Computational antigenic epitope prediction of clinical Indonesian Dengue virus NS1 protein

Abstract The identification of human Non-Structural-1 (NS1) protein epitopes will help us better understand Dengue virus (DENV) immunopathogenesis. In this study, several online and offline bioinformatic prediction tools were exploited to predict and analyze T-cell and B-cell epitopes of DENV NS1 consensus sequences originated from Indonesian clinical isolates. We identified a potential peptide at NS1155--163 (VEDYGFGIF) which interact with MHC-I allele HLA-B*40:01 and showed high binding affinity (IC50) scores ranging between 63.8 nM to 183.9 nM for all Indonesian DENV serotypes. Furthermore, we have succeeded identified a region at the C-terminal of Indonesian DENV NS1 protein between 325--344 as part of discontinuous antigenic epitope which conserved for all serotypes. Our analyses showed this region could induce strong and persistent antibody against all DENV serotypes by interacting with MHC-I molecule and also recognized by B-cell receptor. The identification of DENV NS1 T-cell and B-cell epitopes may help in the development of a new vaccine, drug discovery, and diagnostic system to help eradicate dengue infection.

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

10.1101/2020.07.30.228221 ◽

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.

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Comparison of Neutralizing Dengue Virus B Cell Epitopes and Protective T Cell Epitopes With Those in Three Main Dengue Virus Vaccines

Frontiers in Immunology ◽

10.3389/fimmu.2021.715136 ◽

2021 ◽

Vol 12 ◽

Author(s):

Josilene Ramos Pinheiro ◽

Esther Camilo dos Reis ◽

Rayane da Silva Oliveira Souza ◽

Ana Luíza Silva Rocha ◽

Lincoln Suesdek ◽

...

Keyword(s):

T Cell ◽

Dengue Virus ◽

B Cell ◽

Public Health Problem ◽

Phase Iii ◽

World Health ◽

Human Populations ◽

T Cell Epitopes ◽

Dengue Vaccine ◽

B Cell Epitopes

The four serotypes of Dengue virus (DENV1-4) are arboviruses (arthropod-borne viruses) that belong to the Flavivirus genus, Flaviviridae family. They are the causative agents of an infectious disease called dengue, an important global public health problem with significant social-economic impact. Thus, the development of safe and effective dengue vaccines is a priority according to the World Health Organization. Only one anti-dengue vaccine has already been licensed in endemic countries and two formulations are under phase III clinical trials. In this study, we aimed to compare the main anti-dengue virus vaccines, DENGVAXIA®, LAV-TDV, and TAK-003, regarding their antigens and potential to protect. We studied the conservation of both, B and T cell epitopes involved in immunological control of DENV infection along with vaccine viruses and viral isolates. In addition, we assessed the population coverage of epitope sets contained in each vaccine formulation with regard to different human populations. As main results, we found that all three vaccines contain the main B cell epitopes involved in viral neutralization. Similarly, LAV-TDV and TAK-003 contain most of T cell epitopes involved in immunological protection, a finding not observed in DENGVAXIA®, which explains main limitations of the only licensed dengue vaccine. In summary, the levels of presence and absence of epitopes that are target for protective immune response in the three main anti-dengue virus vaccines are shown in this study. Our results suggest that investing in vaccines that contain the majority of epitopes involved in protective immunity (cellular and humoral arms) is an important issue to be considered.

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

10.26434/chemrxiv.12116943 ◽

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>

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

10.26434/chemrxiv.12116943.v1 ◽

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

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

PLoS ONE ◽

10.1371/journal.pone.0248061 ◽

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.

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Characterisation of B cell epitopes of dengue virus NS1 protein using bioinformatics approach

Journal of the National Science Foundation of Sri Lanka ◽

10.4038/jnsfsr.v44i4.8024 ◽

2016 ◽

Vol 44 (4) ◽

pp. 417 ◽

Cited By ~ 1

Author(s):

PD Pushpakumara ◽

PH Premarathne ◽

CL Goonasekara

Keyword(s):

Dengue Virus ◽

B Cell ◽

Ns1 Protein ◽

B Cell Epitopes

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Potential T-cell and B-cell Epitopes of 2019-nCoV

10.1101/2020.02.19.955484 ◽

2020 ◽

Cited By ~ 27

Author(s):

Ethan Fast ◽

Russ B. Altman ◽

Binbin Chen

Keyword(s):

Experimental Data ◽

T Cell ◽

B Cell ◽

Antigen Presentation ◽

Spike Protein ◽

Receptor Binding Domain ◽

Computational Pipeline ◽

Mhc I ◽

B Cell Epitopes ◽

Protein Receptor

As of early March, 2019-nCoV has infected more than one hundred thousand people and claimed thousands of lives. 2019-nCoV is a novel form of coronavirus that causes COVID-19 and has high similarity with SARS-CoV. No approved vaccine yet exists for any form of coronavirus. Here we use computational tools from structural biology and machine learning to identify 2019-nCoV T-cell and B-cell epitopes based on viral protein antigen presentation and antibody binding properties. These epitopes can be used to develop more effective vaccines and identify neutralizing antibodies. We identified 405 viral peptides with good antigen presentation scores for both human MHC-I and MHC-II alleles, and two potential neutralizing B-cell epitopes near the 2019-nCoV spike protein receptor binding domain (440-460 and 494-506). Analyzing mutation profiles of 68 viral genomes from four continents, we identified 96 coding-change mutations. These mutations are more likely to occur in regions with good MHC-I presentation scores (p=0.02). No mutations are present near the spike protein receptor binding domain. Based on these findings, the spike protein is likely immunogenic and a potential vaccine candidate. We validated our computational pipeline with SARS-CoV experimental data.Significance StatementThe novel coronavirus 2019-nCoV has affected more than 100 countries and continues to spread. There is an immediate need for effective vaccines that contain antigens which trigger responses from human T-cells and B-cells (known as epitopes). Here we identify potential T-cell epitopes through an analysis of human antigen presentation, as well as B-cell epitopes through an analysis of protein structure. We identify a list of top candidates, including an epitope located on 2019-nCoV spike protein that potentially triggers both T-cell and B-cell responses. Analyzing 68 samples, we observe that viral mutations are more likely to happen in regions with strong antigen presentation, a potential form of immune evasion. Our computational pipeline is validated with experimental data from SARS-CoV.

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In silico prediction of T‐cell and B‐cell epitopes of human papillomavirus type 16 L1 protein

Biotechnology and Applied Biochemistry ◽

10.1002/bab.2128 ◽

2021 ◽

Author(s):

Shahab Mahmoudvand ◽

Somayeh Shokri ◽

Manoochehr Makvandi ◽

Reza Taherkhani ◽

Mohammad Rashno ◽

...

Keyword(s):

Human Papillomavirus ◽

T Cell ◽

B Cell ◽

In Silico ◽

In Silico Prediction ◽

B Cell Epitopes ◽

Human Papillomavirus Type 16 ◽

L1 Protein

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Development of Bacteriophage Virus-Like Particle Vaccines Displaying Conserved Epitopes of Dengue Virus Non-Structural Protein 1

Vaccines ◽

10.3390/vaccines9070726 ◽

2021 ◽

Vol 9 (7) ◽

pp. 726

Author(s):

Nikole L. Warner ◽

Kathryn M. Frietze

Keyword(s):

Dengue Virus ◽

Population Based ◽

Ns1 Protein ◽

Structural Protein ◽

Denv Serotypes ◽

Conserved Regions ◽

Virus Like Particle ◽

Dependent Cell ◽

Infected Cells ◽

Plasma Leakage

Dengue virus (DENV) is a major global health problem, with over half of the world’s population at risk of infection. Despite over 60 years of efforts, no licensed vaccine suitable for population-based immunization against DENV is available. Here, we describe efforts to engineer epitope-based vaccines against DENV non-structural protein 1 (NS1). NS1 is present in DENV-infected cells as well as secreted into the blood of infected individuals. NS1 causes disruption of endothelial cell barriers, resulting in plasma leakage and hemorrhage. Immunizing against NS1 could elicit antibodies that block NS1 function and also target NS1-infected cells for antibody-dependent cell cytotoxicity. We identified highly conserved regions of NS1 from all four DENV serotypes. We generated synthetic peptides to these regions and chemically conjugated them to bacteriophage Qβ virus-like particles (VLPs). Mice were immunized two times with the candidate vaccines and sera were tested for the presence of antibodies that bound to the cognate peptide, recombinant NS1 from all four DENV serotypes, and DENV-2-infected cells. We found that two of the candidate vaccines elicited antibodies that bound to recombinant NS1, and one candidate vaccine elicited antibodies that bound to DENV-infected cells. These results show that an epitope-specific vaccine against conserved regions of NS1 could be a promising approach for DENV vaccines or therapeutics to bind circulating NS1 protein.

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