An in-depth in silico and immunoinformatics approach for designing a potential multi-epitope construct for the effective development of vaccine to combat against SARS-CoV-2 encompassing variants of concern and interest

Saba, Abdullah Al; Adiba, Maisha; Saha, Piyal; Hosen, Md. Ismail; Chakraborty, Sajib; Nabi, Ahm Nurun

doi:10.1016/j.compbiomed.2021.104703

Cited by 19 publications

(12 citation statements)

References 92 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…On the other hand, no response Th17 was found in the in silico assay, a common response that characterizes the severe COVID-19 profile ( Wu & Yang, 2020 ). Additionally, the multi-epitope had low binding energy and high stability of in silico structure interactions with TLR3 and TLR4 similar to other computational studies ( Kar et al, 2020 ; Rahman et al, 2020 ; Yang, Bogdan & Nazarian, 2021 ; Nemati et al, 2021 ; Saba et al, 2021 ). This interaction is important since TLR is an innate immune receptor that recognizes viral proteins and triggers infection resistance ( O’Neill, Golenbock & Bowie, 2013 ).…”

Section: Discussionsupporting

confidence: 84%

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

Ferreira

Martins

Souza

et al. 2021

PeerJ

View full text Add to dashboard Cite

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.

show abstract

Section: Discussionsupporting

confidence: 84%

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

Ferreira

Martins

Souza

et al. 2021

PeerJ

View full text Add to dashboard Cite

show abstract

“…The peptide-based vaccines or multiepitope vaccines have been shown to be the better choice for safe vaccination because they use short, nonallergenic peptide fragments to stimulate extremely targeted immunoprotective responses Li et al (2014) . Several previous in silico studies demonstrate the efficacy and effects of prototype multiepitope vaccines Yazdani et al, 2020 , Rakib et al, 2020 , AlSaba et al, 2021 , Silva et al, 2021 . Moreover, vaccine development in this manner has already gained momentum, with immunogenic potential demonstrated through in vivo experiments Lei et al, 2019 , Zhao et al, 2021 and clinical trials Elliott et al, 2008 , Lennerz et al, 2014 .…”

Section: Resultsmentioning

confidence: 94%

Exploiting reverse vaccinology approach for the design of a multiepitope subunit vaccine against the major SARS-CoV-2 variants

Campos

Silva

Barbosa

et al. 2022

Computational Biology and Chemistry

View full text Add to dashboard Cite

“…There have been several reports employing immunoinformatics to identify T-cell epitopes and formulate a vaccine for SARS-CoV-2 infection. PubMed search using keywords 'peptide-based vaccine', 'SARS-CoV-2', and 'immunoinformatics' conducted on 14 October 2021 resulted in 15 research articles [94][95][96][97][98][99][100][101][102][103][104][105][106][107][108]. In this study, we made a prediction based on the HLA alleles that are present with at least 5% frequency in the Indonesian population.…”

Section: Discussionmentioning

confidence: 99%

Immunoinformatics Analysis of SARS-CoV-2 ORF1ab Polyproteins to Identify Promiscuous and Highly Conserved T-Cell Epitopes to Formulate Vaccine for Indonesia and the World Population

et al. 2021

View full text Add to dashboard Cite

SARS-CoV-2 and its variants caused the COVID-19 pandemic. Vaccines that target conserved regions of SARS-CoV-2 and stimulate protective T-cell responses are important for reducing symptoms and limiting the infection. Seven cytotoxic (CTL) and five helper T-cells (HTL) epitopes from ORF1ab were identified using NetCTLpan and NetMHCIIpan algorithms, respectively. These epitopes were generated from ORF1ab regions that are evolutionary stable as reflected by zero Shannon’s entropy and are presented by 56 human leukocyte antigen (HLA) Class I and 22 HLA Class II, ensuring good coverage for the Indonesian and world population. Having fulfilled other criteria such as immunogenicity, IFNγ inducing ability, and non-homology to human and microbiome peptides, the epitopes were assembled into a vaccine construct (VC) together with β-defensin as adjuvant and appropriate linkers. The VC was shown to have good physicochemical characteristics and capability of inducing CTL as well as HTL responses, which stem from the engagement of the vaccine with toll-like receptor 4 (TLR4) as revealed by docking simulations. The most promiscuous peptide 899WSMATYYLF907 was shown via docking simulation to interact well with HLA-A*24:07, the most predominant allele in Indonesia. The data presented here will contribute to the in vitro study of T-cell epitope mapping and vaccine design in Indonesia.

show abstract

An in-depth in silico and immunoinformatics approach for designing a potential multi-epitope construct for the effective development of vaccine to combat against SARS-CoV-2 encompassing variants of concern and interest

Cited by 19 publications

References 92 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

Exploiting reverse vaccinology approach for the design of a multiepitope subunit vaccine against the major SARS-CoV-2 variants

Immunoinformatics Analysis of SARS-CoV-2 ORF1ab Polyproteins to Identify Promiscuous and Highly Conserved T-Cell Epitopes to Formulate Vaccine for Indonesia and the World Population

Contact Info

Product

Resources

About