An immunoinformatics approach to epitope-based vaccine design against PspA in Streptococcus pneumoniae

Brooks LRK, Mias GI (2018) Streptococcus pneumoniae’s virulence and host immunity: aging, diagnostics, and prevention. Front Immunol 9:1366 Van der Poll T, Opal SM (2009) Pathogenesis, treatment, and prevention of pneumococcal pneumonia. Lancet (London, England) 374:1543–1556 Shaper M, Hollingshead SK, Benjamin WHJ, Briles DE (2004) PspA protects Streptococcus pneumoniae from killing by apolactoferrin, and antibody to PspA enhances killing of pneumococci by apolactoferrin [corrected]. Infect Immun 72:5031–5040 Allegrucci M, Sauer K (2007) Characterization of colony morphology variants isolated from Streptococcus pneumoniae biofilms. J Bacteriol 189:2030–2038 Hammerschmidt S, Bethe G, Remane PH, Chhatwal GS (1999) Identification of pneumococcal surface protein A as a lactoferrin-binding protein of Streptococcus pneumoniae. Infect Immun 67:1683–1687 Mitchell AM, Mitchell TJ (2010) Streptococcus pneumoniae: virulence factors and variation. Clin Microbiol Infect Off Publ Eur Soc Clin Microbiol Infect Dis 16:411–418 Ortqvist A, Hedlund J, Kalin M (2005) Streptococcus pneumoniae: epidemiology, risk factors, and clinical features. Semin Respir Crit Care Med 26:563–574 Zhao W, Pan F, Wang B, Wang C, Sun Y, Zhang T et al (2019) Epidemiology characteristics of Streptococcus pneumoniae from children with pneumonia in Shanghai: a retrospective study. Front Cell Infect Microbiol 9:258 Wahl B, O’Brien KL, Greenbaum A, Majumder A, Liu L, Chu Y et al (2018) Burden of Streptococcus pneumoniae and Haemophilus influenzae type b disease in children in the era of conjugate vaccines: global, regional, and national estimates for 2000–15. Lancet Glob Heal 6:e744–e757 Von Mollendorf C, Tempia S, von Gottberg A, Meiring S, Quan V, Feldman C et al (2017) Estimated severe pneumococcal disease cases and deaths before and after pneumococcal conjugate vaccine introduction in children younger than 5 years of age in South Africa. PLoS One 12:1–19 Kumar R, Arora N, Santosham M (2016) South Asia symposium on pneumococcal disease and the promise of vaccines – meeting report. Vaccine 34:2622–2626 Bahadori Z, Shafaghi M, Madanchi H, Ranjbar MM, Shabani AA, Mousavi SF (2022) In silico designing of a novel epitope ‑ based candidate vaccine against Streptococcus pneumoniae with introduction of a new domain of PepO as adjuvant. J Transl Med 20:1–28 Kim GL, Seon SH, Rhee DK (2017) Pneumonia and Streptococcus pneumoniae vaccine. Arch Pharm Res 40:885–893 Dorosti H, Eslami M, Nezafat N, Fadaei F, Ghasemi Y (2019) Designing self-assembled peptide nanovaccine against Streptococcus pneumoniae : an in silico strategy. Mol Cell Probes 48:101446 Kolla HB, Tirumalasetty C, Sreerama K, Ayyagari VS (2021) An immunoinformatics approach for the design of a multi-epitope vaccine targeting super antigen TSST-1 of Staphylococcus aureus. J Genet Eng Biotechnol 19:69 Elliott SL, Suhrbier A, Miles JJ, Lawrence G, Pye SJ, Le TT et al (2008) Phase I Trial of a CD8+ T-cell peptide epitope-based vaccine for infectious mononucleosis. J Virol 82:1448–1457 Shahab M, Hayat C, Sikandar R, Zheng G, Akter S (2022) In silico designing of a multi-epitope vaccine against Burkholderia pseudomallei: reverse vaccinology and immunoinformatics. J Genet Eng Biotechnol 20:100 Jahan Z, Deeba IM, Akter S, Rahman T, Nabi A, Yasmin M et al (2016) Immunogenicity of Streptococcus pneumoniae 74 kDa surface protein in rabbit model. Bangladesh J Microbiol 31:25–28 Munia M, Mahmud S, Mohasin M, Kibria KMK (2021) Informatics in medicine unlocked In silico design of an epitope-based vaccine against choline binding protein A of Streptococcus pneumoniae. Informatics Med Unlocked 23:100546 Tarahomjoo S, Ghaderi S (2017) Novel vaccines against Streptococcus pneumoniae based on the immunoprotective B-cell epitope region of pneumococcal choline binding protein D and Salmonella Enteritidis flagellin. Am J Microbiol Res, 5(6):118-123 Tarahomjoo S, Ghaderi S (2019) In silico design of a novel serotype independent vaccine against Streptococcus pneumoniae based on B-cell epitope regions of fibronectin binding protein, choline binding protein D, and D-alanyl-D-alanine carboxypeptidase. Lett Drug Des Discov 16(4):372–381. https://doi.org/10.2174/1570180815666180815150600 Dorosti H, Eslami M, Negahdaripour M, Ghoshoon MB, Gholami A, Heidari R et al (2019) Vaccinomics approach for developing multi-epitope peptide pneumococcal vaccine. J Biomol Struct Dyn 37:3524–3535 McDaniel LS, Yother J, Vijayakumar M, McGarry L, Guild WR, Briles DE (1987) Use of insertional inactivation to facilitate studies of biological properties of pneumococcal surface protein A (PspA). J Exp Med 165:381–394 Park SS, Gonzalez-Juarbe N, Martínez E, Hale JY, Lin YH, Huffines JT et al (2021) Streptococcus pneumoniae binds to host lactate dehydrogenase via PspA and PspC to enhance virulence. MBio 12:e00673 Ren B, Szalai AJ, Thomas O, Hollingshead SK, Briles DE (2003) Both family 1 and family 2 PspA proteins can inhibit complement deposition and confer virulence to a capsular serotype 3 strain of Streptococcus pneumoniae. Infect Immun 71:75–85 Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410 Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797 Tamura K, Stecher G, Kumar S (2021) MEGA11: molecular evolutionary genetics analysis version 11. Mol Biol Evol 38:3022–3027 Doytchinova IA, Flower DR (2007) VaxiJen: a server for prediction of protective antigens, tumour antigens and subunit vaccines. BMC Bioinformatics 8:4 Dimitrov I, Bangov I, Flower DR, Doytchinova I (2014) AllerTOP vol 2–a server for in silico prediction of allergens. J Mol Model 20:2278 Larsen MV, Lundegaard C, Lamberth K, Buus S, Lund O, Nielsen M (2007) Large-scale validation of methods for cytotoxic T-lymphocyte epitope prediction. BMC Bioinformatics 8:424 Gupta S, Kapoor P, Chaudhary K, Gautam A, Kumar R, Raghava GPS et al (2013) In silico approach for predicting toxicity of peptides and proteins. PLoS One 8:e73957 Vita R, Mahajan S, Overton JA, Dhanda SK, Martini S, Cantrell JR et al (2019) The immune epitope database (IEDB): 2018 update. Nucleic Acids Res 47:D339–D343 Dhanda SK, Vir P, Raghava GPS (2013) Designing of interferon-gamma inducing MHC class-II binders. Biol Direct 8:30 Pandey RK, Bhatt TK, Prajapati VK (2018) Novel immunoinformatics approaches to design multi-epitope subunit vaccine for malaria by investigating anopheles salivary protein. Sci Rep 8:1–11 Islam SI, Mou MJ, Sanjida S, Tariq M, Nasir S, Mahfuj S (2022) Designing a novel mRNA vaccine against Vibrio harveyi infection in fish: an immunoinformatics approach. Genomics and Informatics 20:1–20 Abdellrazeq GS, Fry LM, Elnaggar MM, Bannantine JP, Schneider DA, Chamberlin WM et al (2020) Simultaneous cognate epitope recognition by bovine CD4 and CD8 T cells is essential for primary expansion of antigen-specific cytotoxic T-cells following ex vivo stimulation with a candidate Mycobacterium avium subsp. paratuberculosis peptide vaccine. Vaccine 38:2016–25 Gasteiger E, Gattiker A, Hoogland C, Ivanyi I, Appel RD, Bairoch A (2003) ExPASy: the proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res 31:3784–3788 Magnan CN, Randall A, Baldi P (2009) SOLpro: accurate sequence-based prediction of protein solubility. Bioinformatics 25:2200–2207 Cheng J, Randall AZ, Sweredoski MJ, Baldi P (2005) SCRATCH: a protein structure and structural feature prediction server. Nucleic Acids Res 33(Web Server issue):W72-6 Heo L, Park H, Seok C (2013) GalaxyRefine: protein structure refinement driven by side-chain repacking. Nucleic Acids Res 41(Web Server issue):W384-8 Laskowski RA, Rullmannn JA, MacArthur MW, Kaptein R, Thornton JM (1996) AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J Biomol NMR 8:477–486 Colovos C, Yeates TO (1993) Verification of protein structures: patterns of nonbonded atomic interactions. Protein Sci 2:1511–1519 Kozakov D, Hall DR, Xia B, Porter KA, Padhorny D, Yueh C et al (2017) The ClusPro web server for protein-protein docking. Nat Protoc 12:255–278 Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H et al (2000) The Protein Data Bank. Nucleic Acids Res 28:235–242 (2021) BIOVIA, Dassault Systèmes, Discovery studio, San Diego: Dassault Systèmes The PyMOL Molecular Graphics System, Version 2.0 Schrödinger, LLC. Laskowski RA, Jabłońska J, Pravda L, Vařeková RS, Thornton JM (2018) PDBsum: structural summaries of PDB entries. Protein Sci 27:129–134 López-Blanco JR, Aliaga JI, Quintana-Ortí ES, Chacón P (2014) iMODS: internal coordinates normal mode analysis server. Nucleic Acids Res 42(Web Server issue):W271-6 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:e9862 Madeira F, Pearce M, Tivey ARN, Basutkar P, Lee J, Edbali O, et al (2022) Search and sequence analysis tools services from EMBL-EBI in 2022. Nucleic Acids Res 50:gkac240 Grote A, Hiller K, Scheer M, Münch R, Nörtemann B, Hempel DC et al (2005) JCat: a novel tool to adapt codon usage of a target gene to its potential expression host. Nucleic Acids Res 33(Web Server issue):W526-31 Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425 Mazumder L, Hasan MR, Fatema K, Islam MZ, Tamanna SK (2022) Structural and Functional Annotation and Molecular Docking Analysis of a Hypothetical Protein from Neisseria gonorrhoeae: An In-Silico Approach. Biomed Res Int. 2022;2022:4302625. https://doi.org/10.1155/2022/4302625 Luckheeram RV, Zhou R, Verma AD, Xia B (2012) CD4 +T cells: differentiation and functions. Clin Dev Immunol 2012:925135 El-Manzalawy Y, Dobbs D, Honavar VG (2017) In silico prediction of linear B-cell epitopes on proteins. Methods Mol Biol 1484:255–264 Akter S, Shahab M, Sarkar MMH, Hayat C, Banu TA, Goswami B et al (2022) Immunoinformatics approach to epitope-based vaccine design against the SARS-CoV-2 in Bangladeshi patients. J Genet Eng Biotechnol 20:136