Immunoinformatics and Epitope Prediction

Ramana, Jayashree; Mehla, Kusum

doi:10.1007/978-1-0716-0389-5_6

Cited by 12 publications

(11 citation statements)

References 45 publications

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“…Several studies have used immunoinformatic approaches to select B cell and T cell SARS-CoV-2 epitopes for epitopes-based vaccine formulation ( Ramana & Mehla, 2020 ; Oli et al, 2020 ; Siracusano, Pastori & Lopalco, 2020 ; Yoshida et al, 2021 ; Ribes, Chaccour & Moncunill, 2021 ; Jin et al, 2021 ). However, current computational methods are limited since they identify a large number of epitopes and need different web servers for accurate selection ( Bui et al, 2006 ; Doytchinova & Flower, 2007b ; Gupta et al, 2013 ).…”

Section: Discussionmentioning

confidence: 99%

“…The peptide-based vaccine design requires the immunoinformatic approach as part of the computational vaccinology strategy for epitopes prediction ( Ramana & Mehla, 2020 ; Oli et al, 2020 ; Lu et al, 2021 ). This approach regards the wide availability of the SARS-CoV-2 NGS (Next-Generation Sequencing) information associated with human leukocyte antigen (HLA) profile ( Kazi et al, 2018 ; Oli et al, 2020 ; Sharma et al, 2020 ) to identify T cell epitopes.…”

Section: Introductionmentioning

confidence: 99%

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EpiCurator: an immunoinformatic workflow to predict and prioritize SARS-CoV-2 epitopes

Ferreira

Martins

Souza

et al. 2021

PeerJ

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The ongoing coronavirus 2019 (COVID-19) pandemic, triggered by the emerging SARS-CoV-2 virus, represents a global public health challenge. Therefore, the development of effective vaccines is an urgent need to prevent and control virus spread. One of the vaccine production strategies uses the in silico epitope prediction from the virus genome by immunoinformatic approaches, which assist in selecting candidate epitopes for in vitro and clinical trials research. This study introduces the EpiCurator workflow to predict and prioritize epitopes from SARS-CoV-2 genomes by combining a series of computational filtering tools. To validate the workflow effectiveness, SARS-CoV-2 genomes retrieved from the GISAID database were analyzed. We identified 11 epitopes in the receptor-binding domain (RBD) of Spike glycoprotein, an important antigenic determinant, not previously described in the literature or published on the Immune Epitope Database (IEDB). Interestingly, these epitopes have a combination of important properties: recognized in sequences of the current variants of concern, present high antigenicity, conservancy, and broad population coverage. The RBD epitopes were the source for a multi-epitope design to in silico validation of their immunogenic potential. The multi-epitope overall quality was computationally validated, endorsing its efficiency to trigger an effective immune response since it has stability, high antigenicity and strong interactions with Toll-Like Receptors (TLR). Taken together, the findings in the current study demonstrated the efficacy of the workflow for epitopes discovery, providing target candidates for immunogen development.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

EpiCurator: an immunoinformatic workflow to predict and prioritize SARS-CoV-2 epitopes

Ferreira

Martins

Souza

et al. 2021

PeerJ

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“…B cell epitopes were selected as synthetic peptide candidates due to the fact that B cells are the main cells of antibody production while T cells are responsible for cell-based toxicity and complement activation. However B cell epitopes can be continuous or discontinuous and generally discontinuous ones dominate most antigenic epitope families 27 . For this reason, Linear B cell epitopes were selected.…”

Section: Peptide Design and Synthesismentioning

confidence: 99%

Usage of Peptide Antigens for Antibody-Based BoNT Detection System

Işik

Bilici

Çine

et al. 2021

Kocaeli Üniversitesi Sağlık Bilimleri Dergisi

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Objective: In the current study, we aimed to elicit a BoNT-specific immune response via using peptides designed by using bioinformatics tools instead of using intact native BoNT A toxin itself and to demonstrate the usage of these anti-peptide antibodies in a toxin detection system. Methods: Synthetic epitopic regions specific to LC, HN and HC regions of BoNT A were selected as antigen using B cell “Epitope Prediction Tools” form IEDB and shown to be on the surface of BoNT A with a software (Discovery Studio 4.0). Selected peptides were used in mice immunizations and the interaction between developed anti-peptide antibodies and the native intact BoNT A was examined. Results: The detection of native intact BoNT A at picogram levels per milliliter was performed with anti-peptide antibodies developed against three different peptides (P1, P2, and P3) in mice. Conclusion: The current study shows that synthetic peptides are at least as effective as the native toxin or the toxoid itself for raising high-affinity antibodies against toxins. In addition, considering the need for a quick diagnosis of botulism and, already used test systems in which many experimental animals are sacrificed, these results demonstrate the necessity of synthetic peptide immunogens usage to reduce both the number of animals and the amount of toxin usage.

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“…Antigenic epitopes, including B-and T-cell epitopes, are the regions of an antigen that bind to antigen-specific membrane receptors on lymphocytes or secreted antibodies (Ramana & Mehla, 2020).…”

Section: Introductionmentioning

confidence: 99%

“…Antigenic epitopes, including B‐ and T‐cell epitopes, are the regions of an antigen that bind to antigen‐specific membrane receptors on lymphocytes or secreted antibodies (Ramana & Mehla, 2020). Multiple epitope‐based vaccines have been developed for some bacterial diseases, such as Mycobacterium tuberculosis , Helicobacter pylori and Vibrio mimicus infection (Groot et al, 2005; Guo et al, 2012; Zhang et al, 2014).…”

Section: Introductionmentioning

confidence: 99%

First identification of Nocardia seriolaeGapA adhesion function and its three B‐cell epitopes with cell‐binding activity

Guo

Yue

Chang

et al. 2022

Journal of Fish Diseases

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Fish nocardiosis mainly caused by Nocardia seriolae (N. seriolae) is a serious threat to aquaculture. Bacterial adhesion to host cells mediated by adhesin is an initial step of pathogenesis. But it is not clear whether glyceraldehyde‐3‐phosphate dehydrogenase (GapA) is an adhesin of N. seriolae. Here, recombinant GapA protein (rGapA) was prokaryotic expressed, and its role in the bacterial adhesion to Ctenopharyngodon idella kidney cells was investigated by indirect immunofluorescence, protein‐binding assay and adhesion inhibition assay. The results showed that an obvious green fluorescence was observed on the surface of the cells co‐incubated with rGapA protein; the cytomembrane proteins of the cells pretreated with rGapA could react with anti‐rGapA antibody; and the antibody significantly inhibited the adhesion ability of the bacteria. Subsequently, B‐cell linear epitopes of GapA protein were identified by using a immunoinformatics approach combined with peptide ELISA and Western blot for the first time. It was found that four predicted epitopes (Ep58‐69, Ep139‐150, Ep186‐197, Ep318‐329) could all react with anti‐rGapA antibody and obviously inhibit the immunoreactivity between rGapA and anti‐rGapA antibody, and they were confirmed as indeed B‐cell linear epitopes of the protein. Furthermore, flow cytometry analysis found the percentage of positive cells co‐incubated with FITC‐labelled epitope peptides (Ep139‐150, Ep186‐197, Ep318‐329) was significantly higher than those in the FITC‐labelled Ep58‐69, unrelated control peptide and cell control. Collectively, GapA is an adhesin of N. seriolae, and epitope peptides (Ep139‐150, Ep186‐197, Ep318‐329) possess cell‐binding activity, which are potential candidates for developing a multiple epitopes‐based adhesin vaccine against fish nocardiosis.

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Immunoinformatics and Epitope Prediction

Cited by 12 publications

References 45 publications

EpiCurator: an immunoinformatic workflow to predict and prioritize SARS-CoV-2 epitopes

EpiCurator: an immunoinformatic workflow to predict and prioritize SARS-CoV-2 epitopes

Usage of Peptide Antigens for Antibody-Based BoNT Detection System

First identification of Nocardia seriolaeGapA adhesion function and its three B‐cell epitopes with cell‐binding activity

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