Multi Epitope Vaccine Prediction Against Aichi Virus using Immunoinformatic Approach

AbstractAichi virus, AiV is single stranded negative sense RNA genome belonging to the genus Kobuviru, a family of Picornaviridae that causes severe gastroenteritis. There is no treatment or vaccine for it, thus the aim of this study is to design a peptide vaccine using immunoinformatic approaches to analyze the viral Protein VP1 of AiV-1 strain, to determine the conserved region which is further studied to predict all possible epitopes that can be used as a peptide vaccine. A total of 38 Aichi virus VP1 retrieved from NCBI database were aligned to determine the conservancy and to predict the epitopes using IEDB analysis resource. Three epitopes predicted as a peptide vaccine for B cell was (PLPPDT, PPLPTP, and LPPLPTP). For T cell, two epitopes showed high affinity to MHC class I (FSIPYTSPL and TMVSFSIPY) and high coverage against the whole world population. Also, in MHC class II, three epitopes that interact with most frequent MHC class II alleles (FTYIAADLR and YMAEVPVSA) with high coverage in the whole world population. For both MHCI and MHCII the T-cell peptide with the strongest affinity to the worldwide population was FSIPYTSPL.Peptide vaccine against AiV is powerfully displace the normal produced vaccines based on the experimental biochemistry tools, as it designed to handle with a wide range of mutated strains, which will effectively minimize the frequent outbreaks and their massive economical wastage consequences.

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Epitope-Based Peptide Vaccine against Bombali Ebolavirus Viral Protein 40: An Immunoinformatics Combined with Molecular Docking Studies

10.1101/2020.12.28.424637 ◽

2020 ◽

Author(s):

Mujahed I. Mustafa ◽

Shaza W. Shantier ◽

Miyssa I. Abdelmageed ◽

Abdelrafie M. Makhawi

Keyword(s):

Molecular Docking ◽

T Cell ◽

Mhc Class Ii ◽

Peptide Vaccine ◽

Class Ii ◽

Population Coverage ◽

Antigenic Protein ◽

Wide Range ◽

The World ◽

Hla Molecules

AbstractBackgroundBombali Ebolavirus is RNA viruses belong to the Filoviridae family. They are causing lethal hemorrhagic fever with high mortality rate. Despite having available molecular knowledge of this virus, no approved vaccine or antiviral drugs have been developed yet for the eradication of Bombali Ebolavirus infections in humans.Objectivethe present study described a multi epitope-based peptide vaccine against Bombali Ebolavirus matrix protein VP40, using several immunoinformatics tools.Materials and MethodsThe six strains of Ebolavirus were retrieved from NCBI and Uniprot databases and submitted to VaxiJen to identify the most antigenic protein among all. Then PSIPRED, SOPMA, QMEAN, and PROCHECK tools were used to check the protein quality. T-cell prediction, population coverage, and molecular docking analysis were achieved to select peptides containing multiple Bombali VP40 epitopes showing interaction with multiple HLA molecules for expected immune response across the world.ResultBombali Ebola (YP_009513276.1) was found to be the most antigenic protein among all. Which it has been used in all required analysis. For T cell three epitopes showed high affinity to MHC class I (YSFDSTTAA, VQLPQYFTF, and MVNVISGPK) and high population coverage against Africa and the world. Furthermore in MHC class II, six promising epitopes that associated with most common MHC class II alleles.ConclusionThe above result conclude that, these peptides capable of provoking T-cell response and being interacted with a wide range of HLA molecules have a strong potential to be a vaccine against Bombali Ebolavirus.

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Design of multi epitope-based peptide vaccine against E protein of human COVID-19: An immunoinformatics approach

10.1101/2020.02.04.934232 ◽

2020 ◽

Cited By ~ 20

Author(s):

Miyssa I. Abdelmageed ◽

Abdelrahman H. Abdelmoneim ◽

Mujahed I. Mustafa ◽

Nafisa M. Elfadol ◽

Naseem S. Murshed ◽

...

Keyword(s):

T Cell ◽

Mhc Class Ii ◽

Envelope Protein ◽

Peptide Vaccine ◽

World Health ◽

Comparative Genomic ◽

World Population ◽

T Cell Epitopes ◽

Novel Coronavirus ◽

Health Organization

AbstractBackgroundNew endemic disease has been spread across Wuhan City, China on December 2019. Within few weeks, the World Health Organization (WHO) announced a novel coronavirus designated as coronavirus disease 2019 (COVID-19). In late January 2020, WHO declared the outbreak of a “public-health emergency of international concern” due to the rapid and increasing spread of the disease worldwide. Currently, there is no vaccine or approved treatment for this emerging infection; thus the objective of this study is to design a multi epitope peptide vaccine against COVID-19 using immunoinformatics approach.MethodSeveral techniques facilitating the combination of immunoinformatics approach and comparative genomic approach were used in order to determine the potential peptides for designing the T cell epitopes-based peptide vaccine using the envelope protein of 2019-nCoV as a target.ResultsExtensive mutations, insertion and deletion were discovered with comparative sequencing in COVID-19 strain. Additionally, ten peptides binding to MHC class I and MHC class II were found to be promising candidates for vaccine design with adequate world population coverage of 88.5% and 99.99%, respectively.ConclusionT cell epitopes-based peptide vaccine was designed for COVID-19 using envelope protein as an immunogenic target. Nevertheless, the proposed vaccine is rapidly needed to be validated clinically in order to ensure its safety, immunogenic profile and to help on stopping this epidemic before it leads to devastating global outbreaks.

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Design of a Multiepitope-Based Peptide Vaccine against the E Protein of Human COVID-19: An Immunoinformatics Approach

BioMed Research International ◽

10.1155/2020/2683286 ◽

2020 ◽

Vol 2020 ◽

pp. 1-12 ◽

Cited By ~ 30

Author(s):

Miyssa I. Abdelmageed ◽

Abdelrahman H. Abdelmoneim ◽

Mujahed I. Mustafa ◽

Nafisa M. Elfadol ◽

Naseem S. Murshed ◽

...

Keyword(s):

T Cell ◽

Mhc Class Ii ◽

Envelope Protein ◽

Peptide Vaccine ◽

Cell Epitope ◽

World Health ◽

Comparative Genomic ◽

World Population ◽

T Cell Epitope ◽

Novel Coronavirus

Background. A new endemic disease has spread across Wuhan City, China, in December 2019. Within few weeks, the World Health Organization (WHO) announced a novel coronavirus designated as coronavirus disease 2019 (COVID-19). In late January 2020, WHO declared the outbreak of a “public-health emergency of international concern” due to the rapid and increasing spread of the disease worldwide. Currently, there is no vaccine or approved treatment for this emerging infection; thus, the objective of this study is to design a multiepitope peptide vaccine against COVID-19 using an immunoinformatics approach. Method. Several techniques facilitating the combination of the immunoinformatics approach and comparative genomic approach were used in order to determine the potential peptides for designing the T-cell epitope-based peptide vaccine using the envelope protein of 2019-nCoV as a target. Results. Extensive mutations, insertion, and deletion were discovered with comparative sequencing in the COVID-19 strain. Additionally, ten peptides binding to MHC class I and MHC class II were found to be promising candidates for vaccine design with adequate world population coverage of 88.5% and 99.99%, respectively. Conclusion. The T-cell epitope-based peptide vaccine was designed for COVID-19 using the envelope protein as an immunogenic target. Nevertheless, the proposed vaccine rapidly needs to be validated clinically in order to ensure its safety and immunogenic profile to help stop this epidemic before it leads to devastating global outbreaks.

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Faculty Opinions recommendation of T-cell engagement of dendritic cells rapidly rearranges MHC class II transport.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1009215.122659 ◽

2002 ◽

Author(s):

Peter Jensen

Keyword(s):

Dendritic Cells ◽

T Cell ◽

Mhc Class Ii ◽

Class Ii

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Faculty Opinions recommendation of T cell receptor-independent CD4 signalling: CD4-MHC class II interactions regulate intracellular calcium and cyclic AMP.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1013876.192002 ◽

2003 ◽

Author(s):

Richard Williams

Keyword(s):

T Cell ◽

Cyclic Amp ◽

Intracellular Calcium ◽

T Cell Receptor ◽

Mhc Class Ii ◽

Cell Receptor ◽

Class Ii

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Faculty Opinions recommendation of Peptide-MHC class II dimers as therapeutics to modulate antigen-specific T cell responses in autoimmune diabetes.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1016402.200705 ◽

2003 ◽

Author(s):

Matthias von Herrath

Keyword(s):

T Cell ◽

Mhc Class Ii ◽

Autoimmune Diabetes ◽

T Cell Responses ◽

Class Ii ◽

Cell Responses

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Faculty Opinions recommendation of Cutting edge: Conditional MHC class II expression reveals a limited role for B cell antigen presentation in primary and secondary CD4 T cell responses.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.718020496.793480946 ◽

2013 ◽

Author(s):

Tim Manser

Keyword(s):

T Cell ◽

B Cell ◽

Antigen Presentation ◽

Mhc Class Ii ◽

T Cell Responses ◽

Class Ii ◽

Cutting Edge ◽

Cd4 T Cell ◽

Cell Antigen ◽

Cell Responses

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Decreased expression of MHC class II and cathepsin E in dendritic cells might contribute to impaired induction of antigen-specific T cell response in NC/Nga mice

The Journal of Medical Investigation ◽

10.2152/jmi.59.95 ◽

2012 ◽

Vol 59 (1,2) ◽

pp. 95-101 ◽

Cited By ~ 1

Author(s):

Tohru Sakai ◽

Emi Shuto ◽

Tomoyo Taki ◽

Honami Imamura ◽

Miku Kioka ◽

...

Keyword(s):

Dendritic Cells ◽

T Cell ◽

Mhc Class Ii ◽

Cell Response ◽

Class Ii ◽

T Cell Response ◽

Cathepsin E

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T-cell Epitope-based Vaccine Design for Nipah Virus by Reverse Vaccinology Approach

Combinatorial Chemistry & High Throughput Screening ◽

10.2174/1386207323666200427114343 ◽

2020 ◽

Vol 23 (8) ◽

pp. 788-796

Author(s):

Praveen K.P. Krishnamoorthy ◽

Sekar Subasree ◽

Udhayachandran Arthi ◽

Mohammad Mobashir ◽

Chirag Gowda ◽

...

Keyword(s):

T Cell ◽

Mhc Class Ii ◽

Vaccine Development ◽

Nipah Virus ◽

3D Structure ◽

Cell Epitope ◽

Class Ii ◽

Class I ◽

Reverse Vaccinology ◽

Stable Complex

Aim and Objective: Nipah virus (NiV) is a zoonotic virus of the paramyxovirus family that sporadically breaks out from livestock and spreads in humans through breathing resulting in an indication of encephalitis syndrome. In the current study, T cell epitopes with the NiV W protein antigens were predicted. Materials and Methods: Modelling of unavailable 3D structure of W protein followed by docking studies of respective Human MHC - class I and MHC - class II alleles predicted was carried out for the highest binding rates. In the computational analysis, epitopes were assessed for immunogenicity, conservation, and toxicity analysis. T – cell-based vaccine development against NiV was screened for eight epitopes of Indian - Asian origin. Results: Two epitopes, SPVIAEHYY and LVNDGLNII, have been screened and selected for further docking study based on toxicity and conservancy analyses. These epitopes showed a significant score of -1.19 kcal/mol and 0.15 kcal/mol with HLA- B*35:03 and HLA- DRB1 * 07:03, respectively by using allele - Class I and Class II from AutoDock. These two peptides predicted by the reverse vaccinology approach are likely to induce immune response mediated by T – cells. Conclusion: Simulation using GROMACS has revealed that LVNDGLNII epitope forms a more stable complex with HLA molecule and will be useful in developing the epitope-based Nipah virus vaccine.

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