Epitope‐based peptide vaccine design and target site depiction against Ebola viruses: an immunoinformatics study

Khan, Mukhtar A.; Hossain, Mohammad Uzzal; Shah, Zaman; Morshed, Md. Niaz

doi:10.1111/sji.12302

Cited by 69 publications

(48 citation statements)

References 65 publications

(61 reference statements)

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“…As the selection of effective therapeutics targets are the crucial things for the vaccine and drug design (Hasan et al, 2015; Khan et al, 2015; Oany et al, 2015; Hossain et al, 2016a,b; Hossain and Oany, 2016d) as well as for the building of networking (protein-protein interaction; Hossain et al, 2016c), our subtractive strategy will have a great impact in therapeutics discovery against S. flexneri .…”

Section: Resultsmentioning

confidence: 99%

Finding Potential Therapeutic Targets against Shigella flexneri through Proteome Exploration

Hossain

Khan²,

Hashem³

et al. 2016

Front. Microbiol.

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Background: Shigella flexneri is a gram negative bacteria that causes the infectious disease “shigellosis.” S. flexneri is responsible for developing diarrhea, fever, and stomach cramps in human. Antibiotics are mostly given to patients infected with shigella. Resistance to antibiotics can hinder its treatment significantly. Upon identification of essential therapeutic targets, vaccine and drug could be effective therapy for the treatment of shigellosis.Methods: The study was designed for the identification and qualitative characterization for potential drug targets from S. flexneri by using the subtractive proteome analysis. A set of computational tools were used to identify essential proteins those are required for the survival of S. flexneri. Total proteome (13,503 proteins) of S. flexneri was retrieved from NCBI and further analyzed by subtractive channel analysis. After identification of the metabolic proteins we have also performed its qualitative characterization to pave the way for the identification of promising drug targets.Results: Subtractive analysis revealed that a list of 53 targets of S. flexneri were human non-homologous essential metabolic proteins that might be used for potential drug targets. We have also found that 11 drug targets are involved in unique pathway. Most of these proteins are cytoplasmic, can be used as broad spectrum drug targets, can interact with other proteins and show the druggable properties. The functionality and drug binding site analysis suggest a promising effective way to design the new drugs against S. flexneri.Conclusion: Among the 53 therapeutic targets identified through this study, 13 were found highly potential as drug targets based on their physicochemical properties whilst only one was found as vaccine target against S. flexneri. The outcome might also be used as module as well as circuit design in systems biology.

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Section: Resultsmentioning

confidence: 99%

Finding Potential Therapeutic Targets against Shigella flexneri through Proteome Exploration

Hossain

Khan²,

Hashem³

et al. 2016

Front. Microbiol.

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“…Although our initial aim was to design a specific epitope which would elicit immunity through both humoral and cell‐mediated immune responses, we found a cluster of B cell‐ and T cell‐specific epitopes as the best potential candidates for designing and developing vaccine. Recently, other studies have predicted epitopes from RNA‐dependent RNA polymerase of Ebola virus . However, in this study out of the class I restricted most probable epitopes predicted from different protein sequences, ‘LANETTQAL’ and ‘FLYDRLAST’ from glycoprotein were considered as the most potent considering their interaction with the highest number of different HLA alleles, conservancy, percentage of population coverage and docking analysis.…”

Section: Discussionmentioning

confidence: 97%

B and T Cell Epitope‐Based Peptides Predicted from Evolutionarily Conserved and Whole Protein Sequences of Ebola Virus as Vaccine Targets

Yasmin

Nabi

2016

Scand J Immunol

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Ebola virus (EBV) has become a serious threat to public health. Different approaches were applied to predict continuous and discontinuous B cell epitopes as well as T cell epitopes from the sequence-based and available three-dimensional structural analyses of each protein of EBV. Peptides '(79) VPSATKRWGFRSGVPP(94) ' from GP1 and '(515) LHYWTTQDEGAAIGLA(530) ' from GP2 of Ebola were found to be the consensus peptidic sequences predicted as linear B cell epitope of which the latter contains a region (519) TTQDEG(524) that fulfilled all the criteria of accessibility, hydrophilicity, flexibility and beta turn region for becoming an ideal B cell epitope. Different nonamers as T cell epitopes were obtained that interacted with different numbers of MHC class I and class II alleles with a binding affinity of <100 nm. Interestingly, these alleles also bound to the MHC class I alleles mostly prevalent in African and South Asian regions. Of these, 'LANETTQAL' and 'FLYDRLAST' nonamers were predicted to be the most potent T cell epitopes and they, respectively, interacted with eight and twelve class I alleles that covered 63.79% and 54.16% of world population, respectively. These nonamers were found to be the core sequences of 15mer peptides that interacted with the most common class II allele, HLA-DRB1*01:01. They were further validated for their binding to specific class I alleles using docking technique. Thus, these predicted epitopes may be used as vaccine targets against EBV and can be validated in model hosts to verify their efficacy as vaccine.

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“…The alternative approach to stimulate the immune response, such as humoral and cell-mediated immune response, is the identification of peptide sequences or epitopes that have a protective immune response. Therefore, these epitopes can have no risk of mutation and they would be more stable, and also, there can be fewer side effects [24,25]. This approach is called peptide-based vaccine designing.…”

Section: Candidate For Designing Peptide-based Vaccines Against Ebolamentioning

confidence: 99%

Predicting Candidate Epitopes on Ebola Virus for Possible Vaccine Development

Hemmati¹,

Raoufi²,

Fallahi³

2018

Advances in Ebola Control

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Zaire ebolavirus, a member of family Filoviridae is the cause of hemorrhagic fever. Due to lack of appropriate antiviral or vaccine, this disease is very lethal. In this study, we tried to find epitopes for superficial glycoprotein and nucleoprotein of Zaire ebolavirus (that have high antigenicity for MHC I, II and B cells) by using in silico methods and immunoinformatics approach. By using CTLPred, SYFPEITHI and ProPred web applications for MHC class I and SYFPEITHI and ProPred1 web applications for MHC class II, we had been able to find epitopes (peptides) that have the highest score. Also ElliPro, IgPred and DiscoTope web tools had been performed to predict B cells conformational epitopes. Linear epitope prediction for B cell was performed with six methods from IEDB. All of the results that including candidate epitopes for T cells and B cells were reported. It was expected that these peptides could be stimulated immune response and used for designing the multipeptide vaccine against ZEV but these results should be reliable with experimental analysis.

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Epitope‐based peptide vaccine design and target site depiction against Ebola viruses: an immunoinformatics study

Cited by 69 publications

References 65 publications

Finding Potential Therapeutic Targets against Shigella flexneri through Proteome Exploration

Finding Potential Therapeutic Targets against Shigella flexneri through Proteome Exploration

B and T Cell Epitope‐Based Peptides Predicted from Evolutionarily Conserved and Whole Protein Sequences of Ebola Virus as Vaccine Targets

Predicting Candidate Epitopes on Ebola Virus for Possible Vaccine Development

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