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Research Articles

HPV and molecular mimicry in systemic lupus erythematosus and an impact of compiling B-cell epitopes and MHC-class II binding profiles with in silico evidence

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Pages 12338-12346 | Received 13 Oct 2022, Accepted 01 Jan 2023, Published online: 06 Feb 2023

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.
  • Altschu, 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.
  • 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.
  • Daura, X., Mark, A. E., & Van Gunsteren, W. F. (1998). Parametrization of aliphatic CHn united atoms of GROMOS96 force field. Journal of Computational Chemistry. 19(5), 535–547.
  • Delgado-Vega, A. M.,Martínez-Bueno, M.,Oparina, N. Y.,López Herráez, D.,Kristjansdottir, H.,Steinsson, K.,Kozyrev, S. V., &Alarcón-Riquelme, M. E. (2018). Whole Exome Sequencing of Patients from Multicase Families with Systemic Lupus Erythematosus Identifies Multiple Rare Variants. Scientific Reports, 8(1)10.1038/s41598-018-26274-y
  • Dey, J., Mahapatra, S.R., Patnaik, S., Lata, S., Kushwaha, G. S., Panda, R. K., Misra, N., & Suar, M. (2022a). Molecular characterization and designing of a novel multiepitope vaccine construct against Pseudomonas aeruginosa. International Journal of Peptide Research and Therapeutics, 28, 49.
  • Dey, J., Mahapatra, S. R., Raj, T. K., Kaur, T., Jain, P., Tiwari, A., Patro, S., Misra, N., & Suar, M. (2022b). Designing a novel multi-epitope vaccine to evoke a robust immune response against pathogenic multidrug-resistant Enterococcus faecium bacterium. Gut Pathogens, 14(1), 21. https://doi.org/10.1186/s13099-022-00495-z
  • Dey, J., Mahapatra, S. R., Singh, P., Patro, S., Kushwaha, G. S., Misra, N., & Suar, M. (2021). B and T cell epitope-based peptides predicted from clumping factor protein of Staphylococcus aureus as vaccine targets. Microbial Pathogenesis, 160, 105171.
  • Dimitrov, I., Bangov, I., Flower, D. R., & Doytchinova, I. (2014). AllerTOP v.2–a server for in silico prediction of allergens. Journal of Molecular Modeling, 20(6), 2278. https://doi.org/10.1007/s00894-014-2278-5
  • Edgar, R. C. (2004). MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research, 32(5), 1792–1797.https://doi.org/10.1093/nar/gkh340
  • Elkon, K. (1995). Autoantibodies in systemic lupus erythematosus. Current opinion in Rheumatology, 7(5), 384–388. https://doi.org/10.1097/00002281-199509000-00004
  • García-Carrasco, M., Mendoza-Pinto, C., Rojas-Villarraga, A., Molano-González, N., Vallejo-Ruiz, V., Munguía-Realpozo, P., Colombo, A. L., & Cervera, R. (2019). Prevalence of cervical HPV infection in women with systemic lupus erythematosus: A systematic review and meta-analysis. Autoimmunity Reviews, 18(2), 184–191.
  • Gupta, S., Kapoor, P., Chaudhary, K., Gautam, A., Kumar, R., & Raghava, G. P. S. (2013). In silico approach for predicting toxicity of peptides and proteins. Volume 8 PLoS One.
  • Harari, A., Chen, Z., & Burk, R. D. (2014). HPV genomics: Past, present and future. Current Problems in Dermatology, 45, 1–18. https://doi.org/10.1159/000355952
  • Horst, A. K., Kumashie, K. G., Neumann, K., Diehl, L., & Tiegs, G. (2021). Antigen presentation, autoantibody production, and therapeutic targets in autoimmune liver disease. Cellular & Molecular Immunology, 18(1), 92–111. https://doi.org/10.1038/s41423-020-00568-6
  • Hung, T.,Pratt, G. A.,Sundararaman, B.,Townsend, M. J.,Chaivorapol, C.,Bhangale, T.,Graham, R. R.,Ortmann, W.,Criswell, L. A.,Yeo, G. W., &Behrens, T. W. (2015). The Ro60 autoantigen binds endogenous retroelements and regulates inflammatory gene expression. Science (New York, N.Y.), 350(6259), 455–459. 10.1126/science.aac7442 26382853
  • Jog, N. R., & James, J. A. (2021). Epstein Barr virus and autoimmune responses in systemic lupus erythematosus. Frontiers in Immunology, 11, 623944.
  • Kamen, D. L. (2014). Environmental influences on systemic Lupus Erythematosus expression. Rheumatic Diseases Clinics of North America, 40(3), 401–412, vii. https://doi.org/10.1016/j.rdc.2014.05.003
  • Kanduc, D.,Stufano, A.,Lucchese, G., &Kusalik, A. (2008). Massive peptide sharing between viral and human proteomes. Peptides, 29(10), 1755–1766. 10.1016/j.peptides.2008.05.022 18582510
  • Kanduc, D., & Shoenfeld, Y. (2019). Human papillomavirus epitope mimicry and autoimmunity: The molecular truth of peptide sharing. Pathobiology, 86(5–6), 285–295.
  • Klumb, E., Pinto, A., Jesus, G., Araujo, M., Jascone, L., Gayer, C., Ribeiro, F. M., Albuquerque, E. M. N., & Macedo, J. M. B. (2010). Are women with lupus at higher risk of HPV infection? Lupus, 19(13), 1485–1491.
  • Kogay, R., & Schönbach, C. (2019). Epitope predictions. In: Ranganathan, S., Gribskov, M., Nakai, K., & Schönbach C. (Eds), Encyclopedia of bioinformatics and computational biology [Internet] (pp. 952–971). Academic Press. https://www.sciencedirect.com/science/article/pii/B9780128096338202483
  • Koscielny, G., An, P., Carvalho-Silva, D., Cham, J. A., Fumis, L., Gasparyan, R., Hasan, S., Karamanis, N., Maguire, M., Papa, E., Pierleoni, A., Pignatelli, M., Platt, T., Rowland, F., Wankar, P., Bento, A. P., Burdett, T., Fabregat, A., Forbes, S., … Dunham, I. (2017). Open Targets: A platform for therapeutic target identification and validation. Nucleic Acids Research, 45(D1), D985–D994. https://doi.org/10.1093/nar/gkw1055
  • 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.
  • Mahapatra, S. R., Dey, J., Jaiswal, A., Roy, R., Misra, N., & Suar, M. (2022). Immunoinformatics-guided designing of epitope-based subunit vaccine from Pilus assembly protein of Acinetobacter baumannii bacteria. Journal of Immunological Methods, 508, 113325. 113325.
  • Mahapatra, S. R., Dey, J., Kaur, T., Sarangi, R., Bajoria, A. A., Kushwaha, G. S., Misra, N., & Suar, M. (2021). Immunoinformatics and molecular docking studies reveal a novel Multi-Epitope peptide vaccine against pneumonia infection. Vaccine, 39(42), 6221–6237. https://doi.org/10.1016/j.vaccine.2021.09.025
  • Manczinger, M., & Kemény, L. (2018). Peptide presentation by HLA-DQ molecules is associated with the development of immune tolerance. PeerJ, 6, e5118.
  • Mohd, A. R., Zubair, S., & Azhar, A. (2015). Ligand docking and binding site analysis with pymol and autodock/vina. IJBAS, 4(2), 168.
  • Parrinello, M., & Rahman, A. (1981). Polymorphic transitions in single crystals: A new molecular dynamics method. Journal of Applied Physics, 52(12), 7182–7190.
  • Pathak, S., & Mohan, C. (2011). Cellular and molecular pathogenesis of systemic lupus erythematosus: Lessons from animal models. Arthritis Research & Therapy, 13(5), 241.
  • Pawar, S. S., & Rohane, S. H. (2021). Review on discovery studio: An important tool for molecular docking. Asian Journal of Research in Chemistry, 14(1), 86–88.
  • Rosen, A., & Casciola-Rosen, L. (2009). Autoantigens in systemic autoimmunity: Critical partner in pathogenesis. Journal of Internal Medicine, 265(6), 625–631. https://doi.org/10.1111/j.1365-2796.2009.02102.x
  • Saha, S., & Raghava, G. P. S. (2006). AlgPred: Prediction of allergenic proteins and mapping of IgE epitopes. Nucleic Acids Research, 34(Web Server issue), W202–209. https://doi.org/10.1093/nar/gkl343
  • Sahu, M., & Prasuna, J. (2016). Twin studies: A unique epidemiological tool. Indian Journal of Community Medicine, 41(3), 177–182. https://doi.org/10.4103/0970-0218.183593
  • Singh, J., Malik, D., & Raina, A. (2021). Immuno-informatics approach for B-cell and T-cell epitope based peptide vaccine design against novel COVID-19 virus. Vaccine, 39(7), 1087–1095. https://doi.org/10.1016/j.vaccine.2021.01.011
  • Singh, H., & Raghava, G. P. S. (2001). ProPred: Prediction of HLA-DR binding sites. Bioinformatics (Oxford, England), 17(12), 1236–1237. https://doi.org/10.1093/bioinformatics/17.12.1236
  • Smatti, M. K., Cyprian, F. S., Nasrallah, G. K., A., Thani, A. A., Almishal, R. O., & Yassine, H. M. (2019). Viruses and autoimmunity: A review on the potential interaction and molecular mechanisms. Viruses, 11(8), 762.
  • Tamura, K., Stecher, G., & Kumar, S. (2021). Molecular evolutionary genetics analysis version 11. Molecular Biology and Evolution, 38(7):3022–3027.
  • The UniProt Consortium. (2015). UniProt: A hub for protein information. Nucleic Acids Research, 43(Database issue), D204–12.
  • Trott, O., & Olson, A. J. (2009). AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry, 31, 455–461.
  • Tugnet, N., Rylance, P., Roden, D., Trela, M., & Nelson, P. (2013). Human endogenous retroviruses (HERVs) and autoimmune rheumatic disease: Is there a link? TORJ, 7(1), 13–21.
  • Venigalla, S. S. K., Premakumar, S., & Janakiraman, V. (2020 ). A possible role for autoimmunity through molecular mimicry in alphavirus mediated arthritis. Scientific Reports, 10(1), 938.
  • Zard, E., Arnaud, L., Mathian, A., Chakhtoura, Z., Hie, M., Touraine, P., Heard, I., & Amoura, Z. (2014). Increased risk of high grade cervical squamous intraepithelial lesions in systemic lupus erythematosus: A meta-analysis of the literature. Autoimmunity Reviews, 13(7), 730–735. https://doi.org/10.1016/j.autrev.2014.03.001
  • Zhao, P., Xu, L., Wang, P., Liang, X., Qi, J., Liu, P., Guo, C., Zhang, L., Ma, C., & Gao, L. (2010). Increased expression of human T-cell immunoglobulin- and mucin-domain-containing molecule-4 in peripheral blood mononuclear cells from patients with system lupus erythematosus. Cellular & Molecular Immunology, 7(2), 152–156.
  • Zoete, V., Cuendet, M. A., Grosdidier, A., & Michielin, O. (2011). SwissParam: A fast force field generation tool for small organic molecules. Journal of Computational Chemistry, 32(11), 2359–2368. https://doi.org/10.1002/jcc.21816

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