Immunoinformatics-aided design of a new multi-epitope vaccine adjuvanted with domain 4 of pneumolysin against Streptococcus pneumoniae strains

[1]  Elnaz Afshari,et al.  In-silico design and evaluation of an epitope-based serotype-independent promising vaccine candidate for highly cross-reactive regions of pneumococcal surface protein A , 2023, Journal of Translational Medicine.

[2]  A. Shabani,et al.  In silico designing of a novel epitope-based candidate vaccine against Streptococcus pneumoniae with introduction of a new domain of PepO as adjuvant , 2022, Journal of Translational Medicine.

[3]  A. Shabani,et al.  In silico designing of a novel epitope-based candidate vaccine against Streptococcus pneumoniae with introduction of a new domain of PepO as adjuvant , 2022, Journal of translational medicine.

[4]  B. Kundu,et al.  In-silico design of an immunoinformatics based multi-epitope vaccine against Leishmania donovani , 2022, BMC Bioinformatics.

[5]  Muhammad Sadeqi Nezhad,et al.  In silico design of a multi-epitope vaccine against HPV16/18 , 2022, BMC Bioinformatics.

[6]  Sepideh Fereshteh,et al.  In Silico Analyses of Extracellular Proteins of Acinetobacter baumannii as Immunogenic Candidates , 2022, Iranian journal of pharmaceutical research : IJPR.

[7]  I. Pakzad,et al.  Immunoinformatics Insights into the Internalin A and B Proteins to Design a Multi-Epitope Subunit Vaccine for L. monocytogenes , 2022, International Journal of Peptide Research and Therapeutics.

[8]  Elnaz Afshari,et al.  In-silico Analysis of Pneumococcal Heat-Shock Protein (DnaJ) to Predict Novel Multi-Epitope Vaccine Candidates , 2021, Vaccine Research.

[9]  Giuseppe Alessandro Parasiliti Palumbo,et al.  In silico design of recombinant multi-epitope vaccine against influenza A virus , 2021, BMC Bioinformatics.

[10]  Matin Fathollahi,et al.  In silico vaccine design and epitope mapping of New Delhi metallo-beta-lactamase (NDM): an immunoinformatics approach , 2021, BMC Bioinformatics.

[11]  M. Salehi,et al.  Design of a multi-epitope vaccine against cervical cancer using immunoinformatics approaches , 2021, Scientific Reports.

[12]  A. Shabani,et al.  Rational design of hyper-glycosylated human follicle-stimulating hormone analogs (a bioinformatics approach) , 2021, Journal of biomolecular structure & dynamics.

[13]  V. Sender,et al.  Virus-Induced Changes of the Respiratory Tract Environment Promote Secondary Infections With Streptococcus pneumoniae , 2021, Frontiers in Cellular and Infection Microbiology.

[14]  Eduardo H. B. Maia,et al.  Immunoinformatics Design of Multi-Epitope Peptide-Based Vaccine Against Schistosoma mansoni Using Transmembrane Proteins as a Target , 2021, Frontiers in Immunology.

[15]  E. Tuomanen,et al.  Multi-Valent Protein Hybrid Pneumococcal Vaccines: A Strategy for the Next Generation of Vaccines , 2021, Vaccines.

[16]  Mirian Domenech,et al.  Pneumococcal Choline-Binding Proteins Involved in Virulence as Vaccine Candidates , 2021, Vaccines.

[17]  Maria G. A. Oliveira,et al.  Propedia: a database for protein–peptide identification based on a hybrid clustering algorithm , 2021, BMC Bioinformatics.

[18]  Syed Shujait Ali,et al.  Proteome-wide mapping and reverse vaccinology-based B and T cell multi-epitope subunit vaccine designing for immune response reinforcement against Porphyromonas gingivalis , 2020, Journal of biomolecular structure & dynamics.

[19]  A. Shabani,et al.  Rational Design of Hyper-glycosylated Human Chorionic Gonadotropin Analogs (A Bioinformatics Approach) , 2020 .

[20]  Behzad Pourhossein,et al.  Design of a multi-epitope vaccine against SARS-CoV-2 using immunoinformatics approach , 2020, International Journal of Biological Macromolecules.

[21]  Amjad Ali,et al.  Designing Multi-Epitope Vaccines to Combat Emerging Coronavirus Disease 2019 (COVID-19) by Employing Immuno-Informatics Approach , 2020, Frontiers in Immunology.

[22]  Z. Amirghofran,et al.  Designing a multi-epitope vaccine against blood-stage of Plasmodium falciparum by in silico approaches. , 2020, Journal of molecular graphics & modelling.

[23]  F. Castiglione,et al.  A candidate multi-epitope vaccine against SARS-CoV-2 , 2020, Scientific Reports.

[24]  W. Lim,et al.  Co-infections in people with COVID-19: a systematic review and meta-analysis , 2020, Journal of Infection.

[25]  Sepideh Fereshteh,et al.  New putative vaccine candidates against Acinetobacter baumannii using the reverse vaccinology method. , 2020, Microbial pathogenesis.

[26]  C. Poh,et al.  Development of Next Generation Streptococcus pneumoniae Vaccines Conferring Broad Protection , 2020, Vaccines.

[27]  D. Odimegwu,et al.  Immunoinformatics and Vaccine Development: An Overview , 2020, ImmunoTargets and therapy.

[28]  A. Janani,et al.  Relationship Between Prevalence of Pneumococcal Serotypes and Their Neuraminidases in Carriers, Predictive Facts? , 2020 .

[29]  L. Leite,et al.  The long search for a serotype independent pneumococcal vaccine , 2020, Expert review of vaccines.

[30]  N. Shahrokhi,et al.  Assessment of PhtD C-Terminal Immunogenicity by Opsonophagocytosis Assay (OPA) with OMVs as Adjuvants , 2019 .

[31]  F. Kazemi-Lomedasht,et al.  Protective responses of an engineered PspA recombinant antigen against Streptococcus pneumoniae , 2019, Biotechnology reports.

[32]  Chuntao Zhang,et al.  Immunoinformatics prediction of OMP2b and BCSP31 for designing multi-epitope vaccine against Brucella. , 2019, Molecular immunology.

[33]  Shu-Pei Lien,et al.  Domain 4 of pneumolysin from Streptococcus pneumoniae is a multifunctional domain contributing TLR4 activating and hemolytic activity. , 2019, Biochemical and biophysical research communications.

[34]  Y. Ghasemi,et al.  Designing self-assembled peptide nanovaccine against Streptococcus pneumoniae: An in silico strategy , 2019, Molecular and Cellular Probes.

[35]  N. Pang,et al.  Bioinformatics analysis of EgA31 and EgG1Y162 proteins for designing a multi-epitope vaccine against Echinococcus granulosus. , 2019, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

[36]  E. Gosselin,et al.  Bacterial Protein Toll-Like-Receptor Agonists: A Novel Perspective on Vaccine Adjuvants , 2019, Front. Immunol..

[37]  A. Abiri,et al.  In silico analysis of transmembrane protein 31 (TMEM31) antigen to design novel multiepitope peptide and DNA cancer vaccines against melanoma. , 2019, Molecular immunology.

[38]  Mona Shafaghi,et al.  Rational design of hyper-glycosylated human luteinizing hormone analogs (a bioinformatics approach) , 2019, Comput. Biol. Chem..

[39]  Martijn D. B. van de Garde,et al.  Prediction and Validation of Immunogenic Domains of Pneumococcal Proteins Recognized by Human CD4+ T Cells , 2019, Infection and Immunity.

[40]  J. Routsias,et al.  Novel Protein-Based Pneumococcal Vaccines: Assessing the Use of Distinct Protein Fragments Instead of Full-Length Proteins as Vaccine Antigens , 2019, Vaccines.

[41]  Y. Ghasemi,et al.  Vaccinomics approach for developing multi-epitope peptide pneumococcal vaccine , 2019, Journal of biomolecular structure & dynamics.

[42]  E. Lefkowitz,et al.  The diversity of the proline-rich domain of pneumococcal surface protein A (PspA): Potential relevance to a broad-spectrum vaccine. , 2018, Vaccine.

[43]  J. Greenbaum,et al.  Improved methods for predicting peptide binding affinity to MHC class II molecules , 2018, Immunology.

[44]  Lavida R. K. Brooks,et al.  Streptococcus pneumoniae’s Virulence and Host Immunity: Aging, Diagnostics, and Prevention , 2018, Front. Immunol..

[45]  Torsten Schwede,et al.  SWISS-MODEL: homology modelling of protein structures and complexes , 2018, Nucleic Acids Res..

[46]  S. Abdollahi,et al.  Antibiotic Susceptibility and Prevalence of Adhesion Genes in Streptococcus pneumoniae Isolates Detected in Carrier Children in Tehran , 2018 .

[47]  D. Briles,et al.  Transcutaneous immunization with pneumococcal surface protein A in mice , 2018, The Laryngoscope.

[48]  C. Colaco,et al.  Safety and immunogenicity of a novel multiple antigen pneumococcal vaccine in adults: A Phase 1 randomised clinical trial. , 2017, Vaccine.

[49]  Radka Svobodová Vařeková,et al.  PDBsum: Structural summaries of PDB entries , 2017, Protein science : a publication of the Protein Society.

[50]  L. Leite,et al.  Rational selection of broadly cross-reactive family 2 PspA molecules for inclusion in chimeric pneumococcal vaccines. , 2017, Microbial pathogenesis.

[51]  Hamid Reza Nouri,et al.  Development of a multi-epitope peptide vaccine inducing robust T cell responses against brucellosis using immunoinformatics based approaches. , 2017, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

[52]  Navid Nezafat,et al.  Immunoinformatics analysis and in silico designing of a novel multi-epitope peptide vaccine against Staphylococcus aureus. , 2017, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

[53]  Dima Kozakov,et al.  The ClusPro web server for protein–protein docking , 2017, Nature Protocols.

[54]  L. Leite,et al.  Systemic immunization with rPotD reduces Streptococcus pneumoniae nasopharyngeal colonization in mice. , 2017, Vaccine.

[55]  M. Feizabadi,et al.  Antimicrobial Resistant Pattern and Capsular Typing of Streptococcus Pneumoniae Isolated from Children in Sistan -Baluchestan. , 2016, Maedica.

[56]  C. D. Dela Cruz,et al.  Pneumococcal Vaccination Strategies. An Update and Perspective. , 2016, Annals of the American Thoracic Society.

[57]  S. A. Kristian,et al.  Generation and Improvement of Effector Function of a Novel Broadly Reactive and Protective Monoclonal Antibody against Pneumococcal Surface Protein A of Streptococcus pneumoniae , 2016, PloS one.

[58]  Chasity M. Shelton,et al.  A Review of Pneumococcal Vaccines: Current Polysaccharide Vaccine Recommendations and Future Protein Antigens. , 2016, The journal of pediatric pharmacology and therapeutics : JPPT : the official journal of PPAG.

[59]  Yujuan He,et al.  Streptococcus pneumoniae Endopeptidase O (PepO) Elicits a Strong Innate Immune Response in Mice via TLR2 and TLR4 Signaling Pathways , 2016, Front. Cell. Infect. Microbiol..

[60]  M. Pichichero,et al.  Next generation protein based Streptococcus pneumoniae vaccines , 2016, Human vaccines & immunotherapeutics.

[61]  John A. Robinson,et al.  A Synthetic Virus-Like Particle Streptococcal Vaccine Candidate Using B-Cell Epitopes from the Proline-Rich Region of Pneumococcal Surface Protein A , 2015, Vaccines.

[62]  Yongge Wu,et al.  Protective Immune Responses Elicited by Fusion Protein Containing PsaA and PspA Fragments , 2015, Immunological investigations.

[63]  Yang Zhang,et al.  The I-TASSER Suite: protein structure and function prediction , 2014, Nature Methods.

[64]  Darren R. Flower,et al.  AllerTOP v.2—a server for in silico prediction of allergens , 2014, Journal of Molecular Modeling.

[65]  E. Miyaji,et al.  Mapping of Epitopes Recognized by Antibodies Induced by Immunization of Mice with PspA and PspC , 2014, Clinical and Vaccine Immunology.

[66]  M. Melin,et al.  Role of Pht Proteins in Attachment of Streptococcus pneumoniae to Respiratory Epithelial Cells , 2014, Infection and Immunity.

[67]  Sandeep Kumar Dhanda,et al.  Designing of interferon-gamma inducing MHC class-II binders , 2013, Biology Direct.

[68]  A. Ogunniyi,et al.  Vaccination against Streptococcus pneumoniae Using Truncated Derivatives of Polyhistidine Triad Protein D , 2013, PloS one.

[69]  F. Shahcheraghi,et al.  Serotyping of Streptococcus pneumoniae isolated from Tehran by Multiplex PCR: Are serotypes of clinical and carrier isolates identical? , 2013, Iranian journal of microbiology.

[70]  A. Ogunniyi,et al.  Surface Association of Pht Proteins of Streptococcus pneumoniae , 2013, Infection and Immunity.

[71]  E. Tuomanen,et al.  The pneumococcus: epidemiology, microbiology, and pathogenesis. , 2013, Cold Spring Harbor perspectives in medicine.

[72]  Harinder Singh,et al.  Improved Method for Linear B-Cell Epitope Prediction Using Antigen’s Primary Sequence , 2013, PloS one.

[73]  L. Leite,et al.  Characterization of Protective Immune Responses Induced by Pneumococcal Surface Protein A in Fusion with Pneumolysin Derivatives , 2013, PloS one.

[74]  Di Wu,et al.  Bioinformatics analysis of the epitope regions for norovirus capsid protein , 2013, BMC Bioinformatics.

[75]  Morten Nielsen,et al.  Reliable B Cell Epitope Predictions: Impacts of Method Development and Improved Benchmarking , 2012, PLoS Comput. Biol..

[76]  D. Rhee,et al.  Pneumococcal Surface Protein A Inhibits Complement Deposition on the Pneumococcal Surface by Competing with the Binding of C-Reactive Protein to Cell-Surface Phosphocholine , 2012, The Journal of Immunology.

[77]  A. Ogunniyi,et al.  Polyhistidine triad proteins of pathogenic streptococci. , 2012, Trends in microbiology.

[78]  Yang Zhang,et al.  Improving the physical realism and structural accuracy of protein models by a two-step atomic-level energy minimization. , 2011, Biophysical journal.

[79]  D. Briles,et al.  Maternal Immunization with Pneumococcal Surface Protein A Protects against Pneumococcal Infections among Derived Offspring , 2011, PloS one.

[80]  S. Kim,et al.  Intranasal immunization with recombinant PspA fused with a flagellin enhances cross-protective immunity against Streptococcus pneumoniae infection in mice. , 2011, Vaccine.

[81]  J. Poolman,et al.  A protein-based pneumococcal vaccine protects rhesus macaques from pneumonia after experimental infection with Streptococcus pneumoniae. , 2011, Vaccine.

[82]  Andreas P. Eichenberger,et al.  Definition and testing of the GROMOS force-field versions 54A7 and 54B7 , 2011, European Biophysics Journal.

[83]  M. Brandileone,et al.  Selection of family 1 PspA molecules capable of inducing broad-ranging cross-reactivity by complement deposition and opsonophagocytosis by murine peritoneal cells. , 2011, Vaccine.

[84]  Pierre Baldi,et al.  High-throughput prediction of protein antigenicity using protein microarray data , 2010, Bioinform..

[85]  T. Mitchell,et al.  Novel mucosal vaccines generated by genetic conjugation of heterologous proteins to pneumolysin (PLY) from Streptococcus pneumoniae. , 2010, Vaccine.

[86]  D. Briles,et al.  The Proline-Rich Region of Pneumococcal Surface Proteins A and C Contains Surface-Accessible Epitopes Common to All Pneumococci and Elicits Antibody-Mediated Protection against Sepsis , 2010, Infection and Immunity.

[87]  Praveen Kumar Sharma,et al.  Helper T Cell Epitope-Mapping Reveals MHC-Peptide Binding Affinities That Correlate with T Helper Cell Responses to Pneumococcal Surface Protein A , 2010, PloS one.

[88]  Pierre Baldi,et al.  SOLpro: accurate sequence-based prediction of protein solubility , 2009, Bioinform..

[89]  R. Dagan.  Serotype replacement in perspective. , 2009, Vaccine.

[90]  Hayyoung Lee,et al.  The structural basis of lipopolysaccharide recognition by the TLR4–MD-2 complex , 2009, Nature.

[91]  R. Malley,et al.  Protection against Pneumococcal Colonization and Fatal Pneumonia by a Trivalent Conjugate of a Fusion Protein with the Cell Wall Polysaccharide , 2009, Infection and Immunity.

[92]  Yvonne Perrie,et al.  Vaccine adjuvant systems: enhancing the efficacy of sub-unit protein antigens. , 2008, International journal of pharmaceutics.

[93]  Wei Li,et al.  ElliPro: a new structure-based tool for the prediction of antibody epitopes , 2008, BMC Bioinformatics.

[94]  John Sidney,et al.  A Systematic Assessment of MHC Class II Peptide Binding Predictions and Evaluation of a Consensus Approach , 2008, PLoS Comput. Biol..

[95]  E. Miyaji,et al.  Recognition of pneumococcal isolates by antisera raised against PspA fragments from different clades. , 2008, Journal of medical microbiology.

[96]  Carsten Kutzner,et al.  GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. , 2008, Journal of chemical theory and computation.

[97]  Mojgan Kavoosi,et al.  Strategy for selecting and characterizing linker peptides for CBM9‐tagged fusion proteins expressed in Escherichia coli , 2007, Biotechnology and bioengineering.

[98]  Manfred J. Sippl,et al.  Thirty years of environmental health research--and growing. , 1996, Nucleic Acids Res..

[99]  Irini A. Doytchinova,et al.  BMC Bioinformatics BioMed Central Methodology article VaxiJen: a server for prediction of protective antigens, tumour , 2007 .

[100]  Sudipto Saha,et al.  Prediction of continuous B‐cell epitopes in an antigen using recurrent neural network , 2006, Proteins.

[101]  Gajendra P. S. Raghava,et al.  AlgPred: prediction of allergenic proteins and mapping of IgE epitopes , 2006, Nucleic Acids Res..

[102]  Dieter Jahn,et al.  JCat: a novel tool to adapt codon usage of a target gene to its potential expression host , 2005, Nucleic Acids Res..

[103]  D. Briles,et al.  PspA Protects Streptococcus pneumoniae from Killing by Apolactoferrin, and Antibody to PspA Enhances Killing of Pneumococci by Apolactoferrin , 2004, Infection and Immunity.

[104]  David Baker,et al.  Protein structure prediction and analysis using the Robetta server , 2004, Nucleic Acids Res..

[105]  A. Hakansson,et al.  Regions of PspA/EF3296 Best Able To Elicit Protection against Streptococcus pneumoniae in a Murine Infection Model , 2003, Infection and Immunity.

[106]  M. Brandileone,et al.  Analysis of Serum Cross-Reactivity and Cross-Protection Elicited by Immunization with DNA Vaccines against Streptococcus pneumoniae Expressing PspA Fragments from Different Clades , 2002, Infection and Immunity.

[107]  R. Medzhitov,et al.  Adjuvants of Immunity , 2002, The Journal of experimental medicine.

[108]  A. Krogh,et al.  Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. , 2001, Journal of molecular biology.

[109]  D. Briles,et al.  Immunization of humans with recombinant pneumococcal surface protein A (rPspA) elicits antibodies that passively protect mice from fatal infection with Streptococcus pneumoniae bearing heterologous PspA. , 2000, The Journal of infectious diseases.

[110]  D. Briles,et al.  Diversity of PspA: Mosaic Genes and Evidence for Past Recombination in Streptococcus pneumoniae , 2000, Infection and Immunity.

[111]  D. Briles,et al.  Immunization of healthy adults with a single recombinant pneumococcal surface protein A (PspA) variant stimulates broadly cross-reactive antibodies to heterologous PspA molecules. , 2000, Vaccine.

[112]  J C Paton,et al.  Effect of defined point mutations in the pneumolysin gene on the virulence of Streptococcus pneumoniae , 1995, Infection and immunity.

[113]  L. McDaniel,et al.  Localization of protection-eliciting epitopes on PspA of Streptococcus pneumoniae between amino acid residues 192 and 260. , 1994, Microbial pathogenesis.

[114]  T. Yeates,et al.  Verification of protein structures: Patterns of nonbonded atomic interactions , 1993, Protein science : a publication of the Protein Society.

[115]  J. Thornton,et al.  PROCHECK: a program to check the stereochemical quality of protein structures , 1993 .

[116]  D. Eisenberg,et al.  Assessment of protein models with three-dimensional profiles , 1992, Nature.

[117]  E. Emini,et al.  Induction of hepatitis A virus-neutralizing antibody by a virus-specific synthetic peptide , 1985, Journal of virology.

[118]  Pamela G. Guren,et al.  Candidates , 1982, Otolaryngology–Head and Neck Surgery.

[119]  R. Doolittle,et al.  A simple method for displaying the hydropathic character of a protein. , 1982, Journal of molecular biology.

[120]  A Ikai,et al.  Thermostability and aliphatic index of globular proteins. , 1980, Journal of biochemistry.

[121]  J. Zubeldia,et al.  Adjuvants in Allergen-Specific Immunotherapy: Modulating and Enhancing the Immune Response. , 2019, Journal of investigational allergology & clinical immunology.

[122]  R D Appel,et al.  Protein identification and analysis tools in the ExPASy server. , 1999, Methods in molecular biology.