Screening of potential antigens from whole proteome and development of multi-epitope vaccine against Rhizopus delemar using immunoinformatics approaches

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. https://doi.org/10.1038/s41598-017-09199-w.
   PubMed Web of Science ®Google Scholar
• Aliramaei, M. R., Khorasgani, M. R., Rahmani, M. R., Zarkesh Esfahani, S. H., & Emamzadeh, R. (2019). Expression of Helicobacter pylori CagL gene in Lactococcus lactis MG1363 and evaluation of its immunogenicity as an oral vaccine in mice. Microbial Pathogenesis, 142, 103926. https://doi.org/10.1016/j.micpath.2019.103926
   PubMed Web of Science ®Google Scholar
• Alvarez-García, E., Alegre-Cebollada, J., Batanero, E., Monedero, V., Pérez-Martínez, G., García-Fernández, R., Gavilanes, J. G., & del Pozo, A. M. (2008). Lactococcus lactis as a vehicle for the heterologous expression of fungal ribotoxin variants with reduced IgE-binding affinity. Journal of Biotechnology, 134(1–2), 1–8. https://doi.org/10.1016/j.jbiotec.2007.12.011
   PubMed Web of Science ®Google Scholar
• Anderson, R. J., Weng, Z., Campbell, R. K., & Jiang, X. (2005). Main-chain conformational tendencies of amino acids. Proteins, 60(4), 679–689. https://doi.org/10.1002/prot.20530
   PubMed Web of Science ®Google Scholar
• Andreatta, M., Alvarez, B., & Nielsen, M. (2017). GibbsCluster: unsupervised clustering and alignment of peptide sequences. Nucleic Acids Research, 45(W1), W458–W463. https://doi.org/10.1093/nar/gkx248
   PubMed Web of Science ®Google Scholar
• Antonio-Herrera, L., Badillo-Godinez, O., Medina-Contreras, O., Tepale-Segura, A., García- Lozano, A., Gutierrez-Xicotencatl, L., Soldevila, G., Esquivel-Guadarrama, F. R., Idoyaga, J., & Bonifaz, L. C. (2018). The nontoxic Cholera B subunit is a potent adjuvant for intradermal DC-targeted vaccination. Frontiers in Immunology, 9, 2212. https://doi.org/10.3389/fimmu.2018.02212PMID: 30319653; PMCID: PMC6171476.
   PubMed Web of Science ®Google Scholar
• Antunes, D. A., Abella, J. R., Devaurs, D., Rigo, M. M., & Kavraki, L. E. (2018). Structure-based methods for binding mode and binding affinity prediction for peptide-MHC complexes. Current Topics in Medicinal Chemistry, 18(26), 2239–2255. https://doi.org/10.2174/1568026619666181224101744
   PubMed Web of Science ®Google Scholar
• Artyomov, M. N., Lis, M., Devadas, S., Davis, M. M., & Chakraborty, A. K. (2010). CD4 and CD8 binding to MHC molecules primarily acts to enhance Lck delivery. Proceedings of the National Academy of Sciences of the United States of America, 107(39), 16916–16921. https://doi.org/10.1073/pnas.1010568107
   PubMed Web of Science ®Google Scholar
• Azim, K. F., Hasan, M., Hossain, M. N., Somana, S. R., Hoque, S. F., Bappy, M., Chowdhury, A. T., & Lasker, T. (2019). Immunoinformatics approaches for designing a novel multi epitope peptide vaccine against human norovirus (Norwalk virus). Infection, Genetics and Evolution: Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases, 74, 103936. https://doi.org/10.1016/j.meegid.2019.103936
   PubMed Web of Science ®Google Scholar
• Azuar, A., Li, Z., Shibu, M. A., Zhao, L., Luo, Y., Shalash, A. O., Khalil, Z. G., Capon, R. J., Hussein, W. M., Toth, I., & Skwarczynski, M. (2021). Poly(hydrophobic amino acid)-based self-adjuvanting nanoparticles for group A streptococcus vaccine delivery. Journal of Medicinal Chemistry, 64(5), 2648–2658. https://doi.org/10.1021/acs.jmedchem.0c01660
   PubMed Web of Science ®Google Scholar
• Baker, R. D. (1957). Mucormycosis; a new disease? Journal of the American Medical Association, 163(10), 805–808. https://doi.org/10.1001/jama.1957.02970450007003
   PubMed Web of Science ®Google Scholar
• Bastola, R., & Lee, S. (2019). Physicochemical properties of particulate vaccine adjuvants: their pivotal role in modulating immune responses. Journal of Pharmaceutical Investigation, 49(3), 279–285. https://doi.org/10.1007/s40005-018-0406-4
   Google Scholar
• Behbahani, M., Moradi, M., & Mohabatkar, H. (2021). In silico design of a multi-epitope peptide construct as a potential vaccine candidate for Influenza A based on neuraminidase protein. In. In Silico Pharmacology, 9(1), 36. https://doi.org/10.1007/s40203-021-00095-w
   PubMedGoogle Scholar
• Berg, J. M., Tymoczko, J. L., & Stryer, L. (2002). Biochemistry (5th ed.). W H Freeman. https://www.ncbi.nlm.nih.gov/books/NBK21154/.
   Google Scholar
• Brown, G. D. (2011). Innate antifungal immunity: the key role of phagocytes. Annual Review of Immunology, 29, 1–21. https://doi.org/10.1146/annurev-immunol-030409-101229
   PubMed Web of Science ®Google Scholar
• Bruserud, Ø. (2013). Bidirectional crosstalk between platelets and monocytes initiated by Toll-like receptor: an important step in the early defense against fungal infections? Platelets, 24(2), 85–97. https://doi.org/10.3109/09537104.2012.678426
   PubMed Web of Science ®Google Scholar
• Buchan, D., & Jones, D. T. (2019). The PSIPRED protein analysis workbench: 20 years on. Nucleic Acids Research, 47(W1), W402–W407. https://doi.org/10.1093/nar/gkz297
   PubMed Web of Science ®Google Scholar
• Calis, J. J., 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
   PubMed Web of Science ®Google Scholar
• Carmon, L., Avivi, I., Kovjazin, R., Zuckerman, T., Dray, L., Gatt, M. E., Or, R., & Shapira, M. Y. (2015). Phase I/II study exploring ImMucin, a pan-major histocompatibility complex, anti-MUC1 signal peptide vaccine, in multiple myeloma patients. British Journal of Haematology, 169(1), 44–56. https://doi.org/10.1111/bjh.13245
   PubMed Web of Science ®Google Scholar
• Carroll, C. S., Grieve, C. L., Murugathasan, I., Bennet, A. J., Czekster, C. M., Liu, H., Naismith, J., & Moore, M. M. (2017). The rhizoferrin biosynthetic gene in the fungal pathogen Rhizopus delemar is a novel member of the NIS gene family. The International Journal of Biochemistry & Cell Biology, 89, 136–146. https://doi.org/10.1016/j.biocel.2017.06.005
   PubMed Web of Science ®Google Scholar
• Carvalho, A., Cunha, C., Bozza, S., Moretti, S., Massi-Benedetti, C., Bistoni, F., Aversa, F., & Romani, L. (2012). Immunity and tolerance to fungi in hematopoietic transplantation: principles and perspectives. Frontiers in Immunology, 3, 156. https://doi.org/10.3389/fimmu.2012.00156
   PubMed Web of Science ®Google Scholar
• Castillo, P., Wright, K. E., Kontoyiannis, D. P., Walsh, T., Patel, S., Chorvinsky, E., Bose, S., Hazrat, Y., Omer, B., Albert, N., Leen, A. M., Rooney, C. M., Bollard, C. M., & Cruz, C. (2018). A new method for reactivating and expanding T cells specific for Rhizopus oryzae. Molecular Therapy. Methods & Clinical Development, 9, 305–312. https://doi.org/10.1016/j.omtm.2018.03.003
   PubMed Web of Science ®Google Scholar
• Chamilos, G., Lewis, R. E., Lamaris, G., Walsh, T. J., & Kontoyiannis, D. P. (2008). Zygomycetes hyphae trigger an early, robust proinflammatory response in human polymorphonuclear neutrophils through toll-like receptor 2 induction but display relative resistance to oxidative damage. Antimicrobial Agents and Chemotherapy, 52(2), 722–724. https://doi.org/10.1128/AAC.01136-07
   PubMed Web of Science ®Google Scholar
• Chander, J., Kaur, M., Singla, N., Punia, R., Singhal, S. K., Attri, A. K., Alastruey-Izquierdo, A., Stchigel, A. M., Cano-Lira, J. F., & Guarro, J. (2018). Mucormycosis: battle with the deadly enemy over a five-year period in India. Journal of Fungi, 4(2), 46. https://doi.org/10.3390/jof4020046
   Web of Science ®Google Scholar
• Chen, X., Zaro, J. L., & Shen, W. C. (2013). Fusion protein linkers: property, design and functionality. Advanced Drug Delivery Reviews, 65(10), 1357–1369. https://doi.org/10.1016/j.addr.2012.09.039
   PubMed Web of Science ®Google Scholar
• Craig, D. B., & Dombkowski, A. A. (2013). Disulfide by Design 2.0: a web-based tool for disulfide engineering in proteins. BMC Bioinformatics, 14, 346. https://doi.org/10.1186/1471-2105-14-346
   PubMed Web of Science ®Google Scholar
• DasGupta, D., Kaushik, R., & Jayaram, B. (2015). From Ramachandran maps to tertiary structures of proteins. The Journal of Physical Chemistry. B, 119(34), 11136–11145. https://doi.org/10.1021/acs.jpcb.5b02999
   PubMed Web of Science ®Google Scholar
• De Luca, A., Iannitti, R. G., Bozza, S., Beau, R., Casagrande, A., D'Angelo, C., Moretti, S., Cunha, C., Giovannini, G., Massi-Benedetti, C., Carvalho, A., Boon, L., Latgé, J. P., & Romani, L. (2012). CD4(+) T cell vaccination overcomes defective cross-presentation of fungal antigens in a mouse model of chronic granulomatous disease. The Journal of Clinical Investigation, 122(5), 1816–1831. https://doi.org/10.1172/JCI60862
   PubMed Web of Science ®Google Scholar
• Delgado, N., Xue, J., Yu, J. J., Hung, C. Y., & Cole, G. T. (2003). A recombinant beta-1,3-glucanosyltransferase homolog of Coccidioides posadasii protects mice against coccidioidomycosis. Infection and Immunity, 71(6), 3010–3019. https://doi.org/10.1128/IAI.71.6.3010-3019.2003.
   PubMed Web of Science ®Google Scholar
• Desta, I. T., Porter, K. A., Xia, B., Kozakov, D., & Vajda, S. (2020). Performance and its limits in rigid body protein-protein docking. Structure (London, England: 1993), 28(9), 1071–1081.e3. https://doi.org/10.1016/j.str.2020.06.006
   PubMed Web of Science ®Google Scholar
• Dhanda, S. K., Gupta, S., Vir, P., & Raghava, G. P. (2013a). Prediction of IL4 inducing peptides. Clinical & Developmental Immunology, 2013, 263952. https://doi.org/10.1155/2013/263952
   PubMedGoogle Scholar
• Dhanda, S. K., Vir, P., & Raghava, G. P. (2013b). Designing of interferon-gamma inducing MHC class-II binders. Biology Direct, 8, 30. https://doi.org/10.1186/1745-6150-8-30.
   PubMed Web of Science ®Google Scholar
• Dimitrov, I., Naneva, L., Doytchinova, I., & Bangov, I. (2014). AllergenFP: allergenicity prediction by descriptor fingerprints. Bioinformatics (Oxford, England), 30(6), 846–851. https://doi.org/10.1093/bioinformatics/btt619
   PubMed Web of Science ®Google Scholar
• Ding, S., Li, Y., Shi, Z., & Yan, S. (2014). A protein structural classes prediction method based on predicted secondary structure and PSI-BLAST profile. Biochimie, 97, 60–65. https://doi.org/10.1016/j.biochi.2013.09.013
   PubMed Web of Science ®Google Scholar
• Dong, R., Chu, Z., Yu, F., & Zha, Y. (2020). Contriving multi-epitope subunit of vaccine for COVID-19: Immunoinformatics approaches. Frontiers in Immunology, 11, 1784. https://doi.org/10.3389/fimmu.2020.01784
   PubMed Web of Science ®Google Scholar
• Dos Santos, A. R., Fraga-Silva, T. F., Almeida, D. F., Dos Santos, R. F., Finato, A. C., Amorim, B. C., Andrade, M. I., Soares, C. T., Lara, V. S., Almeida, N. L., de Arruda, O. S., de Arruda, M. S., & Venturini, J. (2020). Rhizopus-host interplay of disseminated mucormycosis in immunocompetent mice. Future Microbiology, 15, 739–752. https://doi.org/10.2217/fmb-2019-0246
   PubMed Web of Science ®Google Scholar
• Dos Santos, A. R., Fraga-Silva, T. F., de Fátima Almeida-Donanzam, D., Dos Santos, R. F., Finato, A. C., Soares, C. T., Lara, V. S., Almeida, N., Andrade, M. I., de Arruda, O. S., de Arruda, M., & Venturini, J. (2021). IFN-γ mediated signaling improves fungal clearance in experimental pulmonary mucormycosis. Mycopathologia, 2021, 1–16. https://doi.org/10.1007/s11046-021-00598-2
   Google Scholar
• Doytchinova, I. A., & Flower, D. R. (2008). Bioinformatic approach for identifying parasite and fungal candidate subunit vaccines. Open Vaccines Journal, 2008(1), 22–26.
   Google Scholar
• Eisenberg, D., Lüthy, R., & Bowie, J. U. (1997). VERIFY3D: assessment of protein models with three-dimensional profiles. Methods in Enzymology, 277, 396–404. https://doi.org/10.1016/s0076-6879(97)77022-8
   PubMed Web of Science ®Google Scholar
• Elhasan, L. M. E., Hassan, M. B., Elhassan, R. M., Abdelrhman, F. A., Salih, E. A., Ibrahim, H. A., Mohamed, A. A., Osman, H. S., Khalil, M., Alsafi, A. A., Idris, A. B., & Hassan, M. A. (2021). Epitope-based peptide vaccine design against fructose bisphosphate aldolase of Candida glabrata: An immunoinformatics approach. Journal of Immunology Research, 2021, 8280925. https://doi.org/10.1155/2021/8280925
   PubMed Web of Science ®Google Scholar
• El-Manzalawy, Y., Dobbs, D., & Honavar, V. (2008a). Predicting linear B-cell epitopes using string kernels. Journal of Molecular Recognition: JMR, 21(4), 243–255. https://doi.org/10.1002/jmr.893.
   PubMed Web of Science ®Google Scholar
• El-Manzalawy, Y., Dobbs, D., & Honavar, V. (2008b). Predicting flexible length linear B-cell epitopes. Computational Systems Bioinformatics. Computational Systems Bioinformatics Conference, 7, 121–132.
   PubMedGoogle Scholar
• Figueiredo, R. T., Carneiro, L. A., & Bozza, M. T. (2011). Fungal surface and innate immune recognition of filamentous fungi. Frontiers in Microbiology, 2, 248. https://doi.org/10.3389/fmicb.2011.00248.
   PubMed Web of Science ®Google Scholar
• Fleri, W., Paul, S., Dhanda, S. K., Mahajan, S., Xu, X., Peters, B., & Sette, A. (2017). The immune epitope database and analysis resource in epitope discovery and synthetic vaccine design. Frontiers in immunology, 8, 278. https://doi.org/10.3389/fimmu.2017.00278
   PubMed Web of Science ®Google Scholar
• Flory, P. J. (1956). Theory of elastic mechanisms in fibrous proteins. Journal of the American Chemical Society, 78(20), 5222–5235. https://doi.org/10.1021/ja01601a025
   Web of Science ®Google Scholar
• Gasteiger, E., Gattiker, A., Hoogland, C., Ivanyi, I., Appel, R. D., & Bairoch, A. (2003). ExPASy: The proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Research, 31(13), 3784–3788. https://doi.org/10.1093/nar/gkg563.
   PubMed Web of Science ®Google Scholar
• Gebremariam, T., Alkhazraji, S., Soliman, S., Gu, Y., Jeon, H. H., Zhang, L., French, S. W., Stevens, D. A., Edwards, J. E., Jr, Filler, S. G., Uppuluri, P., & Ibrahim, A. S. (2019). Anti-CotH3 antibodies protect mice from mucormycosis by prevention of invasion and augmenting opsonophagocytosis. Science advances, 5(6), eaaw1327. https://doi.org/10.1126/sciadv.aaw1327.
   PubMedGoogle Scholar
• Ghuman, H., & Voelz, K. (2017). Innate and adaptive immunity to mucorales. Journal of Fungi (Basel, Switzerland), 3(3), 48. https://doi.org/10.3390/jof3030048.
   PubMedGoogle Scholar
• Golubovskaya, V., & Wu, L. (2016). Different subsets of T cells, memory, effector functions, and CAR-T immunotherapy. Cancers, 8(3), 36. https://doi.org/10.3390/cancers8030036
   PubMed Web of Science ®Google Scholar
• Griffiths, J. S., Camilli, G., Kotowicz, N. K., Ho, J., Richardson, J. P., & Naglik, J. R. (2021). Role for IL-1 family cytokines in fungal infections. Frontiers in Microbiology, 12, 633047. https://doi.org/10.3389/fmicb.2021.633047
   PubMed Web of Science ®Google Scholar
• Grote, A., Hiller, K., Scheer, M., Münch, R., Nörtemann, B., Hempel, D. C., & Jahn, D. (2005). JCat: a novel tool to adapt codon usage of a target gene to its potential expression host. Nucleic Acids Research, 33(Web Server issue), W526–W531. https://doi.org/10.1093/nar/gki376
   PubMed Web of Science ®Google Scholar
• Gupta, S., Kapoor, P., Chaudhary, K., Gautam, A., Kumar, R., Open Source Drug Discovery Consortium, & Raghava, G. P. (2013). In silico approach for predicting toxicity of peptides and proteins. PloS One, 8(9), e73957. https://doi.org/10.1371/journal.pone.0073957
   PubMed Web of Science ®Google Scholar
• Guruprasad, K., Reddy, B. V., & Pandit, M. W. (1990). Correlation between stability of a protein and its dipeptide composition: a novel approach for predicting in vivo stability of a protein from its primary sequence. Protein Engineering, 4(2), 155–161. https://doi.org/10.1093/protein/4.2.155
   PubMedGoogle Scholar
• Guy, A. J., Irani, V., Beeson, J. G., Webb, B., Sali, A., Richards, J. S., & Ramsland, P. A. (2018). Proteome-wide mapping of immune features onto Plasmodium protein three-dimensional structures. Scientific Reports, 8(1), 4355. https://doi.org/10.1038/s41598-018-22592-3
   PubMedGoogle Scholar
• Hayes, F., Daly, C., & Fitzgerald, G. F. (1990). Identification of the minimal replicon of Lactococcus lactis subsp. lactis UC317 plasmid pCI305. Applied and Environmental Microbiology, 56(1), 202–209. https://doi.org/10.1128/aem.56.1.202-209.1990
   PubMed Web of Science ®Google Scholar
• He, Y., Xiang, Z., & Mobley, H. L. (2010). Vaxign: the first web-based vaccine design program for reverse vaccinology and applications for vaccine development. Journal of Biomedicine and Biotechnology, 2010, 1–15. https://doi.org/10.1155/2010/297505
   Google Scholar
• Hebditch, M., Carballo-Amador, M. A., Charonis, S., Curtis, R., & Warwicker, J. (2017). Protein-Sol: a web tool for predicting protein solubility from sequence. Bioinformatics (Oxford, England), 33(19), 3098–3100. https://doi.org/10.1093/bioinformatics/btx345
   PubMed Web of Science ®Google Scholar
• Hindustan Times. (2021). https://www.hindustantimes.com/india-news/black-fungus-states-with-highest-number-of-mucormycosis-cases-101621559394002.html. Published on May 21, 2021 07:09 AM IST.
   Google Scholar
• Hou, J., Liu, Y., Hsi, J., Wang, H., Tao, R., & Shao, Y. (2014). Cholera toxin B subunit acts as a potent systemic adjuvant for HIV-1 DNA vaccination intramuscularly in mice. Human Vaccines & Immunotherapeutics, 10(5), 1274–1283. https://doi.org/10.4161/hv.28371.
   PubMed Web of Science ®Google Scholar
• Ibrahim, A. S., Edwards, J. E., & Filler, S. G. (2003). Zygomycosis. In W. E. Dismukes, P. G. Pappas, & J. D. Sobel (Eds.), Clinical mycology (pp. 241–251). Oxford University Press.
   Google Scholar
• Ibrahim, A. S., Edwards, J. E., Jr, Bryant, R., & Spellberg, B. (2009). Economic burden of mucormycosis in the United States: can a vaccine be cost-effective? Medical Mycology, 47(6), 592–600. https://doi.org/10.1080/13693780802326001.
   PubMed Web of Science ®Google Scholar
• Ibrahim, A. S., & Kontoyiannis, D. P. (2013). Update on mucormycosis pathogenesis. Current Opinion in Infectious Diseases, 26(6), 508–515. https://doi.org/10.1097/QCO.0000000000000008.
   PubMed Web of Science ®Google Scholar
• Ibrahim, A. S., Spellberg, B., Walsh, T. J., & Kontoyiannis, D. P. (2012). Clinical infectious diseases: an official publication of the Infectious Diseases Society of America. Pathogenesis of Mucormycosis, 54(Suppl 1), S16–S22. https://doi.org/10.1093/cid/cir865.
   Google Scholar
• Iwai, L. K., Yoshida, M., Sidney, J., Shikanai-Yasuda, M. A., Goldberg, A. C., Juliano, M. A., Hammer, J., Juliano, L., Sette, A., Kalil, J., Travassos, L. R., & Cunha-Neto, E. (2003). In silico prediction of peptides binding to multiple HLA-DR molecules accurately identifies immunodominant epitopes from gp43 of Paracoccidioides brasiliensis frequently recognized in primary peripheral blood mononuclear cell responses from sensitized individuals. Molecular Medicine (Cambridge, MA), 9(9–12), 209–219.
   PubMed Web of Science ®Google Scholar
• Jeong, W., Keighley, C., Wolfe, R., Lee, W. L., Slavin, M. A., Kong, D., & Chen, S. C. (2019). The epidemiology and clinical manifestations of mucormycosis: a systematic review and meta-analysis of case reports. Clinical Microbiology and Infection, 25(1), 26–34. https://doi.org/10.1016/j.cmi.2018.07.011
   PubMed Web of Science ®Google Scholar
• Jin, M. S., Kim, S. E., Heo, J. Y., Lee, M. E., Kim, H. M., Paik, S. G., Lee, H., & Lee, J. O. (2007). Crystal structure of the TLR1-TLR2 heterodimer induced by binding of a tri-acylated lipopeptide. Cell, 130(6), 1071–1082. https://doi.org/10.1016/j.cell.2007.09.008
   PubMed Web of Science ®Google Scholar
• John, T. M., Jacob, C. N., & Kontoyiannis, D. P. (2021). When uncontrolled diabetes mellitus and severe COVID-19 converge: The perfect storm for mucormycosis. Journal of Fungi (Basel, Switzerland), 7(4), 298. https://doi.org/10.3390/jof7040298.
   PubMedGoogle Scholar
• Johnson, A. K., Ghazarian, Z., Cendrowski, K. D., & Persichino, J. G. (2021). Pulmonary aspergillosis and mucormycosis in a patient with COVID-19. Medical Mycology Case Reports, 32, 64–67. https://doi.org/10.1016/j.mmcr.2021.03.006
   PubMed Web of Science ®Google Scholar
• Kaba, S. A., Karch, C. P., Seth, L., Ferlez, K., Storme, C. K., Pesavento, D. M., Laughlin, P. Y., Bergmann-Leitner, E. S., Burkhard, P., & Lanar, D. E. (2018). Self-assembling protein nanoparticles with built-in flagellin domains increases protective efficacy of a Plasmodium falciparum based vaccine. Vaccine, 36(6), 906–914. https://doi.org/10.1016/j.vaccine.2017.12.001
   PubMed Web of Science ®Google Scholar
• Kar, T., Narsaria, U., Basak, S., Deb, D., Castiglione, F., Mueller, D. M., & Srivastava, A. P. (2020). A candidate multi-epitope vaccine against SARS-CoV-2. Scientific Reports, 10(1), 10895. https://doi.org/10.1038/s41598-020-67749-1
   PubMed Web of Science ®Google Scholar
• Kazi, A., Chuah, C., Majeed, A., Leow, C. H., Lim, B. H., & Leow, C. Y. (2018). Current progress of immunoinformatics approach harnessed for cellular- and antibody-dependent vaccine design. Pathogens and Global Health, 112(3), 123–131. https://doi.org/10.1080/20477724.2018.1446773
   PubMed Web of Science ®Google Scholar
• Kilander, A., Jertborn, M., Nordstro, I., Czerkinsky, C., & Holmgren, J. A. N. (2001). Local and systemic immune responses to rectal administration of recombinant cholera toxin B subunit in humans. Infection and Immunity, 69(6), 4125–4128. https://doi.org/10.1128/IAI.69.6.4125-4128.2001.
   PubMed Web of Science ®Google Scholar
• Kolaskar, A. S., & Tongaonkar, P. C. (1990). A semi-empirical method for prediction of antigenic determinants on protein antigens. FEBS Letters, 276(1–2), 172–174. https://doi.org/10.1016/0014-5793(90)80535-q
   PubMed Web of Science ®Google Scholar
• Kontoyiannis, D. P., & Lewis, R. E. (2015). Agents of mucormycosis and entomophthoramycosis. In Mandell, Douglas, and Bennett’s principles and practice of infectious diseases (vol. e3, pp. 2909–2919). Elsevier Inc.. https://doi.org/10.1016/b978-1-4557-4801-3.00260-5
   Google Scholar
• Kovjazin, R., & Carmon, L. (2014). The use of signal peptide domains as vaccine candidates. Human Vaccines & Immunotherapeutics, 10(9), 2733–2740. https://doi.org/10.4161/21645515.2014.970916
   PubMed Web of Science ®Google Scholar
• Koymans, K. J., Feitsma, L. J., Brondijk, T. H., Aerts, P. C., Lukkien, E., Lössl, P., van Kessel, K. P., de Haas, C. J., van Strijp, J. A., & Huizinga, E. G. (2015). Structural basis for inhibition of TLR2 by staphylococcal superantigen-like protein 3 (SSL3). Proceedings of the National Academy of Sciences of the United States of America, 112(35), 11018–11023. https://doi.org/10.1073/pnas.1502026112
   PubMed Web of Science ®Google Scholar
• Kozakov, D., Hall, D. R., Xia, B., Porter, K. A., Padhorny, D., Yueh, C., Beglov, D., & Vajda, S. (2017). The ClusPro web server for protein-protein docking. Nature Protocols, 12(2), 255–278. https://doi.org/10.1038/nprot.2016.169
   PubMed Web of Science ®Google Scholar
• Krogh, A., Larsson, B., von Heijne, G., & Sonnhammer, E. L. (2001). Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. Journal of Molecular Biology, 305(3), 567–580. https://doi.org/10.1006/jmbi.2000.4315.
   PubMed Web of Science ®Google Scholar
• Kulmanov, M., & Hoehndorf, R. (2020). DeepGOPlus: improved protein function prediction from sequence. Bioinformatics (Oxford, England), 36(2), 422–429. https://doi.org/10.1093/bioinformatics/btz595.
   PubMed Web of Science ®Google Scholar
• Langley, J. M., MacDonald, L. D., Weir, G. M., MacKinnon-Cameron, D., Ye, L., McNeil, S., Schepens, B., Saelens, X., Stanford, M. M., & Halperin, S. A. (2018). A respiratory syncytial virus vaccine based on the small hydrophobic protein ectodomain presented with a novel lipid-based formulation is highly immunogenic and safe in adults: a first-in-humans study. The Journal of Infectious Diseases, 218(3), 378–387. https://doi.org/10.1093/infdis/jiy177
   PubMed Web of Science ®Google Scholar
• Lei, H., Peng, X., Jiao, H., Zhao, D., & Ouyang, J. (2015). Broadly protective immunity against divergent influenza viruses by oral co-administration of Lactococcus lactis expressing nucleoprotein adjuvanted with cholera toxin B subunit in mice. Microbial Cell Factories, 14, 111. https://doi.org/10.1186/s12934-015-0287-4
   PubMed Web of Science ®Google Scholar
• Li, L., Gao, M., Li, J., Zu, S., Wang, Y., Chen, C., Wan, D., Duan, J., Aliyari, R., Wang, J., Zhang, J., Jin, Y., Huang, W., Jin, X., Shi, M., Wang, Y., Qin, C. F., Yang, H., & Cheng, G. (2021). Methods to identify immunogenic peptides in SARS-CoV-2 spike and protective monoclonal antibodies in COVID-19 patients. Small Methods, 5(7), 2100058. https://doi.org/10.1002/smtd.202100058
   PubMed Web of Science ®Google Scholar
• Liu, M., Spellberg, B., Phan, Q. T., Fu, Y., Fu, Y., Lee, A. S., Edwards, J. E., Filler, S. G., & Ibrahim, A. S. (2010). The endothelial cell receptor GRP78 is required for mucormycosis pathogenesis in diabetic mice. The Journal of Clinical Investigation, 120(6), 1914–1924. https://doi.org/10.1172/JCI42164
   PubMed Web of Science ®Google Scholar
• Livingston, B., Crimi, C., Newman, M., Higashimoto, Y., Appella, E., Sidney, J., & Sette, A. (2002). A rational strategy to design multiepitope immunogens based on multiple Th lymphocyte epitopes. Journal of Immunology (Baltimore, MD: 1950), 168(11), 5499–5506. https://doi.org/10.4049/jimmunol.168.11.5499
   PubMed Web of Science ®Google Scholar
• Li, X., Xing, Y., Guo, L., Lv, X., Song, H., & Xi, T. (2014). Oral immunization with recombinant Lactococcus lactis delivering a multi-epitope antigen CTB-UE attenuates Helicobacter pylori infection in mice. Pathogens and Disease, 72(1), 78–86. https://doi.org/10.1111/2049-632X.12173
   PubMed Web of Science ®Google Scholar
• López-Blanco, J. R., Aliaga, J. I., Quintana-Ortí, E. S., & Chacón, P. (2014). iMODS: internal coordinates normal mode analysis server. Nucleic Acids Research, 42(Web Server issue), W271–W276. https://doi.org/10.1093/nar/gku339
   PubMed Web of Science ®Google Scholar
• Lovell, S. C., Davis, I. W., Arendall, W. B., de Bakker, P. I. W., Word, J. M., Prisant, M. G., Richardson, J. S., & Richardson, D. C. (2003). Structure validation by Calpha geometry: phi,psi and Cbeta deviation. Proteins: Structure, Function, and Bioinformatics, 50(3), 437–450. https://doi.org/10.1002/prot.10286
   PubMed Web of Science ®Google Scholar
• Magnan, C. N., Zeller, M., Kayala, M. A., Vigil, A., Randall, A., Felgner, P. L., & Baldi, P. (2010). High-throughput prediction of protein antigenicity using protein microarray data. Bioinformatics, 26(23), 2936–2943. https://doi.org/10.1093/bioinformatics/btq551
   PubMed Web of Science ®Google Scholar
• Ma, L.-J., Ibrahim, A. S., Skory, C., Grabherr, M. G., Burger, G., Butler, M., Elias, M., Idnurm, A., Lang, B. F., Sone, T., Abe, A., Calvo, S. E., Corrochano, L. M., Engels, R., Fu, J., Hansberg, W., Kim, J.-M., Kodira, C. D., Koehrsen, M. J., … Wickes, B. L. (2009). Genomic analysis of the basal lineage fungus Rhizopus oryzae reveals a whole-genome duplication. PLoS Genetics, 5(7), e1000549. https://doi.org/10.1371/journal.pgen.1000549
   PubMed Web of Science ®Google Scholar
• Maini, A., Tomar, G., Khanna, D., Kini, Y., Mehta, H., & Bhagyasree, V. (2021). Sino- orbital mucormycosis in a COVID-19 patient: A case report. International Journal of Surgery Case Reports, 82, 105957. Advance online publication. https://doi.org/10.1016/j.ijscr.2021.105957
   PubMed Web of Science ®Google Scholar
• Mancha-Agresti, P., de Castro, C. P., Dos Santos, J., Araujo, M. A., Pereira, V. B., LeBlanc, J. G., Leclercq, S. Y., & Azevedo, V. (2017). Recombinant invasive lactococcus lactis carrying a DNA vaccine coding the Ag85A antigen increases INF-γ, IL-6, and TNF-α cytokines after intranasal immunization. Frontiers in Microbiology, 8, 1263. https://doi.org/10.3389/fmicb.2017.01263
   PubMed Web of Science ®Google Scholar
• Marr, K. A., Carter, R. A., Crippa, F., Wald, A., & Corey, L. (2002). Epidemiology and outcome of mould infections in hematopoietic stem cell transplant recipients. Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America, 34(7), 909–917. https://doi.org/10.1086/339202
   PubMed Web of Science ®Google Scholar
• Matsuzaki, G., & Umemura, M. (2018). Interleukin-17 family cytokines in protective immunity against infections: role of hematopoietic cell-derived and non-hematopoietic cell-derived interleukin-17s. Microbiology and Immunology, 62(1), 1–13. https://doi.org/10.1111/1348-0421.12560
   PubMed Web of Science ®Google Scholar
• McLellan, C. A., Whitesell, L., King, O. D., Lancaster, A. K., Mazitschek, R., & Lindquist, S. (2012). Inhibiting GPI anchor biosynthesis in fungi stresses the endoplasmic reticulum and enhances immunogenicity. ACS Chemical Biology, 7(9), 1520–1528. https://doi.org/10.1021/cb300235m
   PubMed Web of Science ®Google Scholar
• Mehta, S., & Pandey, A. (2020). Rhino-orbital mucormycosis associated with COVID-19. Cureus, 12(9), e10726. https://doi.org/10.7759/cureus.10726
   PubMed Web of Science ®Google Scholar
• Meza, B., Ascencio, F., Sierra-Beltrán, A. P., Torres, J., & Angulo, C. (2017). A novel design of a multi-antigenic, multistage and multi-epitope vaccine against Helicobacter pylori: An in silico approach. Infection, Genetics and Evolution: Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases, 49, 309–317. https://doi.org/10.1016/j.meegid.2017.02.007
   PubMed Web of Science ®Google Scholar
• Mizui, M. (2019). Natural and modified IL-2 for the treatment of cancer and autoimmune diseases. Clinical Immunology (Orlando, FL), 206, 63–70. https://doi.org/10.1016/j.clim.2018.11.002
   PubMed Web of Science ®Google Scholar
• Moming, A., Tuoken, D., Yue, X., Xu, W., Guo, R., Liu, D., Li, Y., Hu, Z., Deng, F., Zhang, Y., & Sun, S. (2018). Mapping of B-cell epitopes on the N- terminal and C-terminal segment of nucleocapsid protein from Crimean-Congo hemorrhagic fever virus. PloS One, 13(9), e0204264. https://doi.org/10.1371/journal.pone.0204264
   PubMed Web of Science ®Google Scholar
• Montaño, D. E., & Voigt, K. (2020). Host immune defense upon fungal infections with mucorales: pathogen-immune cell interactions as drivers of inflammatory responses. Journal of Fungi (Basel, Switzerland), 6(3), 173. https://doi.org/10.3390/jof6030173.
   PubMedGoogle Scholar
• Mugunthan, S. P., & Harish, M. C. (2021). Multi-epitope-based vaccine designed by targeting cytoadherence proteins of Mycoplasma gallisepticum. ACS Omega, 6(21), 13742–13755. https://doi.org/10.1021/acsomega.1c01032
   PubMed Web of Science ®Google Scholar
• Mukaka, M. M. (2012). Statistics corner: A guide to appropriate use of correlation coefficient in medical research. Malawi Medical Journal: The Journal of Medical Association of Malawi, 24(3), 69–71.
   PubMed Web of Science ®Google Scholar
• Murugan, R., Scally, S. W., Costa, G., Mustafa, G., Thai, E., Decker, T., Bosch, A., Prieto, K., Levashina, E. A., Julien, J.-P., & Wardemann, H. (2020). Evolution of protective human antibodies against Plasmodium falciparum circumsporozoite protein repeat motifs. Nature Medicine, 26(7), 1135–1145. https://doi.org/10.1038/s41591-020-0881-9
   PubMed Web of Science ®Google Scholar
• Nagpal, G., Usmani, S. S., Dhanda, S. K., Kaur, H., Singh, S., Sharma, M., & Raghava, G. P. (2017). Computer-aided designing of immunosuppressive peptides based on IL-10 inducing potential. Scientific Reports, 7, 42851. https://doi.org/10.1038/srep42851
   PubMed Web of Science ®Google Scholar
• Nagy, G., Kiss, S., Varghese, R., Bauer, K., Szebenyi, C., Kocsubé, S., Homa, M., Bodai, L., Zsindely, N., Nagy, G., Vágvölgyi, C., & Papp, T. (2021). Characterization of three pleiotropic drug resistance transporter genes and their participation in the azole resistance of mucor circinelloides. Frontiers in Cellular and Infection Microbiology, 11, 660347. https://doi.org/10.3389/fcimb.2021.660347
   PubMed Web of Science ®Google Scholar
• Nanjappa, S. G., & Klein, B. S. (2014). Vaccine immunity against fungal infections. Current Opinion in Immunology, 28, 27–33. https://doi.org/10.1016/j.coi.2014.01.014
   PubMed Web of Science ®Google Scholar
• NCBI Resource Coordinators. (2018). Database resources of the National Center for Biotechnology Information. Nucleic Acids Research, 46(D1), D8–D13. https://doi.org/10.1093/nar/gkx1095.
   PubMed Web of Science ®Google Scholar
• Nezafat, N., Karimi, Z., Eslami, M., Mohkam, M., Zandian, S., & Ghasemi, Y. (2016). Designing an efficient multi-epitope peptide vaccine against Vibrio cholerae via combined immunoinformatics and protein interaction based approaches. Computational Biology and Chemistry, 62, 82–95. https://doi.org/10.1016/j.compbiolchem.2016.04.006
   PubMed Web of Science ®Google Scholar
• Nielsen, M., & Andreatta, M. (2016). NetMHCpan-3.0; improved prediction of binding to MHC class I molecules integrating information from multiple receptor and peptide length datasets. Genome Medicine, 8(1), 33. https://doi.org/10.1186/s13073-016-0288-x
   PubMedGoogle Scholar
• Nielsen, M., & Andreatta, M. (2017). NNAlign: a platform to construct and evaluate artificial neural network models of receptor-ligand interactions. Nucleic Acids Research, 45(W1), W344–W349. https://doi.org/10.1093/nar/gkx276
   PubMed Web of Science ®Google Scholar
• Oliveira-Nascimento, L., Massari, P., & Wetzler, L. M. (2012). The role of TLR2 in infection and immunity. Frontiers in Immunology, 3, 79. https://doi.org/10.3389/fimmu.2012.00079
   PubMed Web of Science ®Google Scholar
• Ozkose, E., Akyol, I., Kar, B., Comlekcioglu, U., & Ekinci, M. S. (2009). Expression of fungal cellulase gene in Lactococcus lactis to construct novel recombinant silage inoculants. Folia Microbiol (Praha), 54(4), 335–342. https://doi.org/10.1007/s12223-009-0043-4
   PubMed Web of Science ®Google Scholar
• Paduraru, M., Moreno-Sanz, C., & Olalla Gallardo, J. M. (2016). Primary cutaneous mucormycosis in an immunocompetent patient. BMJ Case Reports, 2016, bcr2016214982. https://doi.org/10.1136/bcr-2016-214982.
   PubMedGoogle Scholar
• Page, L., Weis, P., Müller, T., Dittrich, M., Lazariotou, M., Dragan, M., Waaga-Gasser, A. M., Helm, J., Dandekar, T., Einsele, H., Löffler, J., Ullmann, A. J., & Wurster, S. (2018). Evaluation of Aspergillus and Mucorales specific T-cells and peripheral blood mononuclear cell cytokine signatures as biomarkers of environmental mold exposure. International Journal of Medical Microbiology: IJMM, 308(8), 1018–1026. https://doi.org/10.1016/j.ijmm.2018.09.002
   PubMed Web of Science ®Google Scholar
• Park, H. R., & Voigt, K. (2014). Interaction of Zygomycetes with innate immune cells reconsidered with respect to ecology, morphology, evolution and infection biology: a mini-review. Mycoses, 57 Suppl 3, 31–39. https://doi.org/10.1111/myc.12235
   PubMed Web of Science ®Google Scholar
• Pearson, W. R. (2013). An introduction to sequence similarity ("homology") searching. Current Protocols in Bioinformatics, Chapter 3, Unit3.1. Chapter 3, Unit3.1. https://doi.org/10.1002/0471250953.bi0301s42
   Google Scholar
• Petersen, T. N., Brunak, S., von Heijne, G., & Nielsen, H. (2011). SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods, 8(10), 785–786. https://doi.org/10.1038/nmeth.1701
   PubMed Web of Science ®Google Scholar
• Pierleoni, A., Martelli, P. L., & Casadio, R. (2008). PredGPI: a GPI-anchor predictor. BMC Bioinformatics, 9, 392. https://doi.org/10.1186/1471-2105-9-392
   PubMed Web of Science ®Google Scholar
• Pinto, D., Sauer, M. M., Czudnochowski, N., Low, J. S., Tortorici, M. A., Housley, M. P., Noack, J., Walls, A. C., Bowen, J. E., Guarino, B., Rosen, L. E., di Iulio, J., Jerak, J., Kaiser, H., Islam, S., Jaconi, S., Sprugasci, N., Culap, K., Abdelnabi, R., … Veesler, D. (2021). Broad betacoronavirus neutralization by a stem helix-specific human antibody. Science (New York, NY), 373(6559), 1109–1116. https://doi.org/10.1126/science.abj3321
   Google Scholar
• Ponomarenko, J., Bui, H. H., Li, W., Fusseder, N., Bourne, P. E., Sette, A., & Peters, B. (2008). ElliPro: a new structure-based tool for the prediction of antibody epitopes. BMC Bioinformatics, 9, 514. https://doi.org/10.1186/1471-2105-9-514
   PubMed Web of Science ®Google Scholar
• Potenza, L., Vallerini, D., Barozzi, P., Riva, G., Forghieri, F., Zanetti, E., Quadrelli, C., Candoni, A., Maertens, J., Rossi, G., Morselli, M., Codeluppi, M., Paolini, A., Maccaferri, M., Del Giovane, C., D'Amico, R., Rumpianesi, F., Pecorari, M., Cavalleri, F., … Luppi, M. (2011). Mucorales-specific T cells emerge in the course of invasive mucormycosis and may be used as a surrogate diagnostic marker in high-risk patients. Blood, 118(20), 5416–5419. https://doi.org/10.1182/blood-2011-07-366526
   PubMed Web of Science ®Google Scholar
• Prakash, H., & Chakrabarti, A. (2019). Global Epidemiology of Mucormycosis. Journal of Fungi, 5(1), 26. https://doi.org/10.3390/jof5010026
   Web of Science ®Google Scholar
• Pritam, M., Singh, G., Swaroop, S., Singh, A. K., Pandey, B., & Singh, S. P. (2020). A cutting-edge immunoinformatics approach for design of multi-epitope oral vaccine against dreadful human malaria. International Journal of Biological Macromolecules, 158, 159–179. https://doi.org/10.1016/j.ijbiomac.2020.04.191
   PubMed Web of Science ®Google Scholar
• Pritam, M., Singh, G., Swaroop, S., Singh, A. K., & Singh, S. P. (2019). Exploitation of reverse vaccinology and immunoinformatics as promising platform for genome-wide screening of new effective vaccine candidates against Plasmodium falciparum. BMC Bioinformatics, 19(S13), 468. https://doi.org/10.1186/s12859-018-2482-x
   PubMed Web of Science ®Google Scholar
• Pyasi, S., Sharma, V., Dipti, K., Jonniya, N. A., & Nayak, D. (2021). Immunoinformatics approach to design multi-epitope- subunit vaccine against bovine ephemeral fever disease. Vaccines, 9(8), 925. https://doi.org/10.3390/vaccines9080925
   Web of Science ®Google Scholar
• Rahmani, A., Baee, M., Rostamtabar, M., Karkhah, A., Alizadeh, S., Tourani, M., & Nouri, H. R. (2019). Development of a conserved chimeric vaccine based on helper T-cell and CTL epitopes for induction of strong immune response against Schistosoma mansoni using immunoinformatics approaches. International Journal of Biological Macromolecules, 141, 125–136. https://doi.org/10.1016/j.ijbiomac.2019.08.259
   PubMed Web of Science ®Google Scholar
• Raijmakers, R., Sprenkeler, E., Aleva, F. E., Jacobs, C., Kanneganti, T. D., Joosten, L., van de Veerdonk, F. L., & Gresnigt, M. S. (2017). Toll-like receptor 2 induced cytotoxic T-lymphocyte-associated protein 4 regulates Aspergillus-induced regulatory T-cells with pro-inflammatory characteristics. Scientific Reports, 7(1), 11500. https://doi.org/10.1038/s41598-017-11738-4
   PubMedGoogle Scholar
• Rapin, N., Lund, O., Bernaschi, M., & Castiglione, F. (2010). Computational immunology meets bioinformatics: the use of prediction tools for molecular binding in the simulation of the immune system. PloS One, 5(4), e9862. https://doi.org/10.1371/journal.pone.0009862
   PubMed Web of Science ®Google Scholar
• Ras-Carmona, A., Pelaez-Prestel, H. F., Lafuente, E. M., & Reche, P. A. (2021). BCEPS: A web server to predict linear B cell epitopes with enhanced immunogenicity and cross-reactivity. Cells, 10(10), 2744. https://doi.org/10.3390/cells10102744
   PubMed Web of Science ®Google Scholar
• Revannavar, S. M., P S, S., Samaga, L., & V K, V. (2021). COVID-19 triggering mucormycosis in a susceptible patient: a new phenomenon in the developing world? BMJ Case Reports, 14(4), e241663. https://doi.org/10.1136/bcr-2021-241663
   PubMedGoogle Scholar
• Roilides, E., Kontoyiannis, D. P., & Walsh, T. J. (2012). Host defenses against zygomycetes. Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America, 54 Suppl 1, S61–S66. https://doi.org/10.1093/cid/cir869
   PubMed Web of Science ®Google Scholar
• Romani, L. (2011). Immunity to fungal infections. Nature Reviews. Immunology, 11(4), 275–288. https://doi.org/10.1038/nri2939
   PubMed Web of Science ®Google Scholar
• Rost, B. (2001). Review: protein secondary structure prediction continues to rise. Journal of Structural Biology, 134(2–3), 204–218. https://doi.org/10.1006/jsbi.2001.4336
   PubMed Web of Science ®Google Scholar
• Rostaminia, S., Aghaei, S. S., Farahmand, B., Nazari, R., & Ghaemi, A. (2021). Computational design and analysis of a multi-epitope against influenza A virus. International Journal of Peptide Research and Therapeutics, 27(4), 2614–2625. Advance online publication. https://doi.org/10.1007/s10989-021-10278-w
   Web of Science ®Google Scholar
• Samazan, F., Rokbi, B., Seguin, D., Telles, F., Gautier, V., Richarme, G., Chevret, D., Varela, P. F., Velours, C., & Poquet, I. (2015). Production, secretion and purification of a correctly folded staphylococcal antigen in Lactococcus lactis. Microbial Cell Factories, 14, 104. https://doi.org/10.1186/s12934-015-0271-z
   PubMed Web of Science ®Google Scholar
• Sarkar, B., Ullah, M. A., Araf, Y., & Rahman, M. S. (2020). Engineering a novel subunit vaccine against SARS-CoV-2 by exploring immunoinformatics approach. Informatics in Medicine Unlocked, 21, 100478. https://doi.org/10.1016/j.imu.2020.100478
   PubMedGoogle Scholar
• Sassone-Corsi, M., Chairatana, P., Zheng, T., Perez-Lopez, A., Edwards, R. A., George, M. D., Nolan, E. M., & Raffatellu, M. (2016). Siderophore-based immunization strategy to inhibit growth of enteric pathogens. Proceedings of the National Academy of Sciences of the United States of America, 113(47), 13462–13467. https://doi.org/10.1073/pnas.1606290113
   PubMed Web of Science ®Google Scholar
• Sato, K., Oinuma, K. I., Niki, M., Yamagoe, S., Miyazaki, Y., Asai, K., Yamada, K., Hirata, K., Kaneko, Y., & Kakeya, H. (2017). Identification of a novel rhizopus-specific antigen by screening with a signal sequence trap and evaluation as a possible diagnostic marker of mucormycosis. Medical Mycology, 55(7), 713–719. https://doi.org/10.1093/mmy/myw146
   PubMed Web of Science ®Google Scholar
• Sayed, S. B., Nain, Z., Khan, M., Abdulla, F., Tasmin, R., & Adhikari, U. K. (2020). Exploring lassa virus proteome to design a multi-epitope vaccine through immunoinformatics and immune simulation analyses. International Journal of Peptide Research and Therapeutics, 2020, 1–19. Advance online publication. https://doi.org/10.1007/s10989-019-10003-8.
   Google Scholar
• Schepens, B., Schotsaert, M., & Saelens, X. (2015). Small hydrophobic protein of respiratory syncytial virus as a novel vaccine antigen. Immunotherapy, 7(3), 203–206. https://doi.org/10.2217/imt.15.11
   PubMed Web of Science ®Google Scholar
• Sephton-Clark, P., Muñoz, J. F., Ballou, E. R., Cuomo, C. A., & Voelz, K. (2018). Pathways of pathogenicity: Transcriptional stages of germination in the fatal fungal pathogen Rhizopus delemar. mSphere, 3(5), e00403–18. https://doi.org/10.1128/mSphere.00403-18.
   PubMed Web of Science ®Google Scholar
• Shao, X., Rivera, J., Niang, R., Casadevall, A., & Goldman, D. L. (2005). A dual role for TGF-beta1 in the control and persistence of fungal pneumonia. Journal of Immunology (Baltimore, MD: 1950), 175(10), 6757–6763. https://doi.org/10.4049/jimmunol.175.10.6757
   PubMed Web of Science ®Google Scholar
• Singh, G., Pritam, M., Banerjee, M., Singh, A. K., & Singh, S. P. (2020). Designing of precise vaccine construct against visceral leishmaniasis through predicted epitope ensemble: A contemporary approach. Computational Biology and Chemistry, 86, 107259. https://doi.org/10.1016/j.compbiolchem.2020.107259
   PubMed Web of Science ®Google Scholar
• Sipsas, N. V., Gamaletsou, M. N., Anastasopoulou, A., & Kontoyiannis, D. P. (2018). Therapy of mucormycosis. Journal of Fungi (Basel, Switzerland), 4(3), 90. https://doi.org/10.3390/jof4030090.
   PubMedGoogle Scholar
• Sircar, G., Chakrabarti, H. S., Saha, B., & Gupta-Bhattacharya, S. (2012). Identification of aero-allergens from Rhizopus oryzae: an immunoproteomic approach. Journal of Proteomics, 77, 455–468. https://doi.org/10.1016/j.jprot.2012.09.023
   PubMed Web of Science ®Google Scholar
• Skountzou, I., Quan, F. S., Gangadhara, S., Ye, L., Vzorov, A., Selvaraj, P., Jacob, J., Compans, R. W., & Kang, S. M. (2007). Incorporation of glycosylphosphatidylinositol-anchored granulocyte- macrophage colony-stimulating factor or CD40 ligand enhances immunogenicity of chimeric simian immunodeficiency virus-like particles. Journal of Virology, 81(3), 1083–1094. https://doi.org/10.1128/JVI.01692-06
   PubMed Web of Science ®Google Scholar
• Solanki, V., Tiwari, M., & Tiwari, V. (2019). Prioritization of potential vaccine targets using comparative proteomics and designing of the chimeric multi-epitope vaccine against Pseudomonas aeruginosa. Scientific Reports, 9(1), 5240. https://doi.org/10.1038/s41598-019-41496-4
   PubMedGoogle Scholar
• Spellberg, B. (2007). Prospects for and barriers to a fungal vaccine. Expert Opinion on Biological Therapy, 7(12), 1785–1788. https://doi.org/10.1517/14712598.7.12.1785
   PubMed Web of Science ®Google Scholar
• Spellberg, B., Edwards, J. Jr, & Ibrahim, A. (2005). Novel perspectives on mucormycosis: pathophysiology, presentation, and management. Clinical Microbiology Reviews, 18(3), 556–569. https://doi.org/10.1128/CMR.18.3.556-569.2005
   PubMed Web of Science ®Google Scholar
• Stajich, J. E., Harris, T., Brunk, B. P., Brestelli, J., Fischer, S., Harb, O. S., Kissinger, J. C., Li, W., Nayak, V., Pinney, D. F., Stoeckert, C. J., Jr,., & Roos, D. S. (2012). FungiDB: an integrated functional genomics database for fungi. Nucleic Acids Research, 40(Database issue), D675–D681. https://doi.org/10.1093/nar/gkr918
   PubMedGoogle Scholar
• Stedman, A., Chambers, M. A., & Gutierrez-Merino, J. (2019). Secretion and functional expression of Mycobacterium bovis antigens MPB70 and MPB83 in lactic acid bacteria. Tuberculosis (Edinburgh, Scotland), 117, 24–30. https://doi.org/10.1016/j.tube.2019.05.007
   PubMed Web of Science ®Google Scholar
• Stratmann, T. (2015). Cholera toxin subunit B as adjuvant--An accelerator in protective immunity and a break in autoimmunity. Vaccines, 3(3), 579–596. https://doi.org/10.3390/vaccines3030579
   PubMedGoogle Scholar
• Sugar, A. M. (2005). Agents of mucormycosis and related species. In G. L. Mandell, J. E. Bennett, & R. Dolin (Eds.), Principles and practice of infectious diseases (6th ed., 2979). Elsevier.
   Google Scholar
• Szczepankowska, A. K., Szatraj, K., Sałański, P., Rózga, A., Górecki, R. K., & Bardowski, J. K. (2017). Recombinant lactococcus lactis expressing haemagglutinin from a Polish Avian H5N1 isolate and its immunological effect in preliminary animal trials. BioMed Research International, 2017, 6747482. https://doi.org/10.1155/2017/6747482
   PubMed Web of Science ®Google Scholar
• Tajiri, K., Ozawa, T., Jin, A., Tokimitsu, Y., Minemura, M., Kishi, H., Sugiyama, T., & Muraguchi, A. (2010). Analysis of the epitope and neutralizing capacity of human monoclonal antibodies induced by hepatitis B vaccine. Antiviral Research, 87(1), 40–49. https://doi.org/10.1016/j.antiviral.2010.04.006
   PubMed Web of Science ®Google Scholar
• Tarang, S., Kesherwani, V., LaTendresse, B., Lindgren, L., Rocha-Sanchez, S. M., & Weston, M. D. (2020). In silico design of a multivalent vaccine against Candida albicans. Scientific Reports, 10(1), 1066. https://doi.org/10.1038/s41598-020-57906-x
   PubMed Web of Science ®Google Scholar
• Tenzer, S., Peters, B., Bulik, S., Schoor, O., Lemmel, C., Schatz, M. M., Kloetzel, P. M., Rammensee, H. G., Schild, H., & Holzhütter, H. G. (2005). Modeling the MHC class I pathway by combining predictions of proteasomal cleavage, TAP transport and MHC class I binding. Cellular and Molecular Life Sciences: CMLS, 62(9), 1025–1037. https://doi.org/10.1007/s00018-005-4528-2
   PubMed Web of Science ®Google Scholar
• Thakur, R., & Shankar, J. (2016). In silico identification of potential peptides or allergen shot candidates against Aspergillus fumigatus. BioResearch Open Access, 5(1), 330–341. https://doi.org/10.1089/biores.2016.0035
   PubMedGoogle Scholar
• Torrey, H. L., Kaliaperumal, V., Bramhecha, Y., Weir, G. M., Falsey, A. R., Walsh, E. E., Langley, J. M., Schepens, B., Saelens, X., & Stanford, M. M. (2020). Evaluation of the protective potential of antibody and T cell responses elicited by a novel preventative vaccine towards respiratory syncytial virus small hydrophobic protein. Human Vaccines & Immunotherapeutics, 16(9), 2007–2017. https://doi.org/10.1080/21645515.2020.1756671
   PubMed Web of Science ®Google Scholar
• Urrutia-Baca, V. H., Gomez-Flores, R., De La Garza-Ramos, M. A., Tamez- Guerra, P., Lucio-Sauceda, D. G., & Rodríguez-Padilla, M. C. (2019). Immunoinformatics approach to design a novel epitope-based oral vaccine against Helicobacter pylori. Journal of Computational Biology: Biology, 26(10), 1177–1190. https://doi.org/10.1089/cmb.2019.0062
   PubMed Web of Science ®Google Scholar
• van Zundert, G., Rodrigues, J., Trellet, M., Schmitz, C., Kastritis, P. L., Karaca, E., Melquiond, A., van Dijk, M., de Vries, S. J., & Bonvin, A. (2016). The HADDOCK2.2 Web Server: User-friendly integrative modeling of biomolecular complexes. Journal of Molecular Biology, 428(4), 720–725. https://doi.org/10.1016/j.jmb.2015.09.014
   PubMed Web of Science ®Google Scholar
• Veerasamy, R., Rajak, H., Jain, A., Sivadasan, S., Varghese, C. P., & Agrawal, R. K. (2011). Validation of QSAR models - strategies and importance. International Journal of Drug Design and Discovery, 2(3), 511–519.
   Google Scholar
• Vega, A., Ventura, I., Chamorro, C., Aroca, R., Orovigt, A., Gómez, E., Puente, Y., Martínez, A., Asturias, J. A., & Monteseirín, J. (2011). Neutrophil defensins: their possible role in allergic asthma. Journal of Investigational Allergology & Clinical Immunology, 21(1), 38–43.
   PubMed Web of Science ®Google Scholar
• Veisi, A., Bagheri, A., Eshaghi, M., Rikhtehgar, M. H., Rezaei Kanavi, M., & Farjad, R. (2021). Rhino-orbital mucormycosis during steroid therapy in COVID-19 patients: A case report. European Journal of Ophthalmology. 2021, 1-6, https://doi.org/10.1177/11206721211009450.
   Google Scholar
• Vigneron, N., Ferrari, V., Stroobant, V., Abi Habib, J., & Van den Eynde, B. J. (2017). Peptide splicing by the proteasome. The Journal of Biological Chemistry, 292(51), 21170–21179. https://doi.org/10.1074/jbc.R117.807560
   PubMed Web of Science ®Google Scholar
• Waizel-Haiat, S., Guerrero-Paz, J. A., Sanchez-Hurtado, L., Calleja-Alarcon, S., & Romero-Gutierrez, L. (2021). A case of fatal rhino-orbital mucormycosis associated with new onset diabetic ketoacidosis and COVID-19. Cureus, 13(2), e13163. https://doi.org/10.7759/cureus.13163
   PubMed Web of Science ®Google Scholar
• Wang, S., Li, W., Liu, S., & Xu, J. (2016). RaptorX-Property: a web server for protein structure property prediction. Nucleic Acids Research, 44(W1), W430–W435. https://doi.org/10.1093/nar/gkw306
   PubMed Web of Science ®Google Scholar
• Wang, P., Sidney, J., Dow, C., Mothé, B., Sette, A., & Peters, B. (2008). A systematic assessment of MHC class II peptide binding predictions and evaluation of a consensus approach. PLoS Computational Biology, 4(4), e1000048. https://doi.org/10.1371/journal.pcbi.1000048.
   PubMed Web of Science ®Google Scholar
• Wang, P., Sidney, J., Kim, Y., Sette, A., Lund, O., Nielsen, M., & Peters, B. (2010). Peptide binding predictions for HLA DR, DP and DQ molecules. BMC Bioinformatics, 11, 568. https://doi.org/10.1186/1471-2105-11-568
   PubMed Web of Science ®Google Scholar
• Weng, G., Wang, E., Wang, Z., Liu, H., Zhu, F., Li, D., & Hou, T. (2019). HawkDock: a web server to predict and analyze the protein-protein complex based on computational docking and MM/GBSA. Nucleic Acids Research, 47(W1), W322–W330. https://doi.org/10.1093/nar/gkz397
   PubMed Web of Science ®Google Scholar
• West, A. P., Koblansky, A. A., & Ghosh, S. (2006). Recognition and signaling by toll-like receptors. Annual Review of Cell and Developmental Biology, 22, 409–437. https://doi.org/10.1146/annurev.cellbio.21.122303.115827
   PubMed Web of Science ®Google Scholar
• WHO Emergency Report. (2021). Retrieved August 30, from https://www.who.int/india/emergencies/coronavirus-disease-(covid-19)/mucormycosis
   Google Scholar
• Wilson, W., Ali-Osman, F., Sucher, J., Shirah, G., & Mangram, A. (2019). Invasive fungal wound infection in an otherwise healthy trauma patient (Mucor Trauma). Trauma Case Reports, 24, 100251. https://doi.org/10.1016/j.tcr.2019.100251
   PubMedGoogle Scholar
• Wu, Y., Xu, H., Li, Y., Huang, D., Chen, L., Hu, Y., Li, L., Zhang, D., & Huang, W. (2019). miRNA-344b-1-3p modulates the autophagy of NR8383 cells during Aspergillus fumigatus infection via TLR2. Experimental and Therapeutic Medicine, 18(1), 139–146. https://doi.org/10.3892/etm.2019.7569
   PubMed Web of Science ®Google Scholar
• Wüthrich, K., Wagner, G., Richarz, R., & Braun, W. (1980). Correlations between internal mobility and stability of globular proteins. Biophysical Journal, 32(1), 549–560. https://doi.org/10.1016/S0006-3495(80)84989-7
   PubMed Web of Science ®Google Scholar
• Xiang, Z., & He, Y. (2009). Vaxign: a web-based vaccine target design program for reverse vaccinology. Procedia in Vaccinology, 1(1), 23–29. https://doi.org/10.1016/j.provac.2009.07.005
   Google Scholar
• Xin, H., Cartmell, J., Bailey, J. J., Dziadek, S., Bundle, D. R., & Cutler, J. E. (2012). Self-adjuvanting glycopeptide conjugate vaccine against disseminated candidiasis. PloS One, 7(4), e35106. https://doi.org/10.1371/journal.pone.0035106
   PubMed Web of Science ®Google Scholar
• Xu, D., & Zhang, Y. (2011). Improving the physical realism and structural accuracy of protein models by a two-step atomic-level energy minimization. Biophysical Journal, 101(10), 2525–2534. https://doi.org/10.1016/j.bpj.2011.10.024
   PubMed Web of Science ®Google Scholar
• Yang, Y., Sun, W., Guo, J., Zhao, G., Sun, S., Yu, H., Guo, Y., Li, J., Jin, X., Du, L., Jiang, S., Kou, Z., & Zhou, Y. (2015). In silico design of a DNA-based HIV-1 multi-epitope vaccine for Chinese populations. Human Vaccines & Immunotherapeutics, 11(3), 795–805. https://doi.org/10.1080/21645515.2015.1012017
   PubMed Web of Science ®Google Scholar
• Yano, A., Onozuka, A., Asahi-Ozaki, Y., Imai, S., Hanada, N., Miwa, Y., & Nisizawa, T. (2005). An ingenious design for peptide vaccines. Vaccine, 23(17-18), 2322–2326. https://doi.org/10.1016/j.vaccine.2005.01.031
   PubMed Web of Science ®Google Scholar
• Yazdani, Z., Rafiei, A., Irannejad, H., Yazdani, M., & Valadan, R. (2020). Designing a novel multiepitope peptide vaccine against melanoma using immunoinformatics approach. Journal of Biomolecular Structure and Dynamics, 2020, 1–13. Advance online publication. https://doi.org/10.1080/07391102.2020.1846625
   Google Scholar
• Zeb, A., Ali, S. S., Azad, A. K., Safdar, M., Anwar, Z., Suleman, M., Nizam- Uddin, N., Khan, A., & Wei, D. Q. (2021). Genome-wide screening of vaccine targets prioritization and reverse vaccinology aided design of peptides vaccine to enforce humoral immune response against Campylobacter jejuni. Computers in Biology and Medicine, 133, 104412. Advance online publication. https://doi.org/10.1016/j.compbiomed.2021.104412
   PubMed Web of Science ®Google Scholar
• Zhang, X., Hu, S., Du, X., Li, T., Han, L., & Kong, J. (2016). Heterologous expression of carcinoembryonic antigen in Lactococcus lactis via LcsB-mediated surface displaying system for oral vaccine development. Journal of Microbiology, Immunology, and Infection = Wei mian yu gan ran za zhi, 49(6), 851–858. https://doi.org/10.1016/j.jmii.2014.11.009
   PubMedGoogle Scholar
• Zhong, Z., Liu, L. J., Dong, Z. Q., Lu, L., Wang, M., Leung, C. H., Ma, D. L., & Wang, Y. (2015). Structure-based discovery of an immunomodulatory inhibitor of TLR1-TLR2 heterodimerization from a natural product-like database. Chemical Communications, 51(56), 11178–11181. https://doi.org/10.1039/C5CC02728D
   PubMed Web of Science ®Google Scholar
• Zuker, M. (2003). Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Research, 31(13), 3406–3415. https://doi.org/10.1093/nar/gkg595
   PubMed Web of Science ®Google Scholar