Accepted 03 Apr 2018, Published online: 10 Dec 2018

References

  • Abd El-Baky, N., Uversky, V. N., & Redwan, E. M. (2017). Virucidal activity of cell-penetrating peptides of viral origin. Journal of Biomolecular Structure and Dynamics, 36, 1739–1746.
  • Aggarwal, M., Singh, A., Grover, S., Pandey, B., Kumari, A., & Grover, A. (2018). Role of pncA gene mutations W68R and W68G in pyrazinamide resistance. Journal of Cellular Biochemistry, 119(3), 2567–2578.
  • Anusuya, S., & Gromiha, M. M. (2017). Quercetin derivatives as non-nucleoside inhibitors for dengue polymerase: Molecular docking, molecular dynamics simulation, and binding free energy calculation. Journal of Biomolecular Structure and Dynamics, 35(13), 2895–2909. doi: 10.1080/07391102.2016.1234416.
  • Berendsen, H. J., van der Spoel, D., & van Drunen, R. (1995). GROMACS: A message-passing parallel molecular dynamics implementation. Computer Physics Communications, 91(1-3), 43–56.
  • Bijker, M. S., Melief, C. J., Offringa, R., & Van Der Burg, S. H. (2007). Design and development of synthetic peptide vaccines: past, present and future. Expert review of vaccines, 6(4), 591–603.
  • Blom, N., Gammeltoft, S., & Brunak, S. (1999). Sequence and structure-based prediction of eukaryotic protein phosphorylation sites. Journal of Molecular Biology, 294(5), 1351–1362.
  • Brusic, V., & Petrovsky, N. (2005). Immunoinformatics and its relevance to understanding human immune disease. Expert Review of Clinical Immunology, 1(1), 145–157.
  • Bui, H.-H., Sidney, J., Dinh, K., Southwood, S., Newman, M. J., & Sette, A. (2006). Predicting population coverage of T-cell epitope-based diagnostics and vaccines. BMC Bioinformatics, 7, 153.
  • Chakravarti, A., Kashyap, B., & Matlani, M. (2009). Cytomegalovirus infection: An Indian perspective. Indian Journal of Medical Microbiology, 27(1), 3.
  • Colovos, C., & Yeates, T. O. (1993). Verification of protein structures: Patterns of nonbonded atomic interactions. Protein Science, 2(9), 1511–1519.
  • Compton, T. (2004). Receptors and immune sensors: The complex entry path of human cytomegalovirus. Trends in Cell Biology, 14(1), 5–8.
  • Compton, T., Kurt-Jones, E. A., Boehme, K. W., Belko, J., Latz, E., Golenbock, D. T., & Finberg, R. W. (2003). Human cytomegalovirus activates inflammatory cytokine responses via CD14 and Toll-like receptor 2. Journal of Virology, 77(8), 4588–4596.
  • Compton, T., Nowlin, D. M., & Cooper, N. R. (1993). Initiation of human cytomegalovirus infection requires initial interaction with cell surface heparan sulfate. Virology, 193(2), 834–841.
  • Demmler, G. J. (1991). Infectious Diseases Society of America and Centers for Disease Control: Summary of a workshop on surveillance for congenital cytomegalovirus disease. Review of Infectious Diseases, 13(2), 315–329.
  • Doytchinova, I. A., & Flower, D. R. (2007). VaxiJen: A server for prediction of protective antigens, tumour antigens and subunit vaccines. BMC Bioinformatics, 8(1), 4.
  • Feire, A. L., Koss, H., & Compton, T. (2004). Cellular integrins function as entry receptors for human cytomegalovirus via a highly conserved disintegrin-like domain. Proceedings of the National Academy of Sciences of the United States of America, 101(43), 15470–15475.
  • Gandhoke, I., Aggarwal, R., Lal, S., & Khare, S. (2006). Congenital CMV infection in symptomatic infants in Delhi and surrounding areas. Indian Journal of Pediatrics, 73(12), 1095–1097.
  • Gasteiger, E., Hoogland, C., Gattiker, A., Duvaud, S. E., Wilkins, M. R., Appel, R. D., & Bairoch, A. (2005). Protein identification and analysis tools on the ExPASy server. Berlin-Heidelberg-New York: Springer-Verlag.
  • Guex, N., & Peitsch, M. C. (1997). SWISS‐MODEL and the Swiss‐Pdb Viewer: An environment for comparative protein modeling. Electrophoresis, 18(15), 2714–2723.
  • Ibanez, C. E., Schrier, R., Ghazal, P., Wiley, C., & Nelson, J. A. (1991). Human cytomegalovirus productively infects primary differentiated macrophages. Journal of Virology, 65(12), 6581–6588.
  • Isaacson, M. K., & Compton, T. (2009). Human cytomegalovirus glycoprotein B is required for virus entry and cell-to-cell spread but not for virion attachment, assembly, or egress. Journal of Virology, 83(8), 3891–3903.
  • Kawai, T., & Akira, S. (2005). Pathogen recognition with Toll-like receptors. Current Opinion in Immunology, 17(4), 338–344.
  • Klemin, S. (2008). Molecular biology of the cell, molecular biology of the cell: The problems book. Yale Journal of Biology and Medicine, 81(3), 157.
  • Kumar, A., Cocco, E., Atzori, L., Marrosu, M. G., & Pieroni, E. (2013). Structural and dynamical insights on HLA-DR2 complexes that confer susceptibility to multiple sclerosis in Sardinia: A molecular dynamics simulation study. PloS One, 8(3), e59711.
  • Lazzarotto, T., Guerra, B., Spezzacatena, P., Varani, S., Gabrielli, L., Pradelli, P., … Landini, M. (1998). Prenatal diagnosis of congenital cytomegalovirus infection. Journal of Clinical Microbiology, 36(12), 3540–3544.
  • Lin, S. Y.-H., Cheng, C.-W., & Su, E. C.-Y. (2013). Prediction of B-cell epitopes using evolutionary information and propensity scales. BMC bioinformatics, 14(Suppl 2), S10.
  • Lindahl, E., Hess, B., & Van Der Spoel, D. (2001). GROMACS 3.0: A package for molecular simulation and trajectory analysis. Journal of Molecular Modeling, 7(8), 306–317.
  • Lovell, S. C., Davis, I. W., Arendall, W. B., de Bakker, P. I., Word, J. M., Prisant, M. G., … Richardson, D. C. (2003). Structure validation by Cα geometry: Φ, ψ and Cβ deviation. Proteins: Structure, Function, and Bioinformatics, 50(3), 437–450.
  • Macindoe, G., Mavridis, L., Venkatraman, V., Devignes, M.-D., & Ritchie, D. W. (2010). HexServer: An FFT-based protein docking server powered by graphics processors. Nucleic Acids Research, 38, W445–W449.
  • Moutsopoulos, N., Routsias, J., Vlachoyiannopoulos, P., Tzioufas, A., & Moutsopoulos, H. (2000). B-cell epitopes of intracellular autoantigens: Myth and reality. Molecular Medicine, 6(3), 141–151.
  • Nagpal, N., Goyal, S., Wahi, D., Jain, R., Jamal, S., Singh, A., … Grover, A. (2015). Molecular principles behind Boceprevir resistance due to mutations in hepatitis C NS3/4A protease. Gene, 570(1), 115–121.
  • NCBI. (2016). Database resources of the National Center for Biotechnology Information. Nucleic Acids Research, 44(D1), D7.
  • Omer, A., & Singh, P. (2017). An integrated approach of network-based systems biology, molecular docking, and molecular dynamics approach to unravel the role of existing antiviral molecules against AIDS-associated cancer. Journal of Biomolecular Structure and Dynamics, 35(7), 1547–1558.
  • Pandey, B., Grover, S., Tyagi, C., Goyal, S., Jamal, S., Singh, A., … Grover, A. (2017). Double mutants in DNA gyrase lead to ofloxacin resistance in Mycobacterium tuberculosis. Journal of Cellular Biochemistry, 118(9), 2950–2957.
  • Pass, R. F., Zhang, C., Evans, A., Simpson, T., Andrews, W., Huang, M.-L., … Flanigan, C. (2009). Vaccine prevention of maternal cytomegalovirus infection. New England Journal of Medicine, 360(12), 1191–1199.
  • Patel, K., Tyagi, C., Goyal, S., Jamal, S., Wahi, D., Jain, R., … Grover, A. (2015). Identification of chebulinic acid as potent natural inhibitor of M. tuberculosis DNA gyrase and molecular insights into its binding mode of action. Computational Biology and Chemistry, 59, 37–47.
  • Phillips, S. L., & Bresnahan, W. A. (2011). Identification of binary interactions between human cytomegalovirus virion proteins. Journal of Virology, 85(1), 440–447.
  • Reche, P. A., Glutting, J.-P., & Reinherz, E. L. (2002). Prediction of MHC class I binding peptides using profile motifs. Human Immunology, 63(9), 701–709.
  • Ryan, K. J., & Ray, C. G. (2004). Medical microbiology. New York, NY: McGraw Hill.
  • Saha, S., & Raghava, G. (2006). Prediction of continuous B‐cell epitopes in an antigen using recurrent neural network. Proteins: Structure, Function, and Bioinformatics, 65(1), 40–48.
  • Schirle, M., Weinschenk, T., & Stevanović, S. (2001). Combining computer algorithms with experimental approaches permits the rapid and accurate identification of T cell epitopes from defined antigens. Journal of Immunological Methods, 257(1), 1–16.
  • Schreiner, W., Karch, R., Knapp, B., & Ilieva, N. (2012). Relaxation estimation of RMSD in molecular dynamics immunosimulations. Computational and Mathematical Methods in Medicine, 2012, 173521.
  • Singh, A., Goyal, S., Jamal, S., Subramani, B., Das, M., Admane, N., & Grover, A. (2016). Computational identification of novel piperidine derivatives as potential HDM2 inhibitors designed by fragment-based QSAR, molecular docking and molecular dynamics simulations. Structural Chemistry, 27(3), 993–1003.
  • Singh, A., Grover, S., Sinha, S., Das, M., Somvanshi, P., & Grover, A. (2017). Mechanistic principles behind molecular mechanism of Rifampicin resistance in mutant RNA polymerase beta subunit of Mycobacterium tuberculosis. Journal of Cellular Biochemistry, 118(12), 4594–4606.
  • Singh, A., Singh, A., Grover, S., Pandey, B., Kumari, A., & Grover, A. (2018). Wild-type catalase peroxidase vs G279D mutant type: Molecular basis of Isoniazid drug resistance in Mycobacterium tuberculosis. Gene, 641, 226–234.
  • Singh, H., & Raghava, G. (2001). ProPred: Prediction of HLA-DR binding sites. Bioinformatics, 17(12), 1236–1237.
  • Sinzger, C., Kahl, M., Laib, K., Klingel, K., Rieger, P., Plachter, B., & Jahn, G. (2000). Tropism of human cytomegalovirus for endothelial cells is determined by a post-entry step dependent on efficient translocation to the nucleus. Journal of General Virology, 81(12), 3021–3035.
  • Thévenet, P., Shen, Y., Maupetit, J., Guyon, F., Derreumaux, P., & Tufféry, P. (2012). PEP-FOLD: An updated de novo structure prediction server for both linear and disulfide bonded cyclic peptides. Nucleic Acids Research, 40(W1), W288–W293.
  • Verma, S., Grover, S., Tyagi, C., Goyal, S., Jamal, S., Singh, A., & Grover, A. (2016). Hydrophobic interactions are a key to MDM2 inhibition by polyphenols as revealed by molecular dynamics simulations and MM/PBSA free energy calculations. PloS One, 11(2), e0149014.
  • Verma, S., Singh, A., Kumari, A., Goyal, S., Jamal, S., Sinha, S., & Grover, A. (2017a). Dissecting the role of mutations in chymase inhibition: Free energy and decomposition analysis. Gene, 609, 68–79.
  • Verma, S., Singh, A., Kumari, A., Tyagi, C., Goyal, S., Jamal, S., & Grover, A. (2017b). Natural polyphenolic inhibitors against the antiapoptotic BCL-2. Journal of Receptors and Signal Transduction, 37(4), 391–400.
  • Vora, J., Patel, S., Sinha, S., Sharma, S., Srivastava, A., Chhabria, M., & Shrivastava, N. (2018). Molecular docking, QSAR and ADMET based mining of natural compounds against prime targets of HIV. Journal of Biomolecular Structure and Dynamics 35, 2631–2644.
  • Wang, X., Huong, S.-M., Chiu, M. L., Raab-Traub, N., & Huang, E.-S. (2003). Epidermal growth factor receptor is a cellular receptor for human cytomegalovirus. Nature, 424(6947), 456–461.
  • Wiederstein, M., & Sippl, M. J. (2007). ProSA-web: Interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Research, 35(Suppl 2), W407–W410.
  • Xiao, Y., Lu, Y., & Chen, Y.-H. (2001). Epitope-vaccine as a new strategy against HIV-1 mutation. Immunology Letters, 77(1), 3–6.

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.