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Research Articles

Immunoinformatics based design and prediction of proteome-wide killer cell epitopes of Leishmania donovani: Potential application in vaccine development

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Pages 10578-10591 | Received 09 Jul 2020, Accepted 16 Jun 2021, Published online: 05 Jul 2021

References

  • Ali, M., Pandey, R. K., Khatoon, N., Narula, A., Mishra, A., & Prajapati, V. K. (2017). Exploring dengue genome to construct a multi-epitope based subunit vaccine by utilizing immunoinformatics approach to battle against dengue infection. Scientific Reports, 7(1), 9232.
  • Belkaid, Y., von Stebut, E., Mendez, S., Lira, R., Caler, E., Bertholet, S., Udey, M. C., & Sacks, D. (2002). CD8+ T cells are required for primary immunity in C57BL/6 mice following low-dose, intradermal challenge with Leishmania major. Journal of Immunology (Baltimore, MD: 1950), 168(8), 3992–4000. https://doi.org/10.4049/jimmunol.168.8.3992
  • Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N., & Bourne, P. E. (2000). The protein data bank. Nucleic Acids Research, 28(1), 235–242. https://doi.org/10.1093/nar/28.1.235
  • Bhatia, V., Sinha, M., Luxon, B., & Garg, N. (2004). Utility of the Trypanosoma cruzi sequence database for identification of potential vaccine candidates by in silico and in vitro screening. Infection and Immunity, 72(11), 6245–6254. https://doi.org/10.1128/IAI.72.11.6245-6254.2004
  • Bindu, S., & Rentala, M. (2004). Leishmaniasis: Current status of vaccine development. Current Molecular Medicine, 4(6), 667–679.
  • Bora, B., Biswas, A. D., Gurung, A. B., Bhattacharjee, A., Mattaparthi, V. S. K., & Mukherjee, A. K. (2017). An in silico approach to understand the structure-function properties of a serine protease (Bacifrinase) from Bacillus cereus and experimental evidence to support the interaction of Bacifrinase with fibrinogen and thrombin. Journal of Biomolecular Structure & Dynamics, 35(3), 622–644. https://doi.org/10.1080/07391102.2016.1158665
  • Bui, H.-H., Sidney, J., Li, W., Fusseder, N., & Sette, A. (2007). Development of an epitope conservancy analysis tool to facilitate the design of epitope-based diagnostics and vaccines. BMC Bioinformatics, 8(1), 361. https://doi.org/10.1186/1471-2105-8-361
  • Calis, J. J. A., Maybeno, M., Greenbaum, J. A., Weiskopf, D., De Silva, A. D., Sette, A., Keşmir, C., & Peters, B. (2013). Properties of MHC class I presented peptides that enhance immunogenicity. PLoS Computational Biology, 9(10), e1003266. https://doi.org/10.1371/journal.pcbi.1003266
  • Chappuis, F., Sundar, S., Hailu, A., Ghalib, H., Rijal, S., Peeling, R. W., Alvar, J., & Boelaert, M. (2007). Visceral leishmaniasis: What are the needs for diagnosis, treatment and control? Nature Reviews. Microbiology, 5(11), 873–882. https://doi.org/10.1038/nrmicro1748
  • Cheng, J., Randall, A. Z., Sweredoski, M. J., & Baldi, P. (2005). SCRATCH: A protein structure and structural feature prediction server. Nucleic Acids Research, 33(Web Server issue), W72–W76. https://doi.org/10.1093/nar/gki396
  • Chou, P. Y., & Fasman, G. D. (1974). Conformational parameters for amino acids in helical, beta-sheet, and random coil regions calculated from proteins. Biochemistry, 13(2), 211–222. https://doi.org/10.1021/bi00699a001
  • Connell, N. D., Medina-Acosta, E., McMaster, W. R., Bloom, B. R., & Russell, D. G. (1993). Effective immunization against cutaneous leishmaniasis with recombinant bacille Calmette-Guérin expressing the Leishmania surface proteinase gp63. Proceedings of the National Academy of Sciences of the United States of America, 90(24), 11473–11477. https://doi.org/10.1073/pnas.90.24.11473
  • 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.
  • Doytchinova, I., & Flower, D. (2008). Bioinformatic approach for identifying parasite and fungal candidate subunit vaccines. The Open Vaccine Journal, 1(1), 22–26. https://doi.org/10.2174/1875035400801010022
  • Dumonteil, E. (2007). DNA vaccines against protozoan parasites: Advances and challenges. Journal of Biomedicine & Biotechnology, 2007(6), 90520–90520.
  • Dyrløv Bendtsen, J., Nielsen, H., von Heijne, G., & Brunak, S. (2004). Improved prediction of signal peptides: SignalP 3.0. Journal of Molecular Biology, 340(4), 783–795. https://doi.org/10.1016/j.jmb.2004.05.028
  • Giguère, S., Drouin, A., Lacoste, A., Marchand, M., Corbeil, J., & Laviolette, F. (2013). MHC-NP: Predicting peptides naturally processed by the MHC. Journal of Immunological Methods, 400–401, 30–36. https://doi.org/10.1016/j.jim.2013.10.003
  • Hasan, M. A., Hossain, M., & Alam, M. J. (2013). A computational assay to design an epitope-based peptide vaccine against Saint Louis encephalitis virus. Bioinformatics and Biology Insights, 7, 347–355.
  • He, Y., Rappuoli, R., De Groot, A. S., & Chen, R. T. (2010). Emerging vaccine informatics. Journal of Biomedicine and Biotechnology, 2010, 26.
  • Hernandez-Ruiz, J., Salaiza-Suazo, N., Carrada, G., Escoto, S., Ruiz-Remigio, A., Rosenstein, Y., Zentella, A., & Becker, I. (2010). CD8 cells of patients with diffuse cutaneous leishmaniasis display functional exhaustion: The latter is reversed, in vitro, by TLR2 agonists. PLoS Neglected Tropical Diseases, 4(11), e871. https://doi.org/10.1371/journal.pntd.0000871
  • Herrera-Najera, C., Piña-Aguilar, R., Xacur-Garcia, F., Ramirez-Sierra, M. J., & Dumonteil, E. (2009). Mining the Leishmania genome for novel antigens and vaccine candidates. Proteomics, 9(5), 1293–1301. https://doi.org/10.1002/pmic.200800533
  • Hosen, M. I., Tanmoy, A. M., Mahbuba, D.-A., Salma, U., Nazim, M., Islam, M. T., & Akhteruzzaman, S. (2014). Application of a subtractive genomics approach for in silico identification and characterization of novel drug targets in Mycobacterium tuberculosis F11. Interdisciplinary Sciences, Computational Life Sciences, 6(1), 48–56. https://doi.org/10.1007/s12539-014-0188-y
  • Huber, M., Timms, E., Mak, T. W., Röllinghoff, M., & Lohoff, M. (1998). Effective and long-lasting immunity against the parasite Leishmania major in CD8-deficient mice. Infection and Immunity, 66(8), 3968–3970. https://doi.org/10.1128/IAI.66.8.3968-3970.1998
  • Hussain, H., Al-Harrasi, A., Al-Rawahi, A., Green, I. R., & Gibbons, S. (2014). Fruitful decade for antileishmanial compounds from 2002 to Late 2011. Chemical Reviews, 114(20), 10369–10428. https://doi.org/10.1021/cr400552x
  • Kashif, M., Hira, S. K., Upadhyaya, A., Gupta, U., Singh, R., Paladhi, A., Khan, F. I., Rub, A., & Manna, P. P. (2019). In silico studies and evaluation of antiparasitic role of a novel pyruvate phosphate dikinase inhibitor in Leishmania donovani infected macrophages. International Journal of Antimicrobial Agents, 53(4), 508–514. https://doi.org/10.1016/j.ijantimicag.2018.12.011
  • Kashif, M., Tabrez, S., Husein, A., Arish, M., Kalaiarasan, P., Manna, P. P., Subbarao, N., Akhter, Y., & Rub, A. (2018). Identification of novel inhibitors against UDP-galactopyranose mutase to combat leishmaniasis. Journal of Cellular Biochemistry, 119(3), 2653–2665. https://doi.org/10.1002/jcb.26433
  • Kedzierski, L., Zhu, Y., & Handman, E. (2006). Leishmania vaccines: Progress and problems. Parasitology, 133(S2), S87–S112. https://doi.org/10.1017/S0031182006001831
  • Kim, Y., Ponomarenko, J., Zhu, Z., Tamang, D., Wang, P., Greenbaum, J., Lundegaard, C., Sette, A., Lund, O., Bourne, P. E., Nielsen, M., & Peters, B. (2012). Immune epitope database analysis resource. Nucleic Acids Research, 40(Web Server issue), W525–W530. https://doi.org/10.1093/nar/gks438
  • Krogh, A., Larsson, B., von Heijne, G., & Sonnhammer, E. L. L. (2001). Predicting transmembrane protein topology with a hidden markov model: Application to complete genomes11Edited by F. Cohen. Journal of Molecular Biology, 305(3), 567–580. https://doi.org/10.1006/jmbi.2000.4315
  • Lamiable, A., Thévenet, P., Rey, J., Vavrusa, M., Derreumaux, P., & Tufféry, P. (2016). PEP-FOLD3: Faster de novo structure prediction for linear peptides in solution and in complex. Nucleic Acids Research, 44(W1), W449–W454. https://doi.org/10.1093/nar/gkw329
  • Laoye, B. J., Okurumeh, O. A., Obagaye, O. V., Olagunju, M. O., Bankole, O. O., Olubiyi, O. O., & Ogundele, O. M. (2016). Dopamine binds calmodulin during autoregulation of dopaminergic D2 receptor signaling through CaMKIIα-calmodulin complex. Journal of Receptor and Signal Transduction Research, 36(3), 271–277. https://doi.org/10.3109/10799893.2015.1091476
  • López, J. A., Weilenman, C., Audran, R., Roggero, M. A., Bonelo, A., Tiercy, J.-M., Spertini, F., & Corradin, G. (2001). A synthetic malaria vaccine elicits a potent CD8+ and CD4+ T lymphocyte immune response in humans. Implications for vaccination strategies. European Journal of Immunology, 31(7), 1989–1998. https://doi.org/10.1002/1521-4141(200107)31:7<1989::AID-IMMU1989>3.0.CO;2-M
  • Lundegaard, C., Lamberth, K., Harndahl, M., Buus, S., Lund, O., & Nielsen, M. (2008). NetMHC-3.0: Accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8–11. Nucleic Acids Research, 36(Web Server issue), W509–W512. https://doi.org/10.1093/nar/gkn202
  • Magnan, C. N., Randall, A., & Baldi, P. (2009). SOLpro: Accurate sequence-based prediction of protein solubility. Bioinformatics (Oxford, England), 25(17), 2200–2207. https://doi.org/10.1093/bioinformatics/btp386
  • Maupetit, J., Tuffery, P., & Derreumaux, P. (2007). A coarse-grained protein force field for folding and structure prediction. Proteins, 69(2), 394–408. https://doi.org/10.1002/prot.21505
  • Milon, G., Titus, R. G., Cerottini, J. C., Marchal, G., & Louis, J. A. (1986). Higher frequency of Leishmania major-specific L3T4+ T cells in susceptible BALB/c as compared with resistant CBA mice. Journal of Immunology (Baltimore, MD: 1950), 136(4), 1467.
  • Mohammad, K., Partha, P. M., Yusuf, A., Mohammed, A., & Abdur, R. (2017). Screening of novel inhibitors against Leishmania donovani calcium ion channel to fight leishmaniasis. Infectious Disorder: Drug Targets, 17(2), 120–129.
  • Nielsen, M., Lundegaard, C., Worning, P., Lauemøller, S. L., Lamberth, K., Buus, S., Brunak, S., & Lund, O. (2003). Reliable prediction of T-cell epitopes using neural networks with novel sequence representations. Protein Science: A Publication of the Protein Society, 12(5), 1007–1017. https://doi.org/10.1110/ps.0239403
  • Payab, N., Mahnam, K., & Shakhsi-Niaei, M. (2018). Computational comparison of two new fusion proteins for multiple sclerosis. Research in Pharmaceutical Sciences, 13(5), 394–403. https://doi.org/10.4103/1735-5362.236832
  • Pierleoni, A., Martelli, P. L., & Casadio, R. (2008). PredGPI: A GPI-anchor predictor. BMC Bioinformatics, 9(1), 392. https://doi.org/10.1186/1471-2105-9-392
  • Poland, G. A., Ovsyannikova, I. G., & Jacobson, R. M. (2009). Application of pharmacogenomics to vaccines. Pharmacogenomics, 10(5), 837–852. https://doi.org/10.2217/pgs.09.25
  • Pronk, S., Páll, S., Schulz, R., Larsson, P., Bjelkmar, P., Apostolov, R., Shirts, M. R., Smith, J. C., Kasson, P. M., van der Spoel, D., Hess, B., & Lindahl, E. (2013). GROMACS 4.5: A high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics (Oxford, England), 29(7), 845–854. https://doi.org/10.1093/bioinformatics/btt055
  • Rana, A., Rub, A., & Akhter, Y. (2015). Proteome-wide B and T cell epitope repertoires in outer membrane proteins of Mycobacterium avium subsp. paratuberculosis have vaccine and diagnostic relevance: A holistic approach. Journal of Molecular Recognition: JMR, 28(8), 506–520. https://doi.org/10.1002/jmr.2458
  • Rappuoli, R. (2000). Reverse vaccinology. Current Opinion in Microbiology, 3(5), 445–450. https://doi.org/10.1016/S1369-5274(00)00119-3
  • Ruiz, J. H., & Becker, I. (2007). CD8 cytotoxic T cells in cutaneous leishmaniasis. Parasite Immunology, 29(12), 671–678. https://doi.org/10.1111/j.1365-3024.2007.00991.x
  • Salaiza-Suazo, N., Volkow, P., Pérez Tamayo, R., Moll, H., Gillitzer, R., Pérez-Torres, A., Pérez-Montfort, R., Domínguez, J. D., Velasco-Castrejón, O., Crippa, M., & Becker, I. (1999). Treatment of two patients with diffuse cutaneous leishmaniasis caused by Leishmania mexicana modifies the immunohistological profile but not the disease outcome. Tropical Medicine & International Health: TM & IH, 4(12), 801–811. https://doi.org/10.1046/j.1365-3156.1999.00491.x
  • Seyed, N., Zahedifard, F., Safaiyan, S., Gholami, E., Doustdari F, Azadmanesh, K., Mirzaei, M., Eslami, N. S., Sadegh, A. K., Eslami far, A., Sharifi, I.,& Rafati, S. (2011). In silico analysis of six known leishmania major antigens and in vitro evaluation of specific epitopes eliciting HLA-A2 restricted CD8 T cell response. PLOS Neglected Tropical Diseases 5(9), e1295. https://doi.org/10.1371/journal.pntd.0001295
  • Schuttelkopf, 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. https://doi.org/10.1107/S0907444904011679
  • Shahsavandi, S., Ebrahimi, M. M., Sadeghi, K., & Mahravani, H. (2015). Design of a heterosubtypic epitope-based peptide vaccine fused with hemokinin-1 against influenza viruses. Virologica Sinica, 30(3), 200–207. https://doi.org/10.1007/s12250-014-3504-0
  • Singh, S. P., Roopendra, K., & Mishra, B. N. (2015). Genome-wide prediction of vaccine candidates for Leishmania major: An integrated approach. Journal of Tropical Medicine, 2015, 1–14. https://doi.org/10.1155/2015/709216
  • T, A. K. (2013). CFSSP: Chou and Fasman secondary structure prediction server. WIDE SPECTURM-Research Journal, 1, 15–19.
  • Titus, R. G., Milon, G., Marchal, G., Vassalli, P., Cerottini, J.-C., & Louis, J. A. (1987). Involvement of specific Lyt-2+ T cells in the immunological control of experimentally induced murine cutaneous leishmaniasis. European Journal of Immunology, 17(10), 1429–1433. https://doi.org/10.1002/eji.1830171007
  • van Aalten, D. M. F., Bywater, R., Findlay, J. B. C., Hendlich, M., Hooft, R. W. W., & Vriend, G. (1996). PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules. Journal of Computer-Aided Molecular Design, 10(3), 255–262. https://doi.org/10.1007/BF00355047
  • Vannier-Santos, M. A., Martiny, A., & Souza, W. (2002). Cell Biology of Leishmania spp.: Invading and evading. Current Pharmaceutical Design, 8(4), 297–318. https://doi.org/10.2174/1381612023396230
  • Wallace, A. C., Laskowski, R. A., & Thornton, J. M. (1995). LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions. Protein Engineering, 8(2), 127–134. https://doi.org/10.1093/protein/8.2.127
  • Wang, Z. E., Reiner, S. L., Hatam, F., Heinzel, F. P., Bouvier, J., Turck, C. W., & Locksley, R. M. (1993). Targeted activation of CD8 cells and infection of beta 2-microglobulin-deficient mice fail to confirm a primary protective role for CD8 cells in experimental leishmaniasis. Journal of Immunology (Baltimore, MD: 1950), 151(4), 2077.
  • Yang, J.-M., & Chen, C.-C. (2004). GEMDOCK: A generic evolutionary method for molecular docking. Proteins, 55(2), 288–304. https://doi.org/10.1002/prot.20035

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