Epitope Based Peptide Prediction from Proteome of Enterotoxigenic E.coli

Khan, Fariya; Srivastava, Vivek; Kumar, Ajay

doi:10.1007/s10989-017-9617-1

Cited by 10 publications

(3 citation statements)

References 41 publications

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“…Recently, immunoinformatics-aided vaccine design has received experimental validation, which targeted multi-epitope protein clusters from Mycobacterium tuberculosis that interacted with HLA class I and II molecules and their prediction was experimentally validated through in vitro studies (84). On the other hand, our study was more speci c than some similar studies, for example, a study from Khan et al had selected MHC-I alleles for which the epitopes representing higher a nity (IC 50 < 500 nm), but in our study, we showed that epitopes for MHC I alleles showing higher a nity (IC 50 < 200 nm), as peptides with minimum IC 50 values, exhibited greater inhibition (85,86). In addition, we assessed immunogenicity, allergenicity, and toxicity of the selected epitopes.…”

Section: Discussionmentioning

confidence: 53%

Epitope-based Immunoinformatics Approach on Nucleocapsid Protein of Severe Acute Respiratory Syndrome-Coronavirus-2

Rakib

Sami

Islam

et al. 2020

Preprint

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With an increasing fatality rate, severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) has emerged as a promising threat to human health worldwide. SARS-CoV-2 is a member of the Coronaviridae family, which is transmitted from animal to human and because of being contagious, further it transmitted human to human. Recently, the World Health Organization (WHO) has announced the infectious disease caused by SARS-CoV-2, which is known as coronavirus disease-2019 (COVID-2019) as a global pandemic. But, no specific medications are available for the treatment of COVID-19 so far. As a corollary, there is a need for a potential vaccine to impede the progression of the disease. Lately, it has been documented that the nucleocapsid (N) protein of SARS-CoV-2 is responsible for viral replication as well as interferes with host immune responses. We have comparatively analyzed the sequences of N protein of SARS-CoV-2 for the identification of core attributes and analyzed the ancestry through phylogenetic analysis. Subsequently, we have predicted the most immunogenic epitope for T-cell as well as B-cell. Importantly, our investigation mainly focused on major histocompatibility complex (MHC) class I potential peptides and NTASWFTAL interacted with most human leukocyte antigen (HLA) that are encoded by MHC class I molecules. Further, molecular docking analysis unveiled that NTASWFTAL possessed a greater affinity towards HLA and also available in a greater range of the population. Our study provides a consolidated base for vaccine design and we hope that this computational analysis will pave the way for designing novel vaccine candidates.

show abstract

Section: Discussionmentioning

confidence: 53%

Epitope-based Immunoinformatics Approach on Nucleocapsid Protein of Severe Acute Respiratory Syndrome-Coronavirus-2

Rakib

Sami

Islam

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…Recently, immunoinformatics-aided vaccine design has received experimental validation, which targeted multi-epitope protein clusters from Mycobacterium tuberculosis that interacted with HLA class I and II molecules and their prediction was experimentally validated through in vitro studies [78]. On the other hand, our study was more specific than some similar studies, for example, a study from Khan et al had selected MHC-I alleles for which the epitopes representing higher affinity (IC 50 < 500 nm), but in our study, we showed that epitopes for MHC I alleles showing higher affinity (IC 50 < 200 nm), as peptides with minimum IC 50 values, exhibited greater inhibition [79,80]. In addition, we assessed immunogenicity, allergenicity and toxicity of the selected epitopes.…”

Section: Discussionmentioning

confidence: 57%

Epitope-Based Immunoinformatics Approach on Nucleocapsid Protein of Severe Acute Respiratory Syndrome-Coronavirus-2

Rakib

Sami

et al. 2020

Molecules

View full text Add to dashboard Cite

With an increasing fatality rate, severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) has emerged as a promising threat to human health worldwide. Recently, the World Health Organization (WHO) has announced the infectious disease caused by SARS-CoV-2, which is known as coronavirus disease-2019 (COVID-2019), as a global pandemic. Additionally, the positive cases are still following an upward trend worldwide and as a corollary, there is a need for a potential vaccine to impede the progression of the disease. Lately, it has been documented that the nucleocapsid (N) protein of SARS-CoV-2 is responsible for viral replication and interferes with host immune responses. We comparatively analyzed the sequences of N protein of SARS-CoV-2 for the identification of core attributes and analyzed the ancestry through phylogenetic analysis. Subsequently, we predicted the most immunogenic epitope for the T-cell and B-cell. Importantly, our investigation mainly focused on major histocompatibility complex (MHC) class I potential peptides and NTASWFTAL interacted with most human leukocyte antigen (HLA) that are encoded by MHC class I molecules. Further, molecular docking analysis unveiled that NTASWFTAL possessed a greater affinity towards HLA and also available in a greater range of the population. Our study provides a consolidated base for vaccine design and we hope that this computational analysis will pave the way for designing novel vaccine candidates.

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“…To stimulate the different arms of the immune system, prediction of potential epitopes with the different computational tools was employed (Kumar et al 2013 ). The proteome of the most pathogenic strain E24377A can be helpful in identifying T cell epitopes in designing the vaccine candidates (Khan et al 2018 ). Furthermore, allergic and toxicity prediction, modeling of epitopes with HLA alleles can be studied and the docking of the MHC molecules and identified peptides will be performed.…”

Section: Introductionmentioning

confidence: 99%

An integrative docking and simulation-based approach towards the development of epitope-based vaccine against enterotoxigenic Escherichia coli

Khan

Kumar

2021

Netw Model Anal Health Inform Bioinforma

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Enterotoxigenic E.coli is causing diarrheal illness in children as well as adults with the majority of the cases occurring in developing countries. To reduce the number of cases occurring worldwide, the development of an effectual vaccine against these bacteria can be the only prevention. This conjectural work was performed using modern bioinformatics tools for investigation of proteome of ETEC strain E24377A. Different computational vaccinology approaches were deployed to assess several parameters including antigenicity, allergenicity, stability, localization, molecular weight and toxicity of the predicted epitopes required for good vaccine candidate to elicit immune response against diarrhea. We estimated two known control antigens, epitope 141 STLPETTVV 149 of Hepatitis B virus and epitope 265 ILRGSVAHK 273 of H1N1 Nucleoprotein in an attempt to corroborate our research work. Furthermore molecular docking was performed to evaluate the interaction between HLA allele and peptide, the peptide QYGGGNSAL and peptide LPYFELRWL were considered to be the most promiscuous T cell epitopes with the highest binding energy value of −2.09 kcal/mol and −1.84 kcal/mol, respectively. In addition, dynamic simulation revealed good stability of the vaccine construct as well as population coverage analysis exhibits the highest population coverage in the regions of East Asia, India, Northeast Asia, South Asia and North America. Therefore, these two epitopes can be further synthesized for wet lab analysis and could be considered as a promising vaccine against diarrhea. Supplementary Information The online version contains supplementary material available at 10.1007/s13721-021-00287-6.

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Epitope Based Peptide Prediction from Proteome of Enterotoxigenic E.coli

Cited by 10 publications

References 41 publications

Epitope-based Immunoinformatics Approach on Nucleocapsid Protein of Severe Acute Respiratory Syndrome-Coronavirus-2

Epitope-based Immunoinformatics Approach on Nucleocapsid Protein of Severe Acute Respiratory Syndrome-Coronavirus-2

Epitope-Based Immunoinformatics Approach on Nucleocapsid Protein of Severe Acute Respiratory Syndrome-Coronavirus-2

An integrative docking and simulation-based approach towards the development of epitope-based vaccine against enterotoxigenic Escherichia coli

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