Development of an in silico multi-epitope vaccine against SARS-COV-2 by précised immune-informatics approaches

Zamane, Saad Al; Nobel, Fahim Alam; Jebin, Ruksana Akter; Amin, Mohammed Badrul; Somadder, Pratul Dipta; Antora, Nusrat Jahan; Hossain, I.; Islam, Mohammod Johirul; Ahmed, Kawsar; Moni, Mohammad Ali

doi:10.1016/j.imu.2021.100781

Cited by 20 publications

(9 citation statements)

References 131 publications

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“…16 n depicts EP population per state (cells per mm 3 ). Results obtained in our study are similar in pattern to the results obtained in the following works [ 101 , 108 , 109 ] in which a similar approach was adopted.…”

Section: Resultssupporting

confidence: 90%

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: Resultssupporting

confidence: 90%

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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“…From the picture, it was clear that memory cells existence is higher after both secondary and tertiary injections than in the first one. Al Zamane et al (2021) [ 79 ] stated that the next injection after the initial phase will activate B cells and T cells and they will create long-lasting protection and memory formation followed by antigen clearance during exposures. Furthermore, from the immune simulation result, innate and cytokine based immune regulation were also involved.…”

Section: Resultsmentioning

confidence: 99%

Immunoinformatics Study: Multi-Epitope Based Vaccine Design from SARS-CoV-2 Spike Glycoprotein

et al. 2023

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The coronavirus disease 2019 outbreak has become a huge challenge in the human sector for the past two years. The coronavirus is capable of mutating at a higher rate than other viruses. Thus, an approach for creating an effective vaccine is still needed to induce antibodies against multiple variants with lower side effects. Currently, there is a lack of research on designing a multiepitope of the COVID-19 spike protein for the Indonesian population with comprehensive immunoinformatic analysis. Therefore, this study aimed to design a multiepitope-based vaccine for the Indonesian population using an immunoinformatic approach. This study was conducted using the SARS-CoV-2 spike glycoprotein sequences from Indonesia that were retrieved from the GISAID database. Three SARS-CoV-2 sequences, with IDs of EIJK-61453, UGM0002, and B.1.1.7 were selected. The CD8+ cytotoxic T-cell lymphocyte (CTL) epitope, CD4+ helper T lymphocyte (HTL) epitope, B-cell epitope, and IFN-γ production were predicted. After modeling the vaccines, molecular docking, molecular dynamics, in silico immune simulations, and plasmid vector design were performed. The designed vaccine is antigenic, non-allergenic, non-toxic, capable of inducing IFN-γ with a population reach of 86.29% in Indonesia, and has good stability during molecular dynamics and immune simulation. Hence, this vaccine model is recommended to be investigated for further study.

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“…Still, the AT content in all genes was considerably lower as compared to wild-type sequences. Similarly in silico codon optimization approach has been utilized in various microorganisms such as Mycobacterium tuberculosis (Mani et al, 2010), Aeromonas hydrophila (Singh et al, 2010), influenza A virus (Mani et al, 2011), SARS-COV-2 (Al Zamane et al, 2021), Nipah virus (Gupta et al, 2022), etc.…”

Section: Discussionmentioning

confidence: 99%

In silico optimization of DNA codons in genes encoded by various strains of Ebola Virus

Mathuria,

Ahmed,

Mani

2023

Preprint

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Ebola hemorrhagic fever (HF) is a severe and often lethal disease that occurs in primates, including humans. It was first identified in 1976 during two outbreaks of fatal haemorrhagic fever in Central Africa. Due to its high fatality rate and lack of a widespread cure, Ebola HF poses a considerable challenge in treatment, making Ebola virus disease (EVD) one of the deadliest zoonotic diseases. The viral genome is ~19kb long, linear, non-segmented, and negative single-stranded (-SS) RNA. The genome of the Ebola virus (EBOV) comprises seven genes, namely NP, GP, L, and VP (VP30, VP24, VP40, VP35), which encode nucleoprotein, glycoprotein, RNA polymerase, and viral proteins. By optimizing the DNA sequence through codon adaptation, we observed significant enhancements in the codon adaptation index (CAI) and the GC content compared to the wild-type strain. These findings demonstrate that optimized genes hold the potential for improved expression in the host organism without the production of truncated proteins. Further, these optimized genes can facilitate proper protein folding and function. In conclusion, these results have implications for vaccine production, as higher codon optimization enhances the expression of the genes, making them appropriate amounts for vaccine development.

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Development of an in silico multi-epitope vaccine against SARS-COV-2 by précised immune-informatics approaches

Cited by 20 publications

References 131 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

Immunoinformatics Study: Multi-Epitope Based Vaccine Design from SARS-CoV-2 Spike Glycoprotein

In silico optimization of DNA codons in genes encoded by various strains of Ebola Virus

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