<i>In silico</i> designing of multi-epitope vaccine construct against human coronavirus infections

Devi, Arpita; Chaitanya, Nyshadham S.N.

doi:10.1080/07391102.2020.1804460

Cited by 28 publications

(11 citation statements)

References 57 publications

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“…Immune simulation with DV-1 was predicted to trigger IgG, IgM, B-cell, T-cell and cytokines. Similar to the results of previous immunoinformatics vaccine designed studies 87 – 89 , the designed vaccines may offer protection against DENV.…”

Section: Discussionsupporting

confidence: 70%

Immunoinformatics design of a novel epitope-based vaccine candidate against dengue virus

Fadaka

Sibuyi

Martin

et al. 2021

Sci Rep

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Dengue poses a global health threat, which will persist without therapeutic intervention. Immunity induced by exposure to one serotype does not confer long-term protection against secondary infection with other serotypes and is potentially capable of enhancing this infection. Although vaccination is believed to induce durable and protective responses against all the dengue virus (DENV) serotypes in order to reduce the burden posed by this virus, the development of a safe and efficacious vaccine remains a challenge. Immunoinformatics and computational vaccinology have been utilized in studies of infectious diseases to provide insight into the host–pathogen interactions thus justifying their use in vaccine development. Since vaccination is the best bet to reduce the burden posed by DENV, this study is aimed at developing a multi-epitope based vaccines for dengue control. Combined approaches of reverse vaccinology and immunoinformatics were utilized to design multi-epitope based vaccine from the sequence of DENV. Specifically, BCPreds and IEDB servers were used to predict the B-cell and T-cell epitopes, respectively. Molecular docking was carried out using Schrödinger, PATCHDOCK and FIREDOCK. Codon optimization and in silico cloning were done using JCAT and SnapGene respectively. Finally, the efficiency and stability of the designed vaccines were assessed by an in silico immune simulation and molecular dynamic simulation, respectively. The predicted epitopes were prioritized using in-house criteria. Four candidate vaccines (DV-1–4) were designed using suitable adjuvant and linkers in addition to the shortlisted epitopes. The binding interactions of these vaccines against the receptors TLR-2, TLR-4, MHC-1 and MHC-2 show that these candidate vaccines perfectly fit into the binding domains of the receptors. In addition, DV-1 has a better binding energies of − 60.07, − 63.40, − 69.89 kcal/mol against MHC-1, TLR-2, and TLR-4, with respect to the other vaccines. All the designed vaccines were highly antigenic, soluble, non-allergenic, non-toxic, flexible, and topologically assessable. The immune simulation analysis showed that DV-1 may elicit specific immune response against dengue virus. Moreover, codon optimization and in silico cloning validated the expressions of all the designed vaccines in E. coli. Finally, the molecular dynamic study shows that DV-1 is stable with minimum RMSF against TLR4. Immunoinformatics tools are now applied to screen genomes of interest for possible vaccine target. The designed vaccine candidates may be further experimentally investigated as potential vaccines capable of providing definitive preventive measure against dengue virus infection.

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Section: Discussionsupporting

confidence: 70%

Immunoinformatics design of a novel epitope-based vaccine candidate against dengue virus

Fadaka

Sibuyi

Martin

et al. 2021

Sci Rep

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“…The whole genome sequence of the SARS-CoV2 is made available in the public domain by next generation sequencing. This enabled the design of several multi-epitope in silico vaccine candidates targeting different structural and nonstructural proteins of the SARS-CoV2 (Bhatnager et al, 2020;Bhattacharya et al, 2020;Devi & Chaitanya, 2020;Dong et al, 2020;Enayatkhani et al, 2020;Kar et al, 2020;Lizbeth et al, 2020;Peele et al, 2020;Samad et al, 2020). In the present study, we aimed to design a novel multi-epitope vaccine targeting membrane glycoprotein by immunoinformatics approach.…”

Section: Introductionmentioning

confidence: 99%

Design of a multi-epitope-based vaccine targeting M-protein of SARS-CoV2: an immunoinformatics approach

Ayyagari

Venkateswarulu

et al. 2020

Journal of Biomolecular Structure and Dynamics

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In the present study, one of the targets present on the envelopes of coronaviruses, membrane glycoprotein (M) was chosen for the design of a multi-epitope vaccine by Immunoinformatics approach. The B-cell and T-cell epitopes used for the construction of vaccine were antigenic, nonallergic and nontoxic. An adjuvant, b-defensin and PADRE sequence were included at the N-terminal end of the vaccine. All the epitopes were joined by linkers for decreasing the junctional immunogenicity. Various physicochemical parameters of the vaccine were evaluated. Secondary and tertiary structures were predicted for the vaccine construct. The tertiary structure was further refined, and various parameters related to the refinement of the protein structure were validated by using different tools. Humoral immunity induced by B-cells relies upon the identification of antigenic determinants on the surface of the vaccine construct. In this regard, the vaccine construct was found to consist of several B-cell epitopes in its three-dimensional conformation. Molecular docking of the vaccine was carried out with TLR-3 receptor to study their binding and its strength. Further, protein-protein interactions in the docked complex were visualized using LigPlotþ. Population coverage analysis had shown that the multi-epitope vaccine covers 94.06% of the global population. The vaccine construct was successfully cloned in silico into pET-28a (þ). Immune simulation studies showed the induction of primary, secondary and tertiary immune responses marked by the increased levels of antibodies, INF-c, IL-2, TGF-b, B-cells, CD4þ and CD8þ cells. Finally, the vaccine construct was able to elicit immune response as desired.

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“…Recent vaccine strategies include the delivery of targeted and prolonged peptide antigens to antigen presenting cells (APCs) such as subunit vaccines (Hos et al 2018;Devi and Chaitanya 2020;Yang et al 2021). These APCs present the antigens through MHC and cluster of differentiation (CD) receptors to T and B lymphocytes that secrete lymphokines and antibodies respectively.…”

Section: Discussionmentioning

confidence: 99%

In Silico Analysis of Potential Outer Membrane Beta-Barrel Proteins in Aeromonas hydrophila Pangenome

Awan

Ali

Dong

et al. 2021

Int J Pept Res Ther

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Outer membrane proteins (OMPs) of Aeromonas hydrophila have a variety of functional roles in virulence and pathogenesis and represent promising targets for vaccine development. The main objective of this study was to develop an in-silico model of beta-barrel OMP present among the valid A. hydrophila pangenomes (n = 22). With a program named the β-barrel Outer Membrane Protein Predictor (BOMP), total beta-barrel OMPs (n = 3127) were predicted across 22 genomes with the estimated median number of 64 per genome. In pangenome analysis, only 32 OMPs were found to be conserved. These beta-barrel OMPs also showed variations among source of isolation, COG and KEGG classes. Among 32 conserved OMPs, a highly antigenic protein was identified by utilizing Vaxijen. With B cell epitope predictions, two fragments of amino acid sequences i.e. GLTLGAQFTGNNDPQNADRSN (21 mer) and FKPSLAYLRTDVKDNARGI DDTATEY (26 mer) bearing B-cell binding sites were selected. Further, an epitope (12 amino acids: GLTLGAQFTGNN) that complexes to maximum MHC alleles with a higher antigenicity was determined. The analysis of evolutionary forces on the identified OMP sequence and epitope indicated that none of basic amino acid sites has shown significantly different substitution ratios. This conserved protein and epitope will be helpful in developing a vaccine that may be effective against all the A. hydrophila strains. Also, this study provides a theoretical basis for vaccine design against other pathogenic bacteria.

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In silico designing of multi-epitope vaccine construct against human coronavirus infections

Cited by 28 publications

References 57 publications

Immunoinformatics design of a novel epitope-based vaccine candidate against dengue virus

Immunoinformatics design of a novel epitope-based vaccine candidate against dengue virus

Design of a multi-epitope-based vaccine targeting M-protein of SARS-CoV2: an immunoinformatics approach

In Silico Analysis of Potential Outer Membrane Beta-Barrel Proteins in Aeromonas hydrophila Pangenome

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