Epitope based vaccine prediction for SARS-COV-2 by deploying immuno-informatics approach

Joshi, Amit; Joshi, B. C.; Mannan, M. Amin-ul; Kaushik, Vikas

doi:10.1016/j.imu.2020.100338

Cited by 81 publications

(60 citation statements)

References 36 publications

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“…Approaches which use overlapping peptides, spaced other than single amino acid displacement, may exclude the key peptides. There have been several reports of bioinformatics analyses of SARS-CoV-2 using a variety of platforms (25)(26)(27)(28)(29). Herein, we applied bioinformatics analysis to determine the antigenic potential of the SARS-CoV-2 N protein.…”

Section: Introductionmentioning

confidence: 99%

Immunoinformatic Analysis of SARS-CoV-2 Nucleocapsid Protein and Identification of COVID-19 Vaccine Targets

2020

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COVID-19 is a worldwide emergency; therefore, there is a critical need for foundational knowledge about B and T cell responses to SARS-CoV-2 essential for vaccine development. However, little information is available defining which determinants of SARS-CoV-2 other than the spike glycoprotein are recognized by the host immune system. In this study, we focus on the SARS-CoV-2 nucleocapsid protein as a suitable candidate target for vaccine formulations. Major B and T cell epitopes of the SARS-CoV-2 N protein are predicted and resulting sequences compared with the homolog immunological domains of other coronaviruses that infect human beings. The most dominant of B cell epitope is located between 176-206 amino acids in the SRGGSQASSRSSSRSRNSSRNSTPGSSRGTS sequence. Further, we identify sequences which are predicted to bind multiple common MHC I and MHC II alleles. Most notably there is a region of potential T cell cross-reactivity within the SARS-CoV-2 N protein position 102-110 amino acids that traverses multiple human alpha and betacoronaviruses. Vaccination strategies designed to target these conserved epitope regions could generate immune responses that are cross-reactive across human coronaviruses, with potential to protect or modulate disease. Finally, these predictions can facilitate effective vaccine design against this high priority virus.

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Section: Introductionmentioning

confidence: 99%

Immunoinformatic Analysis of SARS-CoV-2 Nucleocapsid Protein and Identification of COVID-19 Vaccine Targets

2020

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“…The Nucleocapsid peptide (KTFPPTEPK) has the highest binding affinity to the MHC I HLA-A0202 allele ( Table 6). The 2D and 3D interactions are illustrated in According to the AllergenFP v.1.0 [12], AllerCatPro v. 1.7 [13], and ToxinPred servers [14], all the predicted peptides except the spike peptide (EVFNATRFASVYAWN) were Nonallergen and Non-Toxin (Tables 8and 9). The Hydrophobicity scores of the Spike Glycoprotein peptides were not available.…”

Section: Resultsmentioning

confidence: 99%

“…The Nucleocapsid peptides (KTFPPTEPK) and (RWYFYYLGTGPEAGL) showed a higher binding affinity to the MHC I HLA-A0202 allele and the three MHC II alleles HLA-DPA1*01:03/DPB1*02:01, HLA-DQA1*01:02/DQB1*06:02, HLA-DRB1, respectively, however, the total population coverage of the peptides FTISVTTEI and KTFPPTEPK is not high (Table 10). Joshi A, et al in their predictive COVID-19 Peptide-based vaccine study found that the ORF-7A protein's peptide (ITLCFTLKR) binds most effectively with the MHC I HLA alleles HLA-A*11:01, HLA-A*68:01 [13]. Enayatkhani M, et al in their predictive study included Nucleocapsid N, but they studied its interaction with the MHC I HLA-A*11:01 allele [11].…”

Section: Thementioning

confidence: 99%

“…The peptide vaccines are sufficient to stimulate cellular and humoral immunity without allergic responses [9]. They are" safe, simply produced, stable, reproducible, cost-effective" [10], and permits a broad spectrum of immunity [9], consequently, they are the targets for this study as well as they utilized in multiple studies concerning COVID-19 vaccine [11][12][13][14].…”

Section: Introductionmentioning

confidence: 99%

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A Multiple Peptides Vaccine against nCOVID-19 Designed from the Nucleocapsid phosphoprotein (N) and Spike Glycoprotein (S) via the Immunoinformatics Approach

Soa

Al-Nour

Elhag

et al. 2020

Preprint

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Due to the current COVID-19 pandemic, the rapid discovery of a safe and effective vaccine is an essential issue, consequently, this study aims to predict potential COVID-19 peptide-based vaccine utilizing the Nucleocapsid phosphoprotein (N) and Spike Glycoprotein (S) via the Immunoinformatics approach. To achieve this goal, several Immune Epitope Database (IEDB) tools, molecular docking, and safety prediction servers were used. According to the results, The Spike peptide peptides SQCVNLTTRTQLPPAYTNSFTRGVY is predicted to have the highest binding affinity to the B-Cells. The Spike peptide FTISVTTEI has the highest binding affinity to the MHC I HLA-B1503 allele. The Nucleocapsid peptides KTFPPTEPK and RWYFYYLGTGPEAGL have the highest binding affinity to the MHC I HLA-A0202 allele and the three MHC II alleles HLA-DPA1*01:03/DPB1*02:01, HLA-DQA1*01:02/DQB1-*06:02, HLA-DRB1, respectively. Furthermore, those peptides were predicted as non-toxic and non-allergen. Therefore, the combination of those peptides is predicted to stimulate better immunological responses with respectable safety.

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“…We have shared this resource as an online spreadsheet at the following link to encourage community-curated collaboration: https://tinyurl.com/y84n9ttq. From 18 epitopes comprising the nal construct, predicted as PPVPs with targets for HLA-I and II molecules, another ve have been identi ed as possible vaccine targets: P9, P7, P5, P18 (in SP) and P12 (in ORF7) [66][67][68][69][70][71] . Interestingly, there is experimental evidence to show that P9 conserved in SARS-CoV is a potential vaccine target 66 .…”

Section: Discussionmentioning

confidence: 99%

A Multi-Epitope Vaccine Against Sars-Cov-2 Directed Towards the Latin American Population: An Immunoinformatics Approach

Cuspoca

Díaz

Acosta

et al. 2020

Preprint

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The coronavirus pandemic is a major public health crisis affecting global health systems with dire socioeconomic consequences, especially in vulnerable regions such as Latin America. There is an urgent need for a vaccine to help control contagion, reduce mortality and alleviate social costs. In this study, we propose a rational multi-epitope vaccine against SARS-CoV-2. Using bioinformatics, we constructed a library of potential vaccine peptides to predict immunological complexes among antigenic, non-toxic and non-allergenic peptides extracted from the conserved regions of 92 proteomes. We included the most common HLA-I and II molecules in the Latin American population. We also used three-dimensional structures of SARS-CoV-2 proteins to identify potential regions for antibody production. The best HLA-I and II predictions (with increased coverage in common alleles and regions evoking B lymphocyte responses) were grouped into an optimised final construct that meets the necessary safety and physicochemical requirements for conducting experimental tests.

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Epitope based vaccine prediction for SARS-COV-2 by deploying immuno-informatics approach

Cited by 81 publications

References 36 publications

Immunoinformatic Analysis of SARS-CoV-2 Nucleocapsid Protein and Identification of COVID-19 Vaccine Targets

Immunoinformatic Analysis of SARS-CoV-2 Nucleocapsid Protein and Identification of COVID-19 Vaccine Targets

A Multiple Peptides Vaccine against nCOVID-19 Designed from the Nucleocapsid phosphoprotein (N) and Spike Glycoprotein (S) via the Immunoinformatics Approach

A Multi-Epitope Vaccine Against Sars-Cov-2 Directed Towards the Latin American Population: An Immunoinformatics Approach

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Epitope based vaccine prediction for SARS-COV-2 by deploying immuno-informatics approach

Cited by 81 publications

References 36 publications

Immunoinformatic Analysis of SARS-CoV-2 Nucleocapsid Protein and Identification of COVID-19 Vaccine Targets

Immunoinformatic Analysis of SARS-CoV-2 Nucleocapsid Protein and Identification of COVID-19 Vaccine Targets

A Multiple Peptides Vaccine against nCOVID-19 Designed from the Nucleocapsid phosphoprotein (N) and Spike Glycoprotein (S) via the Immunoinformatics Approach

A Multi-Epitope&nbsp;Vaccine Against Sars-Cov-2 Directed Towards the Latin American Population: An Immunoinformatics Approach

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A Multi-Epitope Vaccine Against Sars-Cov-2 Directed Towards the Latin American Population: An Immunoinformatics Approach