scholarly journals Multi-epitope Based Peptide Vaccine Design Using Three Structural Proteins (S, E, and M) of SARS-CoV-2: An In Silico Approach

2020 ◽  
Author(s):  
Arpita Singha Roy ◽  
Mahafujul Islam Quadery Tonmoy ◽  
Atqiya Fariha ◽  
Ithmam Hami ◽  
Ibrahim Khalil Afif ◽  
...  
Keyword(s):  
T Cell ◽  
B Cell ◽  
Peptide Vaccine ◽  
Evolutionary Relationship ◽  
Cell Epitope ◽  
Epitope Prediction ◽  
Vaccine Design ◽  
Structural Proteins ◽  
T Cell Epitopes ◽  
Novel Coronavirus

AbstractSevere Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is the novel coronavirus responsible for the ongoing pandemic of coronavirus disease (COVID-19). No sustainable treatment option is available so far to tackle such a public health threat. Therefore, designing a suitable vaccine to overcome this hurdle asks for immediate attention. In this study, we targeted for a design of multi-epitope based vaccine using immunoinformatics tools. We considered the structural proteins S, E and, M of SARS-CoV-2, since they facilitate the infection of the virus into host cell and using different bioinformatics tools and servers, we predicted multiple B-cell and T-cell epitopes having potential for the required vaccine design. Phylogenetic analysis provided insight on ancestral molecular changes and molecular evolutionary relationship of S, E, and M proteins. Based on the antigenicity and surface accessibility of these proteins, eight epitopes were selected by various B cell and T cell epitope prediction tools. Molecular docking was executed to interpret the binding interactions of these epitopes and three potential epitopes WTAGAAAYY, YVYSRVKNL, and GTITVEELK were selected for their noticeable higher binding affinity scores −9.1, −7.4, and −7.0 kcal/mol, respectively. Targeted epitopes had 91.09% population coverage worldwide. In summary, we identified three epitopes having the most significant properties of designing the peptide-based vaccine against SARS-CoV-2.

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 T Cell Epitope-Based Vaccine Design for Pandemic Novel Coronavirus 2019-nCoV

2020 ◽  
Author(s):  
Dr. Seema Mishra
Keyword(s):  
T Cell ◽  
Cell Epitope ◽  
Structural Proteins ◽  
T Cell Epitope ◽  
T Cell Epitopes ◽  
Consensus Sequences ◽  
Tight Cluster ◽  
Cell Assays ◽  
Novel Coronavirus

Immunoinformatics approach has been used to identify potential T cell epitopes from structural and non-structural proteins for immunotherapy against novel coronavirus 2019-nCoV across populations Two different prediction algorithms, NetCTLpan and Pickpocket were used to generate consensus epitopes against HLA supertypes. All of the 57 epitopes identified had no similarity/identity with the human proteome thus preventing crossreactivity. Many of these epitopes formed a tight cluster around consensus sequences <p>MGYINVFAFPFTIYSLLLC and KVSIWNLDYIINLI across proteins and alleles. These should be urgently tested in <i>in-vitro</i> MHC binding and T cell assays before being tried as vaccines to further prevent pandemic due to this lethal coronavirus.<br></p>

scholarly journals T Cell Epitope-Based Vaccine Design for Pandemic Novel Coronavirus 2019-nCoV

2020 ◽  
Author(s):  
Dr. Seema Mishra
Keyword(s):  
T Cell ◽  
Cell Epitope ◽  
Structural Proteins ◽  
T Cell Epitope ◽  
T Cell Epitopes ◽  
Consensus Sequences ◽  
Tight Cluster ◽  
Cell Assays ◽  
Novel Coronavirus

Immunoinformatics approach has been used to identify potential T cell epitopes from structural and non-structural proteins for immunotherapy against novel coronavirus 2019-nCoV across populations Two different prediction algorithms, NetCTLpan and Pickpocket were used to generate consensus epitopes against HLA supertypes. All of the 57 epitopes identified had no similarity/identity with the human proteome thus preventing crossreactivity. Many of these epitopes formed a tight cluster around consensus sequences <p>MGYINVFAFPFTIYSLLLC and KVSIWNLDYIINLI across proteins and alleles. These should be urgently tested in <i>in-vitro</i> MHC binding and T cell assays before being tried as vaccines to further prevent pandemic due to this lethal coronavirus.<br></p>

scholarly journals An Integrated In-Silico Approach to Develop Epitope-Based Peptide Vaccine against SARS-CoV-2

2020 ◽  
Author(s):  
Prekshi Garg ◽  
Neha Srivastava ◽  
Prachi Srivastava
Keyword(s):  
T Cell ◽  
B Cell ◽  
In Silico ◽  
3D Structure ◽  
Peptide Vaccine ◽  
Cell Epitope ◽  
Peptide Sequence ◽  
T Cell Epitopes ◽  
Mhc I ◽  
In Silico Study

SARS-CoV-2 has been the talk of the town ever since the beginning of 2020. The pandemic has brought the complete world on a halt. Every country is trying all possible steps to combat the disease ranging from shutting the complete economy of the country to repurposing of drugs and vaccine development. The rapid data analysis and widespread tools, software and databases have made bioinformatics capable of giving new insights to the researchers to deal with the current scenario more efficiently. Vaccinomics, the new emerging field of bioinformatics uses concepts of immunogenetics and immunogenomics with in silico tools to give promising results for wet lab experiments. This approach is highly validated for the designing and development of potent vaccines. The present in-silico study was attempted to identify peptide fragments from spike surface glycoprotein that can be efficiently used for the designing and development of epitope-based vaccine designing approach. Both B-cell and T-cell epitopes are predicted using integrated computational tools. VaxiJen server was used for prediction of protective antigenicity of the protein. NetCTL was studied for analyzing most potent T cell epitopes and its subsequent MHC-I interaction through tools provided by IEDB. 3D structure prediction of peptides and MHC-I alleles (HLA-C*03:03) was further done to carry out docking studies using AutoDock4.0. Various tools from IEDB were used to predict B-cell epitopes on the basis of different essential parameters like surface accessibility, beta turns and many more. Based on results interpretation, the peptide sequence from 1138-1145 amino acid and sequence WTAGAAAYY and YDPLQPEL were obtained as a potential B-cell epitope and T-cell epitope respectively. This in-silico study will help us to identify novel epitope-based peptide vaccine target in spike protein of SARS-CoV-2. Further, in-vitro and in-vivo study needed to validate the findings.

scholarly journals A Multiple Antigen Peptide Vaccine Containing CD4+ T Cell Epitopes Enhances Humoral Immunity against Trichinella spiralis Infection in Mice

2020 ◽  
Vol 2020 ◽  
pp. 1-14 ◽  
Author(s):  
Yuan Gu ◽  
Ximeng Sun ◽  
Jingjing Huang ◽  
Bin Zhan ◽  
Xinping Zhu
Keyword(s):  
T Cell ◽  
B Cell ◽  
Trichinella Spiralis ◽  
Peptide Vaccine ◽  
Cell Epitope ◽  
Muscle Larva ◽  
T Cell Epitopes ◽  
Protein Vaccine ◽  
B Cell Epitopes ◽  
Multiple Antigen

Multiepitope peptide vaccine has some advantages over traditional recombinant protein vaccine due to its easy and fast production and possible inclusion of multiple protective epitopes of pathogens. However, it is usually poorly immunogenic and needs to conjugate to a large carrier protein. Peptides conjugated to a central lysine core to form multiple antigen peptides (MAPs) will increase the immunogenicity of peptide vaccine. In this study, we constructed a MAP consisting of CD4+ T cell and B cell epitopes of paramyosin (Pmy) of Trichinella spiralis (Ts-Pmy), which has been proved to be a good vaccine candidate in our previous work. The immunogenicity and induced protective immunity of MAP against Trichinella spiralis (T. spiralis) infection were evaluated in mice. We demonstrated that mice immunized with MAP containing CD4+ T cell and B cell epitopes (MAP-TB) induced significantly higher protection against the challenge of T. spiralis larvae (35.5% muscle larva reduction) compared to the MAP containing B cell epitope alone (MAP-B) with a 12.4% muscle larva reduction. The better protection induced by immunization of MAP-TB was correlated with boosted antibody titers (both IgG1 and IgG2a) and mixed Th1/Th2 cytokine production secreted by the splenocytes of immunized mice. Further flow cytometry analysis of lymphocytes in spleens and draining lymph nodes demonstrated that mice immunized with MAP-TB specifically enhanced the generation of T follicular helper (Tfh) cells and germinal center (GC) B cells, while inhibiting follicular regulatory CD4+ T (Tfr) cells and regulatory T (Treg) cells. Immunofluorescence staining of spleen sections also confirmed that MAP-TB vaccination enhanced the formation of GCs. Our results suggest that CD4+ T cell epitope of Ts-Pmy is crucial in vaccine component for inducing better protection against T. spiralis infection.

An Integrated In-Silico Approach to Develop Epitope-Based Peptide Vaccine against SARS-CoV-2

Coronaviruses ◽  
2021 ◽  
Vol 02 ◽  
Author(s):  
Prekshi Garg ◽  
Neha Srivastava ◽  
Prachi Srivastava
Keyword(s):  
Amino Acid ◽  
T Cell ◽  
B Cell ◽  
In Silico ◽  
Peptide Vaccine ◽  
Cell Epitope ◽  
Peptide Sequence ◽  
T Cell Epitopes ◽  
Mhc I ◽  
In Silico Study

Background: SARS-CoV-2 has been the talk of the town ever since the beginning of 2020. Every country is trying all possible steps to combat the disease ranging from shutting the complete economy of the country to the repurposing of drugs and vaccine development. The rapid data analysis and widespread tools have made bioinformatics capable of giving new insights to deal with the current scenario more efficiently through an emerging field, Vaccinomics. Objective: The present in-silico study was attempted to identify peptide fragments from spike surface glycoprotein of SARS-CoV-2 that can be efficiently used for the development of an epitope-based vaccine designing approach. Methodology: The epitopes of B and T-cell are predicted using integrated computational tools. VaxiJen server, NetCTL, and IEDB tools were used to study, analyze, and predict potent T-cell epitopes, its subsequent MHC-I interactions, and B-cell epitopes. The 3D structure prediction of peptides and MHC-I alleles (HLA-C*03:03) was further done using AutoDock4.0. Result: Based on result interpretation, the peptide sequence from 1138-1145 amino acid and sequence WTAGAAAYY and YDPLQPEL were obtained as potential B-cell and T-cell epitopes respectively. Conclusion: The peptide sequence WTAGAAAYY and the amino acid sequence from 1138-1145 of the spike protein of SARS-CoV-2 can be used as a probable B-cell epitope candidate. Also, the amino acid sequence YDPLQPEL can be used as a potent T-cell epitope. This in-silico study will help us to identify novel epitope-based peptide vaccine targets in the spike protein of SARS-CoV-2. Further, the in-vitro and in-vivo study needed to validate the findings.

scholarly journals T Cell Epitope-Based Vaccine Design for Pandemic Novel Coronavirus 2019-nCoV

2020 ◽  
Author(s):  
Dr. Seema Mishra
Keyword(s):  
T Cell ◽  
Cell Epitope ◽  
Structural Proteins ◽  
T Cell Epitope ◽  
T Cell Epitopes ◽  
Consensus Sequences ◽  
Tight Cluster ◽  
Cell Assays ◽  
Novel Coronavirus

Immunoinformatics approach has been used to identify potential T cell epitopes from structural and non-structural proteins for immunotherapy against novel coronavirus 2019-nCoV across populations Two different prediction algorithms, NetCTLpan and Pickpocket were used to generate consensus epitopes against HLA supertypes. All of the 57 epitopes identified had no similarity/identity with the human proteome thus preventing crossreactivity. Many of these epitopes formed a tight cluster around consensus sequences <p>MGYINVFAFPFTIYSLLLC and KVSIWNLDYIINLI across proteins and alleles. These should be urgently tested in <i>in-vitro</i> MHC binding and T cell assays before being tried as vaccines to further prevent pandemic due to this lethal coronavirus.<br></p>

scholarly journals Vaccination With a FAT1-Derived B Cell Epitope Combined With Tumor-Specific B and T Cell Epitopes Elicits Additive Protection in Cancer Mouse Models

2018 ◽  
Vol 8 ◽  
Author(s):  
Alberto Grandi ◽  
Laura Fantappiè ◽  
Carmela Irene ◽  
Silvia Valensin ◽  
Michele Tomasi ◽  
...  
Keyword(s):  
T Cell ◽  
B Cell ◽  
Mouse Models ◽  
Cell Epitope ◽  
T Cell Epitopes ◽  
B Cell Epitope
Sign in / Sign up

Export Citation Format

Share Document