Comprehensive Analysis and Annotation of Available Fungal Allergens for the Presence of T-cell and B-cell epitopes and Development of the SVM Based Classifiers for in silico Prediction of Novel Allergen Sequences

2018 ◽  
Vol 15 (2) ◽  
Author(s):  
Mehak Dangi ◽  
Bharat Singh ◽  
Sandeep Kumar Dhanda ◽  
Renu Chaudhary ◽  
Anil K. Chhillar
Keyword(s):  
T Cell ◽  
B Cell ◽  
In Silico ◽  
Comprehensive Analysis ◽  
In Silico Prediction ◽  
B Cell Epitopes ◽  
Fungal Allergens

In silico prediction of T‐cell and B‐cell epitopes of human papillomavirus type 16 L1 protein

2021 ◽  
Author(s):  
Shahab Mahmoudvand ◽  
Somayeh Shokri ◽  
Manoochehr Makvandi ◽  
Reza Taherkhani ◽  
Mohammad Rashno ◽  
...  
Keyword(s):  
Human Papillomavirus ◽  
T Cell ◽  
B Cell ◽  
In Silico ◽  
In Silico Prediction ◽  
B Cell Epitopes ◽  
Human Papillomavirus Type 16 ◽  
L1 Protein

scholarly journals Homology modeling of Amb a 4 and Amb a 6 ragweed allergens and in silico prediction of their T-cell and B-cell epitopes for peptide-based immunotherapy

Alergologia ◽  
2021 ◽  
Vol 4 (7) ◽  
pp. 188
Author(s):  
Michael-Bogdan Mărgineanu ◽  
Didier Barradas Bautista ◽  
Kuan-Wei Chen ◽  
Virgil Păunescu ◽  
Carmen Panaitescu
Keyword(s):  
T Cell ◽  
Homology Modeling ◽  
B Cell ◽  
In Silico ◽  
In Silico Prediction ◽  
B Cell Epitopes

scholarly journals Immuno-informatics Design of a Multimeric Epitope Peptide Based Vaccine Targeting SARS-CoV-2 Spike Glycoprotein

2020 ◽  
Author(s):  
Onyeka S. Chukwudozie ◽  
Clive M. Gray ◽  
Tawakalt A. Fagbayi ◽  
Rebecca C. Chukwuanukwu ◽  
Victor O. Oyebanji ◽  
...  
Keyword(s):  
T Cell ◽  
B Cell ◽  
In Silico ◽  
Peptide Vaccine ◽  
Spike Protein ◽  
Cell Mediated Immunity ◽  
Epitope Peptide ◽  
Mhc I ◽  
B Cell Epitopes ◽  
Antibody Recognition

ABSTRACTDeveloping an efficacious vaccine to SARS-CoV-2 infection is critical to stem COVID-19 fatalities and providing the global community with immune protection. We have used a bioinformatic approach to aid in the design of an epitope peptide-based vaccine against the spike protein of the virus. Five antigenic B cell epitopes with viable antigenicity and a total of 27 discontinuous B cell epitopes were mapped out structurally in the spike protein for antibody recognition. We identified eight CD8+ T cell 9-mers along with 12 CD4+ T cell 14-15-mer as promising candidate epitopes putatively restricted by a large number of MHC-I and II alleles respectively. We used this information to construct an in silico chimeric peptide vaccine whose translational rate was highly expressed when cloned in pET28a (+) vector. The vaccine construct was predicted to elicit high antigenicity and cell-mediated immunity when given as a homologous prime-boost, with triggering of toll-like receptor 5 by the adjuvant linker. The vaccine was characterized by an increase in IgM and IgG and an array of Th1 and Th2 cytokines. Upon in silico challenge with SARS-CoV-2, there was a decrease in antigen levels using our immune simulations. We therefore propose that potential vaccine designs consider this approach.

scholarly journals In silico prediction of B cell epitopes of the hemolysis-associated protein 1 for vaccine design against leptospirosis

2020 ◽  
Vol 1 (1) ◽  
pp. 32-37
Author(s):  
Sakineh Poorhosein Fookolaee ◽  
Somayyeh Talebishelimaki ◽  
Mohammad Taha Saadati Rad ◽  
Mostafa Akbarian Rokni
Keyword(s):  
B Cell ◽  
In Silico ◽  
Vaccine Design ◽  
In Silico Prediction ◽  
B Cell Epitopes

scholarly journals Molecular cloning, expression, purification and in silico epitope prediction of cobalamin-independent methionine synthase (Mor a 2), as a novel allergen from Morus alba pollen

2021 ◽  
Author(s):  
Yunus AKSÜT
Keyword(s):  
T Cell ◽  
B Cell ◽  
In Silico ◽  
Allergic Diseases ◽  
Structural Features ◽  
Morus Alba ◽  
Methionine Synthase ◽  
Antigenic Peptides ◽  
T Cell Epitopes ◽  
B Cell Epitopes

IntroductionMorus alba (white mulberry) pollen is an aero-allergen source that can trigger allergic diseases. Cobalamin-independent methionine synthase (MetE) in M. alba pollen has been proved to be one of the major allergens for some patients living in Istanbul (Turkey). The aim of the present study was the recombinant production and identification of MetE (Mor a 2), a novel allergen from M. alba pollen. The IgE binding reactivity of rMor a 2 produced for the first time was evaluated and some structural features were investigated by in silico methods to better understand its immunogenicity.Material and methodsThe gene encoding Mor a 2 was cloned in fission yeast, Schizosaccharomyces pombe ura4-D18h- strain, using pSLF1073 vector. This is the first report of the production of recombinant pollen allergen in S. pombe. After the purification, immunoreactivity of rMor a 2 was confirmed by immunoblotting using sera of patient allergic to M. alba pollen. Besides, B-cell epitopes of rMor a 2 were predicted using various bioinformatic tools, namely Bioinformatics Predicted Antigenic Peptides, BepiPred 2.0 and Immune Epitope Database whereas T-cell epitopes were estimated using NetMHCIIpan-3.2 and NetMHCII 2.3 servers.ResultsThe immunoblotting analysis yielded 11 of 11 positive reactions to rMor a 2. In silico predictions exerted seven B-cell epitopes (22-33, 384-394, 407-423, 547-553, 571-577, 671-678, 736-741) and seven T-cell epitopes (54-62, 161-170, 197-205, 347-358, 622-630, 657-665, 756-764).ConclusionsThese findings may help the use of rMor a 2 in the diagnosis and treatment of allergic diseases associated with M. alba and/or MetE.

In silico prediction of B-cell epitopes for twenty-five mite allergens: The therapeutic potentials for immunotherapy

2019 ◽  
Vol 46 ◽  
pp. 101408
Author(s):  
Narjes Ebrahimi ◽  
Navid Nezafat ◽  
Hossein Esmaeilzadeh ◽  
Younes Ghasemi ◽  
Seyed Hesamodin Nabavizadeh ◽  
...  
Keyword(s):  
B Cell ◽  
In Silico ◽  
In Silico Prediction ◽  
B Cell Epitopes

scholarly journals Immuno-informatics design of a multimeric epitope peptide based vaccine targeting SARS-CoV-2 spike glycoprotein

PLoS ONE ◽  
2021 ◽  
Vol 16 (3) ◽  
pp. e0248061
Author(s):  
Onyeka S. Chukwudozie ◽  
Clive M. Gray ◽  
Tawakalt A. Fagbayi ◽  
Rebecca C. Chukwuanukwu ◽  
Victor O. Oyebanji ◽  
...  
Keyword(s):  
T Cell ◽  
B Cell ◽  
In Silico ◽  
Peptide Vaccine ◽  
Spike Protein ◽  
Cell Mediated Immunity ◽  
Epitope Peptide ◽  
Mhc I ◽  
B Cell Epitopes ◽  
Antibody Recognition

Developing an efficacious vaccine for SARS-CoV-2 infection is critical to stemming COVID-19 fatalities and providing the global community with immune protection. We have used a bioinformatic approach to aid in designing an epitope peptide-based vaccine against the spike protein of the virus. Five antigenic B cell epitopes with viable antigenicity and a total of 27 discontinuous B cell epitopes were mapped out structurally in the spike protein for antibody recognition. We identified eight CD8+ T cell 9-mers and 12 CD4+ T cell 14-15-mer as promising candidate epitopes putatively restricted by a large number of MHC I and II alleles, respectively. We used this information to construct an in silico chimeric peptide vaccine whose translational rate was highly expressed when cloned in pET28a (+) vector. With our In silico test, the vaccine construct was predicted to elicit high antigenicity and cell-mediated immunity when given as a homologous prime-boost, triggering of toll-like receptor 5 by the adjuvant linker. The vaccine was also characterized by an increase in IgM and IgG and an array of Th1 and Th2 cytokines. Upon in silico challenge with SARS-CoV-2, there was a decrease in antigen levels using our immune simulations. We, therefore, propose that potential vaccine designs consider this approach.

scholarly journals In Silico screening of T-cell and B-cell Epitopes of Rotavirus VP7 and VP4 proteins for Effective Vaccine Design

2019 ◽  
Vol 35 (1) ◽  
pp. 45-55
Author(s):  
Md Sadikur Rahman Shuvo ◽  
Sanjoy Kumar Mukharjee ◽  
Firoz Ahmed
Keyword(s):  
Developing Countries ◽  
T Cell ◽  
B Cell ◽  
In Silico ◽  
Child Death ◽  
Vaccine Design ◽  
Effective Vaccine ◽  
World Population ◽  
Promising Alternative ◽  
B Cell Epitopes

Rotavirus is one of the deadliest causative agents of childhood diarrhea which causes half a million child death across the globe, mostly in developing countries. However, effective vaccine strategies against rotavirus are yet to be established to prevent these unwanted premature deaths. In this regard, in silico vaccine design for rotavirus could be a promising alternative for developing countries due to its efficiency in shortening valuable time and cost. The present study described an epitope-based peptide vaccine design against rotavirus, using a combination of T-cell and B-cell epitope predictions and molecular docking approach. To perform this, sequences of rotavirus VP7 and VP4 proteins were retrieved from the NCBI database and subjected to different bioinformatics tools to predict most immunogenic T-cell and B-cell epitopes. From the identified epitopes, the sequence VMSKRSRSL of VP7 and TQFTDFVSL of VP4 was identified as the most potential epitopes based on their antigenicity, conservancy and interaction with major histocompatability complex I (MHC-I) alleles. Moreover, the peptide VMSKRSRSL interacted with human leukocyte antigen, HLA-B*08:01 and TQFTDFVSL interacted with HLA-A*02:06 with considerable binding energy and affinity score. Combined population coverage for our identified epitopes was found 70.53% and 45.64% for world population and South Asian population respectively. All these results suggest that, the epitopes identified in this study could be a very good vaccine candidate for the strains of rotavirus circulating in Bangladesh. However, as this study is completely dependent on computational prediction algorithms, further in vivo screening is required to come up in a precise conclusion about these epitopes for effective rotavirus vaccination. Bangladesh J Microbiol, Volume 35 Number 1 June 2018, pp 45-55

scholarly journals In silico prediction of B cell epitopes and experimental validation on wheat allergens

2014 ◽  
Vol 4 (S2) ◽  
Author(s):  
Sandra Denery-Papini ◽  
Virginie Lollier ◽  
Hamza Mameri ◽  
Manon Pietri ◽  
Colette Larre ◽  
...  
Keyword(s):  
B Cell ◽  
In Silico ◽  
Experimental Validation ◽  
In Silico Prediction ◽  
B Cell Epitopes
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