Immunoinformatics Approach for the Identification and Characterization of T Cell and B Cell Epitopes towards the Peptide-Based Vaccine against SARS-CoV-2

Chakraborty, Chiranjib; Sharma, Ashish Ranjan; Bhattacharya, Manojit; Sharma, Garima; Lee, Sang-Soo

doi:10.1016/j.arcmed.2021.01.004

Cited by 30 publications

(20 citation statements)

References 85 publications

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“…The research conducted by Sarkar and colleagues [ 98 ], also engaged in designing epitope-based vaccines against SARS-CoV-2. Chakraborty and colleagues [ 99 ], adopted immunoinformatic approach to develop peptide-based vaccines against SARS-CoV-2. Fathollahi and colleagues also engaged in immunoinformatics approaches for vaccine design [ 100 ].…”

Section: Resultsmentioning

confidence: 99%

Computational construction of a glycoprotein multi-epitope subunit vaccine candidate for old and new South-African SARS-CoV-2 virus strains

Oluwagbemi

Oladipo

Dairo

et al. 2022

Informatics in Medicine Unlocked

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The discovery of a new SARS-CoV-2 virus strain in South Africa presents a major public health threat, therefore contributing to increased infections and transmission rates during the second wave of the global pandemic. This study lays the groundwork for the development of a novel subunit vaccine candidate from the circulating strains of South African SARS-CoV-2 and provides an understanding of the molecular epidemiological trend of the circulating strains. A total of 475 whole-genome nucleotide sequences from South Africa submitted between December 1, 2020 and February 15, 2021 available at the GISAID database were retrieved based on its size, coverage level and hosts. To obtain the distribution of the clades and lineages of South African SARS-CoV-2 circulating strains, the metadata of the sequence retrieved were subjected to an epidemiological analysis. There was a prediction of the cytotoxic T lymphocytes (CTL), Helper T cells (HTL) and B-cell epitopes. Furthermore, there was allergenicity, antigenicity and toxicity predictions on the epitopes. The analysis of the physicochemical properties of the vaccine construct was performed; the secondary structure, tertiary structure and B-cell 3D conformational structure of the vaccine construct were predicted. Also, molecular binding simulations and dynamics simulations were adopted in the prediction of the vaccine construct's stability and binding affinity with TLRs. Result obtained from the metadata analysis indicated lineage B.1.351 to be in higher circulation among various circulating strains of SARS-CoV-2 in South Africa and GH has the highest number of circulating clades. The construct of the novel vaccine was antigenic, non-allergenic and non-toxic. The Instability index (II) score and aliphatic index were estimated as 41.74 and 78.72 respectively. The computed half-life in mammalian reticulocytes was 4.4 h in vitro, for yeast and in E. coli was >20 h and >10 h in vivo respectively. The grand average of hydropathicity (GRAVY) score is estimated to be −0.129, signifying the hydrophilic nature of the protein. The molecular docking indicates that the vaccine construct has a high binding affinity towards the TLRs with TLR 3 having the highest binding energy (−1203.2 kcal/mol) and TLR 9 with the lowest (−1559.5 kcal/mol). These results show that the vaccine construct is promising and should be evaluated using animal model.

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Section: Resultsmentioning

confidence: 99%

Computational construction of a glycoprotein multi-epitope subunit vaccine candidate for old and new South-African SARS-CoV-2 virus strains

Oluwagbemi

Oladipo

Dairo

et al. 2022

Informatics in Medicine Unlocked

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“…This strategy recruits online databases and software to map the immunogenic epitope fragments within the target sequence [ 28 – 30 ]. This method is easy, reliable, cost effective, and widely accepted [ 31 , 32 ]. These epitopes are the building blocks of candidate vaccines.…”

Section: Introductionmentioning

confidence: 99%

Bioengineering of Novel Non-Replicating mRNA (NRM) and Self-Amplifying mRNA (SAM) Vaccine Candidates Against SARS-CoV-2 Using Immunoinformatics Approach

et al. 2022

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Presently, the world needs safe and effective vaccines to overcome the COVID-19 pandemic. Our work has focused on formulating two types of mRNA vaccines that differ in capacity to copy themselves inside the cell. These are non-amplifying mRNA (NRM) and self-amplifying mRNA (SAM) vaccines. Both the vaccine candidates encode an engineered viral replicon which can provoke an immune response. Hence we predicted and screened twelve epitopes from the spike glycoprotein of SARS-CoV-2. We used five CTL, four HTL, and three B-cell-activating epitopes to formulate each mRNA vaccine. Molecular docking revealed that these epitopes could combine with HLA molecules that are important for boosting immunogenicity. The B-cell epitopes were adjoined with GPGPG linkers, while CTL and HTL epitopes were linked with KK linkers. The entire protein chain was reverse translated to develop a specific NRM-based vaccine. We incorporate gene encoding replicase in the upstream region of CDS encoding antigen to design the SAM vaccine. Subsequently, signal sequences were added to human mRNA to formulate vaccines. Both vaccine formulations translated to produce the epitopes in host cells, initiate a protective immune cascade, and generate immunogenic memory, which can counter future SARS-CoV-2 viral exposures before the onset of infection. Supplementary Information The online version contains supplementary material available at 10.1007/s12033-021-00432-6.

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“…This has given rise to a new keyword, called immunoinformatics. 3 Immunoinformatics as a new-emerging field uses computational tools that cover multi dimensions of bioinformatics such as databases management and development definition of both structural and functional signatures and the modeling of predictive algorithms. Immunoinformatics give us a better perception of the immune system of both man and animals to the effective fight against some less predictable pathogenesis.…”

Section: Introductionmentioning

confidence: 99%

Immunoinformatics: A Basic Bibliometric Analysis

Rahimpour

Samad‐Soltani

2021

ImmunoAnalysis

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Background: Traditionally, immunologists have been using experimental methods for a long time, which have generated functional, clinical and epidemiological data. So, it is inevitable to develop and apply novel computational approaches to collect, store, analyze, and report the latent knowledge behind these data. Immunoinformatics as a new-emerging field uses computational tools that cover multi dimensions of bioinformatics such as databases management and development definition of both structural and functional signatures and the modeling of predictive algorithms. Recently, with the dramatic growth in research documents publishing, the need for new methodologies to structure and visualize knowledge emerged. Methods: Capability to analyze huge amounts of published items with a detailed level of granularity and report statistical, mathematical and visual knowledge within it, introduced an approach called bibliometrics analysis. According to the best of our knowledge, there isn’t any bibliometrics analysis based on immunoinformatics keyword. So, the aim of current study was to perform a brief and basic bibliometrics analysis on the immunoinformatics publications to report the most influencers on this field by statistical and mathematical methods to identify key authors, titles, keywords and other parameters that extracted from publication’s metadata. Results: Results were summarized in statistical tables and diagrams. It was revealed that the immunoinformatics is a relatively novel field and the time trends showed that the strategic research plans can be directed to expand this field. Conclusion: We can conclude that the future is the age of immunoinformatics for immunologists and related specialties.

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Immunoinformatics Approach for the Identification and Characterization of T Cell and B Cell Epitopes towards the Peptide-Based Vaccine against SARS-CoV-2

Cited by 30 publications

References 85 publications

Computational construction of a glycoprotein multi-epitope subunit vaccine candidate for old and new South-African SARS-CoV-2 virus strains

Computational construction of a glycoprotein multi-epitope subunit vaccine candidate for old and new South-African SARS-CoV-2 virus strains

Bioengineering of Novel Non-Replicating mRNA (NRM) and Self-Amplifying mRNA (SAM) Vaccine Candidates Against SARS-CoV-2 Using Immunoinformatics Approach

Immunoinformatics: A Basic Bibliometric Analysis

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