scholarly journals Immunoinformatics Approach for Epitope-Based Peptide Vaccine Design and Active Site Prediction against Polyprotein of Emerging Oropouche Virus

2018 ◽  
Vol 2018 ◽  
pp. 1-22 ◽  
Author(s):  
Utpal Kumar Adhikari ◽  
Mourad Tayebi ◽  
M. Mizanur Rahman
Keyword(s):  
T Cell ◽  
Ligand Binding ◽  
B Cell ◽  
Peptide Vaccine ◽  
Vaccine Design ◽  
Binding Interaction ◽  
B Cell Epitopes ◽  
Vaccine Candidates ◽  
Binding Pockets ◽  
Potential Vaccine

Oropouche virus (OROV) is an emerging pathogen which causes Oropouche fever and meningitis in humans. Several outbreaks of OROV in South America, especially in Brazil, have changed its status as an emerging disease, but no vaccine or specific drug target is available yet. Our approach was to identify the epitope-based vaccine candidates as well as the ligand-binding pockets through the use of immunoinformatics. In this report, we identified both T-cell and B-cell epitopes of the most antigenic OROV polyprotein with the potential to induce both humoral and cell-mediated immunity. Eighteen highly antigenic and immunogenic CD8+ T-cell epitopes were identified, including three 100% conserved epitopes (TSSWGCEEY, CSMCGLIHY, and LAIDTGCLY) as the potential vaccine candidates. The selected epitopes showed 95.77% coverage for the mixed Brazilian population. The docking simulation ensured the binding interaction with high affinity. A total of five highly conserved and nontoxic linear B-cell epitopes “NQKIDLSQL,” “HPLSTSQIGDRC,” “SHCNLEFTAITADKIMSL,” “PEKIPAKEGWLTFSKEHTSSW,” and “HHYKPTKNLPHVVPRYH” were selected as potential vaccine candidates. The predicted eight conformational B-cell epitopes represent the accessibility for the entered virus. In the posttherapeutic strategy, ten ligand-binding pockets were identified for effective inhibitor design against emerging OROV infection. Collectively, this research provides novel candidates for epitope-based peptide vaccine design against OROV.

scholarly journals Computational perspectives revealed prospective vaccine candidates from five structural proteins of novel SARS corona virus 2019 (SARS-CoV-2)

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9855
Author(s):  
Rajesh Anand ◽  
Subham Biswal ◽  
Renu Bhatt ◽  
Bhupendra N. Tiwary
Keyword(s):  
T Cell ◽  
B Cell ◽  
Structural Proteins ◽  
T Cell Epitopes ◽  
Population Coverage ◽  
B Cell Epitopes ◽  
Vaccine Candidates ◽  
Conformational Epitopes ◽  
Potential Vaccine ◽  
Linear B

Background The present pandemic COVID-19 is caused by SARS-CoV-2, a single-stranded positive-sense RNA virus from the Coronaviridae family. Due to a lack of antiviral drugs, vaccines against the virus are urgently required. Methods In this study, validated computational approaches were used to identify peptide-based epitopes from six structural proteins having antigenic properties. The Net-CTL 1.2 tool was used for the prediction of CD8+ T-cell epitopes, while the robust tools Bepi-Pred 2 and LBtope was employed for the identification of linear B-cell epitopes. Docking studies of the identified epitopes were performed using HADDOCK 2.4 and the structures were visualized by Discovery Studio and LigPlot+. Antigenicity, immunogenicity, conservancy, population coverage and allergenicity of the predicted epitopes were determined by the bioinformatics tools like VaxiJen v2.0 server, the Immune Epitope Database tools and AllerTOP v.2.0, AllergenFP 1.0 and ElliPro. Results The predicted T cell and linear B-cell epitopes were considered as prime vaccine targets in case they passed the requisite parameters like antigenicity, immunogenicity, conservancy, non-allergenicity and broad range of population coverage. Among the predicted CD8+ T cell epitopes, potential vaccine targets from surface glycoprotein were; YQPYRVVVL, PYRVVVLSF, GVYFASTEK, QLTPTWRVY, and those from ORF3a protein were LKKRWQLAL, HVTFFIYNK. Similarly, RFLYIIKLI, LTWICLLQF from membrane protein and three epitopes viz; SPRWYFYYL, TWLTYTGAI, KTFPPTEPK from nucleocapsid phosphoprotein were the superior vaccine targets observed in our study. The negative values of HADDOCK and Z scores obtained for the best cluster indicated the potential of the epitopes as suitable vaccine candidates. Analysis of the 3D and 2D interaction diagrams of best cluster produced by HADDOCK 2.4 displayed the binding interaction of leading T cell epitopes within the MHC-1 peptide binding clefts. On the other hand, among linear B cell epitopes the majority of potential vaccine targets were from nucleocapsid protein, viz; 59−HGKEDLKFPRGQGVPINTNSSPDDQIGYYRRATRRIRGGDGKMKDLS−105, 227−LNQLE SKMSGKGQQQQGQTVTKKSAAEASKKPRQKRTATK−266, 3−DNGPQNQRNAPRITFGGP−20, 29−GERSGARSKQRRPQGL−45. Two other prime vaccine targets, 370−NSASFSTFKCYGVSPTKLNDLCFTNV−395 and 260−AGAAAYYVGYLQPRT−274 were identified in the spike protein. The potential B-cell conformational epitopes were predicted on the basis of a higher protrusion index indicating greater solvent accessibility. These conformational epitopes were of various lengths and belonged to spike, ORF3a, membrane and nucleocapsid proteins. Conclusions Taken together, eleven T cell epitopes, seven B cell linear epitopes and ten B cell conformational epitopes were identified from five structural proteins of SARS-CoV-2 using advanced computational tools. These potential vaccine candidates may provide important timely directives for an effective vaccine against SARS-CoV-2.

scholarly journals Epitope‐based peptide vaccine design and target site depiction against Middle East Respiratory Syndrome Coronavirus: an immune-informatics study

2019 ◽  
Vol 17 (1) ◽  
Author(s):  
Muhammad Tahir ul Qamar ◽  
Saman Saleem ◽  
Usman Ali Ashfaq ◽  
Amna Bari ◽  
Farooq Anwar ◽  
...  
Keyword(s):  
T Cell ◽  
Middle East ◽  
B Cell ◽  
Mhc Class Ii ◽  
Peptide Vaccine ◽  
Middle East Respiratory Syndrome ◽  
T Cell Epitopes ◽  
Resistance Response ◽  
B Cell Epitopes ◽  
S Protein

Abstract Background Middle East Respiratory Syndrome Coronavirus (MERS-COV) is the main cause of lung and kidney infections in developing countries such as Saudi Arabia and South Korea. This infectious single-stranded, positive (+) sense RNA virus enters the host by binding to dipeptidyl-peptide receptors. Since no vaccine is yet available for MERS-COV, rapid case identification, isolation, and infection prevention strategies must be used to combat the spreading of MERS-COV infection. Additionally, there is a desperate need for vaccines and antiviral strategies. Methods The present study used immuno-informatics and computational approaches to identify conserved B- and T cell epitopes for the MERS-COV spike (S) protein that may perform a significant role in eliciting the resistance response to MERS-COV infection. Results Many conserved cytotoxic T-lymphocyte epitopes and discontinuous and linear B-cell epitopes were predicted for the MERS-COV S protein, and their antigenicity and interactions with the human leukocyte antigen (HLA) B7 allele were estimated. Among B-cell epitopes, QLQMGFGITVQYGT displayed the highest antigenicity-score, and was immensely immunogenic. Among T-cell epitopes, MHC class-I peptide YKLQPLTFL and MHC class-II peptide YCILEPRSG were identified as highly antigenic. Furthermore, docking analyses revealed that the predicted peptides engaged in strong bonding with the HLA-B7 allele. Conclusion The present study identified several MERS-COV S protein epitopes that are conserved among various isolates from different countries. The putative antigenic epitopes may prove effective as novel vaccines for eradication and combating of MERS-COV infection.

scholarly journals Immuno-informatics Design of a Multimeric Epitope Peptide Based Vaccine Targeting SARS-CoV-2 Spike Glycoprotein

2020 ◽  
Author(s):  
Onyeka S. Chukwudozie ◽  
Clive M. Gray ◽  
Tawakalt A. Fagbayi ◽  
Rebecca C. Chukwuanukwu ◽  
Victor O. Oyebanji ◽  
...  
Keyword(s):  
T Cell ◽  
B Cell ◽  
In Silico ◽  
Peptide Vaccine ◽  
Spike Protein ◽  
Cell Mediated Immunity ◽  
Epitope Peptide ◽  
Mhc I ◽  
B Cell Epitopes ◽  
Antibody Recognition

ABSTRACTDeveloping an efficacious vaccine to SARS-CoV-2 infection is critical to stem COVID-19 fatalities and providing the global community with immune protection. We have used a bioinformatic approach to aid in the design of an epitope peptide-based vaccine against the spike protein of the virus. Five antigenic B cell epitopes with viable antigenicity and a total of 27 discontinuous B cell epitopes were mapped out structurally in the spike protein for antibody recognition. We identified eight CD8+ T cell 9-mers along with 12 CD4+ T cell 14-15-mer as promising candidate epitopes putatively restricted by a large number of MHC-I and II alleles respectively. We used this information to construct an in silico chimeric peptide vaccine whose translational rate was highly expressed when cloned in pET28a (+) vector. The vaccine construct was predicted to elicit high antigenicity and cell-mediated immunity when given as a homologous prime-boost, with triggering of toll-like receptor 5 by the adjuvant linker. The vaccine was characterized by an increase in IgM and IgG and an array of Th1 and Th2 cytokines. Upon in silico challenge with SARS-CoV-2, there was a decrease in antigen levels using our immune simulations. We therefore propose that potential vaccine designs consider this approach.

scholarly journals Prediction of T and B Cell Epitopes in the Proteome of SARS-CoV-2 for Potential Use in Diagnostics and Vaccine Design

2020 ◽  
Author(s):  
Parvez Slathia ◽  
Preeti Sharma,
Keyword(s):  
T Cell ◽  
B Cell ◽  
Cell Epitope ◽  
Epitope Prediction ◽  
Vaccine Design ◽  
T Cell Epitopes ◽  
B Cell Epitopes ◽  
The People ◽  
Skilled Manpower ◽  
Prophylactic Measures

<p>The world is currently battling the Covid-19 pandemic for which there is no therapy available. Prophylactic measures like vaccines can effectively thwart the disease burden. The current methods of detection are PCR based and require skilled manpower to operate. The availability of cheap and ready to use diagnostics like serological methods can ease the detection of SARS-CoV-2 virus. In the current study, immunoinformatics tools have been used to predict T and B cell epitopes present in all the proteins of this virus. NetMHCPan, NetCTL and NetMHCII servers were used for T cell epitope prediction while BepiPred and ABCPred were used for B cell epitope prediction. Population coverage analysis for T cell epitopes revealed that these could provide protection to the people throughout world. The T cell epitopes can exclusively used for vaccine design whereas B cell epitopes can be used for both vaccine design and developing diagnostic kits. </p> <p> </p>

scholarly journals Prediction of T and B Cell Epitopes in the Proteome of SARS-CoV-2 for Potential Use in Diagnostics and Vaccine Design

2020 ◽  
Author(s):  
Parvez Slathia ◽  
Preeti Sharma,
Keyword(s):  
T Cell ◽  
B Cell ◽  
Cell Epitope ◽  
Epitope Prediction ◽  
Vaccine Design ◽  
T Cell Epitopes ◽  
B Cell Epitopes ◽  
The People ◽  
Skilled Manpower ◽  
Prophylactic Measures

<p>The world is currently battling the Covid-19 pandemic for which there is no therapy available. Prophylactic measures like vaccines can effectively thwart the disease burden. The current methods of detection are PCR based and require skilled manpower to operate. The availability of cheap and ready to use diagnostics like serological methods can ease the detection of SARS-CoV-2 virus. In the current study, immunoinformatics tools have been used to predict T and B cell epitopes present in all the proteins of this virus. NetMHCPan, NetCTL and NetMHCII servers were used for T cell epitope prediction while BepiPred and ABCPred were used for B cell epitope prediction. Population coverage analysis for T cell epitopes revealed that these could provide protection to the people throughout world. The T cell epitopes can exclusively used for vaccine design whereas B cell epitopes can be used for both vaccine design and developing diagnostic kits. </p> <p> </p>

scholarly journals Structure/epitope-based immunoinformatics analysis of structural proteins of 2019 novel coronavirus

2020 ◽  
Author(s):  
Yuwei Li ◽  
Mi Mao ◽  
Liteng Yang ◽  
Xizhuo Sun ◽  
Nanshan Zhong ◽  
...  
Keyword(s):  
T Cell ◽  
Membrane Protein ◽  
B Cell ◽  
Envelope Protein ◽  
Antiviral Treatment ◽  
Peptide Vaccine ◽  
Structural Proteins ◽  
T Cell Epitopes ◽  
B Cell Epitopes ◽  
Novel Coronavirus

Abstract The newly identified 2019 novel coronavirus (2019-nCoV) has caused more than 81,400 laboratory-confirmed human infections, including 3261 deaths, posing a serious threat to human health. Currently, however, there is no specific antiviral treatment or vaccine. To identify immunodominant peptides for designing global peptide vaccine for combating the infections caused by 2019-nCoV, the structure and immunogenicity of 2019-nCoV structural protein were analyzed by bioinformatics tools. 33 B-cell epitopes and 39 T-cell epitopes were determined in four structural proteins via different immunoinformatic tools in which include spike protein (22 B-cell epitopes, 25 T-cell epitopes ), nucleocapsid protein (7 B-cell epitopes, 6 T-cell epitopes), membrane protein (2 B-cell epitopes, 7 T-cell epitopes), and envelope protein (2 B-cell epitopes, 1T-cell epitopes), respectively. The proportion of epitope residues in primary sequence was used to determine the antigenicity and immunogenicity of proteins. The envelope protein has the largest antigenicity in which residue coverage of B-cell epitopes is 24%. The membrane protein possesses the largest immunogenicity in which residue coverage of T-cell epitopes is 55.86%. The reason that immune storm was caused by 2019-nCoV maybe that the membrane and envelope protein expressed plentifully in cell infected. Further, studies involving experimental validation of these predicted epitopes is warranted to ensure the potential of B-cells and T-cells stimulation for their effective use as vaccine candidates. These findings provide the basis for starting further studies on the pathogenesis, and optimizing the design of diagnostic, antiviral and vaccination strategies for this emerging infection.

scholarly journals Immuno-informatics design of a multimeric epitope peptide based vaccine targeting SARS-CoV-2 spike glycoprotein

PLoS ONE ◽  
2021 ◽  
Vol 16 (3) ◽  
pp. e0248061
Author(s):  
Onyeka S. Chukwudozie ◽  
Clive M. Gray ◽  
Tawakalt A. Fagbayi ◽  
Rebecca C. Chukwuanukwu ◽  
Victor O. Oyebanji ◽  
...  
Keyword(s):  
T Cell ◽  
B Cell ◽  
In Silico ◽  
Peptide Vaccine ◽  
Spike Protein ◽  
Cell Mediated Immunity ◽  
Epitope Peptide ◽  
Mhc I ◽  
B Cell Epitopes ◽  
Antibody Recognition

Developing an efficacious vaccine for SARS-CoV-2 infection is critical to stemming COVID-19 fatalities and providing the global community with immune protection. We have used a bioinformatic approach to aid in designing an epitope peptide-based vaccine against the spike protein of the virus. Five antigenic B cell epitopes with viable antigenicity and a total of 27 discontinuous B cell epitopes were mapped out structurally in the spike protein for antibody recognition. We identified eight CD8+ T cell 9-mers and 12 CD4+ T cell 14-15-mer as promising candidate epitopes putatively restricted by a large number of MHC I and II alleles, respectively. We used this information to construct an in silico chimeric peptide vaccine whose translational rate was highly expressed when cloned in pET28a (+) vector. With our In silico test, the vaccine construct was predicted to elicit high antigenicity and cell-mediated immunity when given as a homologous prime-boost, triggering of toll-like receptor 5 by the adjuvant linker. The vaccine was also characterized by an increase in IgM and IgG and an array of Th1 and Th2 cytokines. Upon in silico challenge with SARS-CoV-2, there was a decrease in antigen levels using our immune simulations. We, therefore, propose that potential vaccine designs consider this approach.

scholarly journals Design of an epitope-based peptide vaccine againstCryptococcus neoformans

2018 ◽  
Author(s):  
Isra Khalil ◽  
Ibtihal Omer ◽  
Islam Zainalabdin Abdalgadir Farh ◽  
Hanaa Abdalla Mohamed ◽  
Hajr Abdallha Elsharif ◽  
...  
Keyword(s):  
T Cell ◽  
B Cell ◽  
Cryptococcus Neoformans ◽  
Tertiary Structure ◽  
Peptide Vaccine ◽  
Population Coverage ◽  
Binding Prediction ◽  
B Cell Epitopes ◽  
Mhc Ii ◽  
Average Population

AbstractIntroductionThis study aimed to design an immunogenic epitope for Cryptococcus neoformans the etiological agent of cryptococcosis using in silico simulations, for epitope prediction, we selected the mannoprotein antigen MP88 which it’s known to induce protective immunity.Material & methodA total of 39 sequences of MP88 protein with length 378 amino acids were retrieved from the National Center for Biotechnology Information database (NCBI) in the FASTA format were used to predict antigenic B-cell and T cell epitopes via different bioinformatics tools at Immune Epitope Database and Analysis Resource (IEDB). The tertiary structure prediction of MP88 was created in RaptorX, and visualized by UCSF Chimera software.ResultA Conserved B-cell epitopesAYSTPA, AYSTPAS, PASSNCK, and DSAYPPhave displayed the most promising B cell epitopes. While theYMAADQFCL, VSYEEWMNYandFQQRYTGTFthey represent the best candidates T-cell conserved epitopes, the 9-mer epitopeYMAADQFCLdisplay the greater interact with 9 MHC-I alleles and HLA-A*02:01 alleles have the best interaction with an epitope. TheVSYEEWMNYandFQQRYTGTFthey are non-allergen whileYMAADQFCLwas an allergen. For MHC class II peptide binding prediction, theYARLLSLNA, ISYGTAMAVandINQTSYARLrepresent the most Three highly binding affinity core epitopes. The core epitopeINQTSYARLwas found to interact with 14 MHC-II. The allergenicity prediction revealsISYGTAMAV, INQTSYARLwere non-allergen andYARLLSLNAwas an allergen. Regarding population coverage theYMAADQFCLexhibit, a higher percentage among the world (69.75%) and the average population coverage was93.01%.In MHC-II,ISYGTAMAVepitope reveal a higher percentage (74.39%) and the average population coverage was (81.94%). This successfully designed a peptide vaccine against Cryptococcus neoformans open up a new horizon in Cryptococcus neoformans research; the results require validation by in vitro and in vivo experiments.

Identification of Generalized Peptide Regions for Designing Vaccine Effective for All Significant Mutated Strains of SARS-CoV-2

2021 ◽  
Vol 24 ◽  
Author(s):  
Subhamoy Biswas ◽  
Smarajit Manna ◽  
Tathagata Dey ◽  
Shreyans Chatterjee ◽  
Sumanta Dey
Keyword(s):  
Comparative Study ◽  
Zika Virus ◽  
Peptide Vaccine ◽  
Vaccine Design ◽  
Current Approach ◽  
Polar Plot ◽  
Vaccine Candidates ◽  
The Future ◽  
Potential Vaccine ◽  
The Comparative Study

Background: Coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 has become a worldwide pandemic and created an utmost crisis across the globe. To mitigate the crisis, the design of vaccines is a crucial solution. The frequent mutation of the virus demands generalized vaccine candidates, which would be effective for all mutated strains at present and for the strains that would evolve due to further new mutations in the virus. Objective: The objective of this study is to identify more frequently occurring mutated variants of SARS-CoV-2 and to suggest peptide vaccine candidates effective in common against the viral strains considered. Method: In this study, we have identified all currently prevailing mutated strains of SARS-CoV-2 through 2D Polar plot and Quotient Radius〖(q〗_R) characterization descriptor. Then, by considering the top eight mutation strains, which are significant due to their frequency of occurrence, peptide regions suitable for vaccine design have been identified with the help of a mathematical model – 2D Polygon Representation, followed by the evaluation of epitope potential and ensuring that there is no case of any autoimmune threat. Lastly, in order to verify whether this entire approach is applicable for vaccine design against any other virus in general, we have made a comparative study between the peptide vaccine candidates prescribed for the Zika virus using the current approach and a list of potential vaccine candidates for the same already established in the past. Results: We have finally suggested three generalized peptide regions which would be suitable as sustainable peptide vaccine candidates against SARS-CoV-2 irrespective of its currently prevailing strains as well any other variant of the same that may appear in the future. We also observed that during the comparative study using the case of E protein of Zika virus, the peptide regions suggested using the new approach matched with the already established results. Conclusion: The study, therefore, illustrates an approach that would help in developing peptide vaccine against SARS-CoV-2 by suggesting those peptide regions which can be targeted irrespective of any mutated form of this virus. The consistency with which this entire approach was also able to figure out similar vaccine candidates for Zika virus with utmost accuracy proves that this protocol can be extended for peptide vaccine design against any other virus in the future.

scholarly journals In Silico screening of T-cell and B-cell Epitopes of Rotavirus VP7 and VP4 proteins for Effective Vaccine Design

2019 ◽  
Vol 35 (1) ◽  
pp. 45-55
Author(s):  
Md Sadikur Rahman Shuvo ◽  
Sanjoy Kumar Mukharjee ◽  
Firoz Ahmed
Keyword(s):  
Developing Countries ◽  
T Cell ◽  
B Cell ◽  
In Silico ◽  
Child Death ◽  
Vaccine Design ◽  
Effective Vaccine ◽  
World Population ◽  
Promising Alternative ◽  
B Cell Epitopes

Rotavirus is one of the deadliest causative agents of childhood diarrhea which causes half a million child death across the globe, mostly in developing countries. However, effective vaccine strategies against rotavirus are yet to be established to prevent these unwanted premature deaths. In this regard, in silico vaccine design for rotavirus could be a promising alternative for developing countries due to its efficiency in shortening valuable time and cost. The present study described an epitope-based peptide vaccine design against rotavirus, using a combination of T-cell and B-cell epitope predictions and molecular docking approach. To perform this, sequences of rotavirus VP7 and VP4 proteins were retrieved from the NCBI database and subjected to different bioinformatics tools to predict most immunogenic T-cell and B-cell epitopes. From the identified epitopes, the sequence VMSKRSRSL of VP7 and TQFTDFVSL of VP4 was identified as the most potential epitopes based on their antigenicity, conservancy and interaction with major histocompatability complex I (MHC-I) alleles. Moreover, the peptide VMSKRSRSL interacted with human leukocyte antigen, HLA-B*08:01 and TQFTDFVSL interacted with HLA-A*02:06 with considerable binding energy and affinity score. Combined population coverage for our identified epitopes was found 70.53% and 45.64% for world population and South Asian population respectively. All these results suggest that, the epitopes identified in this study could be a very good vaccine candidate for the strains of rotavirus circulating in Bangladesh. However, as this study is completely dependent on computational prediction algorithms, further in vivo screening is required to come up in a precise conclusion about these epitopes for effective rotavirus vaccination. Bangladesh J Microbiol, Volume 35 Number 1 June 2018, pp 45-55

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