Construction of Epitope-Based Peptide Vaccine Against SARS-CoV-2: Immunoinformatics Study

Recently, a novel coronavirus (SARS-CoV-2) appeared which is conscientious for the current outbreak in China and rapidly spread worldwide. Unluckily, there is no approved vaccine found against SARS-CoV-2. Therefore, there is an urgent need for designing a suitable peptide vaccine constituent against the SARS-CoV-2. In this study, we characterized the spike glycoprotein of SARS-CoV-2 to obtain immunogenic epitopes. In addition, we used 58 SARS-CoV-2 isolates were retrieved from the Global Initiative on Sharing All Influenza Data (GISAID) and National Center for Biotechnology Information (NCBI), then aligned to obtain the conserved region of SARS-CoV-2 spike glycoprotein. The interaction between the conserved region with ACE2 receptor, a SARS-CoV-2 receptor on the host cell, has been evaluated through molecular docking approach. The B-cell epitope was identified using the immune epitope database (IEDB) web server. Interestingly, we recommend Pep_4 ADHQPQTFVNTELH as a epitope-based peptide vaccine candidate to deal with the SARS-CoV-2 outbreak. Pep_4 has a high level of immunogenicity and does not trigger autoimmune mechanisms. Pep_4 is capable of forming BCR/Fab molecular complexes with the lowest binding energy for activation of transduction signal the direct B-cell immune response. However, further study is suggested for confirmation (in vitro and in vivo).

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A Highly Conserved GEQYQQLR Epitope Has Been Identified in the Nucleoprotein of Ebola Virus by Using an In Silico Approach

Advances in Bioinformatics ◽

10.1155/2015/278197 ◽

2015 ◽

Vol 2015 ◽

pp. 1-8 ◽

Cited By ~ 7

Author(s):

Mohammad Tuhin Ali ◽

Md Ohedul Islam

Keyword(s):

B Cell ◽

Ebola Virus ◽

Cell Epitope ◽

Multiple Sequence ◽

B Cell Epitope ◽

Conserved Region ◽

Immune Epitope Database ◽

The Ideal

Ebola virus (EBOV) is a deadly virus that has caused several fatal outbreaks. Recently it caused another outbreak and resulted in thousands afflicted cases. Effective and approved vaccine or therapeutic treatment against this virus is still absent. In this study, we aimed to predict B-cell epitopes from several EBOV encoded proteins which may aid in developing new antibody-based therapeutics or viral antigen detection method against this virus. Multiple sequence alignment (MSA) was performed for the identification of conserved region among glycoprotein (GP), nucleoprotein (NP), and viral structural proteins (VP40, VP35, and VP24) of EBOV. Next, different consensus immunogenic and conserved sites were predicted from the conserved region(s) using various computational tools which are available in Immune Epitope Database (IEDB). Among GP, NP, VP40, VP35, and VP30 protein, only NP gave a 100% conserved GEQYQQLR B-cell epitope that fulfills the ideal features of an effective B-cell epitope and could lead a way in the milieu of Ebola treatment. However, successful in vivo and in vitro studies are prerequisite to determine the actual potency of our predicted epitope and establishing it as a preventing medication against all the fatal strains of EBOV.

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An Immunoinformatics Study to Predict Epitopes in the Envelope Protein of SARS-COV-2

10.1101/2020.05.26.115790 ◽

2020 ◽

Author(s):

Renu Jakhar ◽

S.K Gakhar

Keyword(s):

B Cell ◽

Envelope Protein ◽

Peptide Vaccine ◽

Cell Epitope ◽

T Helper ◽

Ctl Epitopes ◽

The People ◽

B Cell Epitope

AbstractCOVID-19 is a new viral emergent human disease caused by a novel strain of Coronavirus. This virus has caused a huge problem in the world as millions of the people are affected with this disease in the entire world. We aimed to design a peptide vaccine for COVID-19 particularly for the envelope protein using computational methods to predict epitopes inducing the immune system and can be used later to create a new peptide vaccine that could replace conventional vaccines. A total of available 370 sequences of SARS-CoV-2 were retrieved from NCBI for bioinformatics analysis using Immune Epitope Data Base (IEDB) to predict B and T cells epitopes. Then we docked the best predicted CTL epitopes with HLA alleles. CTL cell epitopes namely interacted with MHC class I alleles and we suggested them to become universal peptides based vaccine against COVID-19. Potentially continuous B cell epitopes were predicted using tools from IEDB. The Allergenicity of predicted epitopes was analyzed by AllerTOP tool and the coverage was determined throughout the worlds. We found these CTL epitopes to be T helper epitopes also. The B cell epitope, SRVKNL and T cell epitope, FLAFVVFLL were suggested to become a universal candidate for peptide-based vaccine against COVID-19. We hope to confirm our findings by adding complementary steps of both in vitro and in vivo studies to support this new universal predicted candidate.

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Conserved B-cell epitope identification of envelope glycoprotein (GP120) HIV-1 to develop multi-strain vaccine candidate through bioinformatics approach

Jurnal Teknologi Laboratorium ◽

10.29238/teknolabjournal.v10i1.274 ◽

2021 ◽

Vol 10 (1) ◽

pp. 06-13

Author(s):

Viol Dhea Kharisma ◽

Arif Nur Muhammad Ansori ◽

Gabrielle Ann Villar Posa ◽

Wahyu Choirur Rizky ◽

Sofy Permana ◽

...

Keyword(s):

B Cell ◽

Cell Activation ◽

Immune Cell ◽

Vaccine Candidate ◽

Peptide Vaccine ◽

Cell Epitope ◽

Vaccine Design ◽

B Cell Epitope ◽

Conserved Region ◽

Hiv 1

Acquired immune deficiency syndrome (AIDS) has been identified from US patients since 1981. AIDS is caused by infection with the human immunodeficiency virus type 1 (HIV-1) which is a retrovirus. HIV-1 gp120 can be recognized by the immune system because it is located outside the virion. The conserved region is identified in gp120, and it is recognized by an immune cell which then initiates specific immune responses, viral mutation escape, and increase vaccine protection coverage, a benefit derived from the conserved region-based vaccine design. However, previous researchers have little knowledge on this conserved region as a target for vaccine design. This paper explains how the conserved region of gp120 HIV-1 is a major target for vaccine design through a bioinformatics approach. The conserved region from gp120 was explored as a vaccine design target with a bioinformatics tool that consists of B-cell epitope mapping, vaccine properties, molecular docking, and dynamic simulation. The peptide vaccine candidate of B5 with the gp120 HIV-1 conserved region was found to provoke B-cell activation through a direct pathway, produce specific antibody, and increase protection from multi-strain viral infection.

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Epitope - based peptide vaccine against glycoprotein GPC precursor of Lujo virus using immunoinformatics approaches

10.1101/2020.09.09.287771 ◽

2020 ◽

Author(s):

Arwa A. Mohammed ◽

Mayada E. Elkhalifa ◽

Khadija E. Elamin ◽

Rawan A. Mohammed ◽

Musab E. Ibrahim ◽

...

Keyword(s):

B Cell ◽

Mhc Class Ii ◽

Peptide Vaccine ◽

Cell Epitope ◽

Hemorrhagic Fever ◽

Population Coverage ◽

B Cell Epitope ◽

Cub Domain ◽

Autodock 4.0

AbstractBackgroundLujo virus (LUJV) is a highly fatal human pathogen belonging to the Arenaviridae family. Lujo virus causes viral hemorrhagic fever (VHF). An In silico molecular docking was performed on the GPC domain of Lujo virus in complex with the first CUB domain of neuropilin-2.The aim of this study is to predict effective epitope-based vaccine against glycoprotein GPC precursor of Lujo virus using immunoinformatics approaches.Methods and Materialsglycoprotein GPC precursor of Lujo virus Sequence was retrieved from NCBI. Different prediction tools were used to analyze the nominee’s epitopes in BepiPred-2.0: Sequential B-Cell Epitope Predictor for B-cell, T-cell MHC class II & I. Then the proposed peptides were docked using Autodock 4.0 software program.Results and ConclusionsThe proposed and promising peptides FWYLNHTKL and YMFSVTLCI shows a very strong binding affinity to MHC class I & II alleles with high population coverage for the world, South Africa and Sudan. This indicates a strong potential to formulate a new vaccine, especially with the peptide YMFSVTLCI which is likely to be the first proposed epitope-based vaccine against glycoprotein GPC of Lujo virus. This study recommends an in-vivo assessment for the most promising peptides especially FWYLNHTKL, YMFSVTLCI and LPCPKPHRLR.

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Immunobioinformatics analysis and phylogenetic tree construction of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Indonesia: spike glycoprotein gene

Jurnal Teknologi Laboratorium ◽

10.29238/teknolabjournal.v9i1.221 ◽

2020 ◽

Vol 9 (1) ◽

pp. 13-20

Author(s):

Arif Nur Muhammad Ansori ◽

Viol Dhea Kharisma ◽

Yulanda Antonius ◽

Martia Rani Tacharina ◽

Fedik Abdul Rantam

Keyword(s):

Severe Acute Respiratory Syndrome ◽

Phylogenetic Tree ◽

Protective Antigen ◽

Cell Epitope ◽

World Health ◽

Spike Glycoprotein ◽

Phylogenetic Tree Construction ◽

Tree Construction

The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19), has spread worldwide and as a result, the World Health Organization (WHO) declared it a pandemic. At present, there are no approved vaccines against SARS-CoV-2. Therefore, the aim of this study was to predict epitope-based vaccines using bioinformatics approaches and phylogenetic tree construction of SARS-CoV-2 against the backdrop of the COVID-19 pandemic. In this study, we employed 27 isolates of SARS-CoV-2 spike glycoprotein genes retrieved from GenBank® (National Center for Biotechnology Information, USA) and the GISAID EpiCoV™ Database (Germany). We analyzed the candidate epitopes using the Immune Epitope Database and Analysis Resource. Furthermore, we performed a protective antigen prediction with VaxiJen 2.0. Data for B-cell epitope prediction, protective antigen prediction, and the underlying phylogenetic tree of SARS-CoV-2 were obtained in this research. Therefore, these data could be used to design an epitope-based vaccine against SARS-CoV-2. However, the advanced study is recommended for confirmation (in vitro and in vivo).

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Regulation of memory B-cell survival by the BH3-only protein Puma

Blood ◽

10.1182/blood-2011-04-347096 ◽

2011 ◽

Vol 118 (15) ◽

pp. 4120-4128 ◽

Cited By ~ 26

Author(s):

Cyril Clybouw ◽

Silke Fischer ◽

Marie Thérèse Auffredou ◽

Patricia Hugues ◽

Catherine Alexia ◽

...

Keyword(s):

Immune Response ◽

B Cells ◽

B Cell ◽

Cell Survival ◽

Family Member ◽

Cell Immune Response ◽

Memory B Cell ◽

B Cell Survival

Abstract Apoptosis is crucial for immune system homeostasis, including selection and survival of long-lived antibody-forming cells and memory cells. The interactions between proapoptotic and pro-survival proteins of the Bcl-2 family are critical for this process. In this report, we show that expression of the proapoptotic BH3-only Bcl-2 family member Puma was selectively up-regulated on in vitro activation with antigens or mitogens of both human and mouse B cells. Puma expression coincided in vivo, with the prosurvival Bcl-2 family member Mcl-1 within the germinal centers and its expression correlates with the germinal center like phenotype of Burkitt lymphoma. Experiments performed in Puma-deficient mice revealed that Puma is essential for apoptosis of mitogen-activated B cells in vitro and for the control of memory B-cell survival. In conclusion, using both human and murine models, our data show that Puma has a major role in the T cell– dependent B-cell immune response. These data demonstrate that Puma is a major regulator of memory B lymphocyte survival and therefore a key molecule in the control of the immune response.

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Epitope-Based Peptide Vaccine against Glycoprotein G of Nipah Henipavirus Using Immunoinformatics Approaches

Journal of Immunology Research ◽

10.1155/2020/2567957 ◽

2020 ◽

Vol 2020 ◽

pp. 1-12

Author(s):

Arwa A. Mohammed ◽

Shaza W. Shantier ◽

Mujahed I. Mustafa ◽

Hind K. Osman ◽

Hashim E. Elmansi ◽

...

Keyword(s):

B Cell ◽

Mhc Class Ii ◽

Nipah Virus ◽

Peptide Vaccine ◽

Cell Epitope ◽

Asymptomatic Infection ◽

Healthcare Facilities ◽

Glycoprotein G ◽

Autodock 4.0

Background. Nipah belongs to the genus Henipavirus and the Paramyxoviridae family. It is an endemic most commonly found at South Asia and has first emerged in Malaysia in 1998. Bats are found to be the main reservoir for this virus, causing disease in both humans and animals. The last outbreak has occurred in May 2018 in Kerala. It is characterized by high pathogenicity and fatality rates which varies from 40% to 70% depending on the severity of the disease and on the availability of adequate healthcare facilities. Currently, there are no antiviral drugs available for NiV disease and the treatment is just supportive. Clinical presentations for this virus range from asymptomatic infection to fatal encephalitis. Objective. This study is aimed at predicting an effective epitope-based vaccine against glycoprotein G of Nipah henipavirus, using immunoinformatics approaches. Methods and Materials. Glycoprotein G of the Nipah virus sequence was retrieved from NCBI. Different prediction tools were used to analyze the epitopes, namely, BepiPred-2.0: Sequential B Cell Epitope Predictor for B cell and T cell MHC classes II and I. Then, the proposed peptides were docked using Autodock 4.0 software program. Results and Conclusions. The two peptides TVYHCSAVY and FLIDRINWI have showed a very strong binding affinity to MHC class I and MHC class II alleles. Furthermore, considering the conservancy, the affinity, and the population coverage, the peptide FLIDRINWIT is highly suitable to be utilized to formulate a new vaccine against glycoprotein G of Nipah henipavirus. An in vivo study for the proposed peptides is also highly recommended.

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Use of a Novel Peptide Welding Technology Platform for the Development of B- and T-Cell Epitope-Based Vaccines

Vaccines ◽

10.3390/vaccines9050526 ◽

2021 ◽

Vol 9 (5) ◽

pp. 526

Author(s):

Francesco Nicoli ◽

Salvatore Pacifico ◽

Eleonora Gallerani ◽

Erika Marzola ◽

Valentina Albanese ◽

...

Keyword(s):

T Cell ◽

B Cell ◽

Cell Epitope ◽

Subcutaneous Administration ◽

T Cell Epitopes ◽

Peptide Vaccines ◽

Peptide Epitope ◽

Welding Technology

Peptide vaccines incorporating B- and T-cell epitopes have shown promise in the context of various cancers and infections. These vaccines are relatively simple to manufacture, but more immunogenic formulations are considered a priority. We developed tetrabranched derivatives for this purpose based on a novel peptide welding technology (PWT). PWTs provide molecular scaffolds for the efficient synthesis of ultrapure peptide dendrimers, which allow the delivery of multiple ligands within a single macromolecular structure. Peptide vaccines incorporating T-cell epitopes derived from melanoma and B-cell epitopes derived from human immunodeficiency virus, synthesized using this approach, elicited primary immune responses in vitro and in vivo. Subcutaneous administration of the B-cell epitope-based vaccines also elicited more potent humoral responses than subcutaneous administration of the corresponding peptides alone. Highly immunogenic peptide epitope-based vaccines can therefore be generated quickly and easily using a novel PWT.

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In Silico Approach To Design a B-cell Epitope Based Vaccine Target Against Yellow Fever Virus

Bangladesh Journal of Microbiology ◽

10.3329/bjm.v35i1.39801 ◽

2019 ◽

Vol 35 (1) ◽

pp. 27-35

Author(s):

Shamira Tabrejee ◽

M Mahboob Hossain

Keyword(s):

Yellow Fever ◽

Yellow Fever Virus ◽

Peptide Vaccine ◽

Cell Epitope ◽

Epitope Prediction ◽

Fever Virus ◽

Young Infants ◽

E Protein

Yellow fever virus is a prototype member of the Flaviviridae family causing high fever and jaundice. Though YF 17D vaccine is administered to yellow fever patients, however it can produce adverse effects in immunocompromised, older people and young infants. The aim of this study is to design an epitope-based peptide vaccine by targeting envelope (E) protein of Yellow Fever Virus. Thirty sequences of E protein of Yellow Fever Virus strains were retrieved from NCBI database. E protein was found to be mostly conserved among all the sequences with little variability and also was identified as a probable antigen. Different epitope prediction tools predicted 4 common epitopes, 3 of which were found to be antigenic. A peptide VKNPTDTGin E protein was predicted to have surface accessibility which overlaps with the VKNPTDTGHGT epitope.So, the whole VKNPTDTGHGT epitope was taken for further analysis. The VKNPTDTGHGT epitope showed 96.67% conservancy and also possesses flexibility, hydrophilicity and non-toxicity. Therefore, VKNPTDTGHGT can be regarded as a potential vaccine candidate against Yellow fever virus with further in vitro and in vivo validation. Bangladesh J Microbiol, Volume 35 Number 1 June 2018, pp 27-35

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Epitope - based peptide vaccine against glycoprotein G of Nipah henipavirus using immunoinformatics approaches

10.1101/678664 ◽

2019 ◽

Cited By ~ 1

Author(s):

Arwa A. Mohammed ◽

Shaza W. Shantier ◽

Mujahed I. Mustafa ◽

Hind K. Osman ◽

Hashim E. Elmansi ◽

...

Keyword(s):

B Cell ◽

Binding Affinity ◽

Mhc Class Ii ◽

Peptide Vaccine ◽

Cell Epitope ◽

Case Fatality ◽

Mhc I ◽

Strong Binding ◽

Glycoprotein G

AbstractBackgroundNipah virus (NiV) is a member of the genus Henipavirus of the family Paramyxoviridae, characterized by high pathogenicity and endemic in South Asia, first emerged in Malaysia in 1998. The case-fatality varies from 40% to 70% depending on the severity of the disease and on the availability of adequate healthcare facilities. At present no antiviral drugs are available for NiV disease and the treatment is just supportive. Clinical presentation ranges from asymptomatic infection to fatal encephalitis. Bats are the main reservoir for this virus, which can cause disease in humans and animals. The last investigated NiV outbreak has occurred in May 2018 in Kerala.ObjectiveThis study aims to predict effective epitope-based vaccine against glycoprotein G of Nipah henipavirus using immunoinformatics approaches.Methods and MaterialsGlycoprotein G of Nipah henipavirus sequence was retrieved from NCBI. Different prediction tools were used to analyze the nominee’s epitopes in BepiPred-2.0: Sequential B-Cell Epitope Predictor for B-cell, T-cell MHC class II & I. Then the proposed peptides were docked using Autodock 4.0 software program.Results and ConclusionsPeptide TVYHCSAVY shows a very strong binding affinity to MHC I alleles while FLIDRINWI shows a very strong binding affinity to MHC II and MHC I alleles. This indicates a strong potential to formulate a new vaccine, especially with the peptide FLIDRINWI that is likely to be the first proposed epitope-based vaccine against glycoprotein G of Nipah henipavirus. This study recommends an in-vivo assessment for the most promising peptides especially FLIDRINWI.

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