Epitope-based vaccine design: a comprehensive overview of bioinformatics approaches

Parvizpour, Sepideh; Pourseif, Mohammad M.; Razmara, Jafar; Rafi, Mohammad; Omidi, Yadollah

doi:10.1016/j.drudis.2020.03.006

Cited by 136 publications

(83 citation statements)

References 55 publications

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“…Recently, there is increasing interest in the development of vaccines which use only minimal components from pathogens. Such vaccines are based on recombinant proteins or even minimal fragments carrying immunological information from this protein, called peptide epitopes [24,30]. Epitopes or antigenic determinants are the minimal immunogenic part of any particular antigen, which are capable of inducing speci c immune responses [24].…”

Section: Discussionmentioning

confidence: 99%

“…The nanotechnology-based approach is considered to be one of the most advantageous methods for the development of peptide-based vaccine [24]. Poly (lactic-co-glycolic) acid (PLGA) is a synthetic copolymer that has been approved by United States Food and Drug Administration (FDA) and European Medicine Agency (EMA) for various medical and pharmaceutical applications in humans [25].…”

Section: Introductionmentioning

confidence: 99%

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A Multi-epitope Peptide rOmp22 Encapsulated in Chitosan-PLGA Nanoparticles as Vaccine Candidate Against Acinetobacter baumannii Infection

Du¹,

Xue²,

Jiang³

et al. 2020

Preprint

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Background: Development of vaccine is a promising and cost-effective strategy to prevent emerging multi-drug resistant (MDR) Acinetobacter baumannii infections. The purpose of this study was to prepare a multi-epitope peptide nanovaccine and evaluate its immunogenicity and protective effect in BALB/c mice.Results: The B-cell and T-cell epitopes of Omp22 from A. baumannii were predicted using bioinformatics method and identified by immunological experiments. Three dominant B-cell epitopes and two T-cell epitopes were linked in series and chemically synthesized to generate multi-epitope peptide rOmp22. Then, rOmp22 was encapsulated by chitosan (CS) and polylactic acid glycolic acid (PLGA) to prepare CS-PLGA-rOmp22 nanoparticles (NPs). CS-PLGA-rOmp22 NPs were small (mean size of 272.83 nm) with apparently spherical structural, positively charged (4.39 mV) and exhibited nontoxicity to A549 cells. We achieved a high encapsulation efficiency (54.94%) and a continuous slow release pattern. Compared with non-encapsulated rOmp22, CS-PLGA-rOmp22 induced more rOmp22-specific IgG in serum and IFN-γ in splenocyte supernatant. Vaccination with CS-PLGA-rOmp22 decreased lung injury, suppressed bacterial burdens in the lung and blood, provided potent protection (57.14%-83.3%) against acute lethal intratracheal A. baumannii challenge in BALB/c mice.Conclusions: CS-PLGA-rOmp22 NPs could elicit specific IgG antibody, Th1 cellular immunity and protection against acute lethal intratracheal A. baumannii challenge. Our results indicate this nanovaccine is a disirable candidate to prevent A. baumannii infection.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

A Multi-epitope Peptide rOmp22 Encapsulated in Chitosan-PLGA Nanoparticles as Vaccine Candidate Against Acinetobacter baumannii Infection

Du¹,

Xue²,

Jiang³

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…In order to select best immunodominant epitopes, antigenicity (>=1) and immunogenicity (>=0.1), both criteria were used (Table-2 When MHC class I molecules binds to epitopes, immune system recognizes these epitopes as a foreign peptide, and the infected cell presents itself as an antigen-presenting cell for self-destruction. For better sensitivity, CD8 + T-cell epitopes should be generated from both structural and non-structural proteins because both types of proteins will be processed by infected cells in the cytoplasm, whereas structural proteins are of interest for CD4 + T-cell epitopes, as it might provide help to cognate interaction [53][54][55].…”

Section: Information Of Expressed Regions Of Viral Genome Is Very Impmentioning

confidence: 99%

SARS-CoV-2 transcriptome analysis and molecular cataloguing of immunodominant epitopes for multi-epitope based vaccine design

Kushwaha

Kesarwani

Choudhury

et al. 2020

Preprint

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SARS-CoV-2 is a single-stranded RNA virus that has caused more than 0.29 million deaths worldwide as of May 2020, and influence of COVID-19 pandemic is increasing continuously in the absence of approved vaccine and drug. Moreover, very limited information is available about SARS-CoV-2 expressed regions and immune responses. In this paper an effort has been made, to facilitate vaccine development by proposing multiple epitopes as potential vaccine candidates by utilising SARS-CoV-2 transcriptome data. Here, publicly available RNA-seq data of SARS-CoV-2 infection in NHBE and A549 human cell lines were used to construct SARS-CoV-2 transcriptome to understand disease pathogenesis and immune responses. In the first step, epitope prediction, MHC class I and II gene identification for epitopes, population coverage, antigenicity, immunogenicity, conservation and crossreactivity analysis with host antigens were performed by using SARS-CoV-2 transcriptome, and in the second step, structural compatibility of identified T-and B-cell epitopes were evaluated with MHC molecules and B-cell receptors through molecular docking studies. Quantification of MHC gene expression was also performed that indicated high variation in allele types and expression level of MHC genes with respect to cell lines. In A549 cell line, HLA-ANHBE cell lines. Prevalence of HLA-A*24 alleles was suggested as risk factors for H1N1 infection, and associated with type-1 diabetes. HLA-C*03:03, linked with male infertility factors was also highly expressed in SARS-CoV-2 infected NHBE cell lines. Finally, three potential T-cell and five B-cell epitopes were selected for molecular docking studies with twenty-two MHC molecules and two B-cell receptors respectively. The results of in silico analysis indicated that proposed epitopes have high potential to recognize immune response of SARS-CoV-2 infection. This study will facilitate in vitro and in vivo vaccine related research studies.

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“…Recent progress in the next-generation sequencing (NGS) technology and the relevant computational approaches have offered vaccinologists to take a holistic and deep analysis of the whole genomes, and proteomes of the EREI pathogens like SARS-CoV-2 9,10 . The vaccine design and delivery strategies can be optimized based on a "vaccine on-demand" approach.…”

Section: Introductionmentioning

confidence: 99%

Prophylactic domain-based vaccine against SARS-CoV-2, causative agent of COVID-19 pandemic

Pourseif

Parvizpour

Jafari

et al. 2020

Preprint

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Coronavirus disease 2019 (COVID-19) is undoubtedly the most challenging pandemic in the current century with more than 253,381 deaths worldwide since its emergence in late 2019 (updated May 6th, 2020). COVID-19 is caused by a novel emerged coronavirus named as Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Today, the world needs crucially to develop a prophylactic vaccine scheme for such emerged and emerging infectious pathogens. In this study, we have targeted spike (S) glycoprotein, as an important surface antigen of SARS-CoV-2, to identify its immunodominant B- and T-cell epitopes. We have conducted a multi-method B-cell epitope (BCE) prediction approach using different predictor algorithms to discover most potential BCEs. Besides, we sought among a pool of MHC class I and II-associated peptide binders provided by the IEDB server through the strict cut-off values. To design a broad-coverage vaccine, we carried out a population coverage analysis for a set of candidate T-cell epitopes and based on the HLA allele frequency in the top most-affected countries by COVID-19 (update 02 April 2020). The final determined B- and T-cell epitopes were mapped on the S glycoprotein sequence, and three potential hub regions covering the largest number of overlapping epitopes were identified for the vaccine designing (I531–N711; T717–C877; and V883–E973). Here, we have designed two domain-based constructs to be produced and delivered through the recombinant protein- and gene-based approaches, including (i) an adjuvanted domain-based protein vaccine construct (DPVC), and (ii) a self-amplifying mRNA vaccine (SAMV) construct. The safety, stability, and immunogenicity of the DPVC were validated using the integrated sequential (i.e. allergenicity, autoimmunity, and physicochemical features) and structural (i.e. molecular docking between the vaccine and human Toll-like receptors (TLRs) 4 and 5) analysis. The stability of the docked complexes was evaluated using the molecular dynamics (MD) simulations. These rigorous in silico validations supported the potential of the DPVC and SAMV to promote both innate and specific immune responses in the animal studies.

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Epitope-based vaccine design: a comprehensive overview of bioinformatics approaches

Cited by 136 publications

References 55 publications

A Multi-epitope Peptide rOmp22 Encapsulated in Chitosan-PLGA Nanoparticles as Vaccine Candidate Against Acinetobacter baumannii Infection

A Multi-epitope Peptide rOmp22 Encapsulated in Chitosan-PLGA Nanoparticles as Vaccine Candidate Against Acinetobacter baumannii Infection

SARS-CoV-2 transcriptome analysis and molecular cataloguing of immunodominant epitopes for multi-epitope based vaccine design

Prophylactic domain-based vaccine against SARS-CoV-2, causative agent of COVID-19 pandemic

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