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

2019 ◽  
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.

scholarly journals Epitope-Based Peptide Vaccine Against Fructose-Bisphosphate Aldolase of Madurella mycetomatis Using Immunoinformatics Approaches

2018 ◽  
Vol 12 ◽  
pp. 117793221880970 ◽  
Author(s):  
Arwa A Mohammed ◽  
Ayman MH ALnaby ◽  
Solima M Sabeel ◽  
Fagr M AbdElmarouf ◽  
Amina I Dirar ◽  
...  
Keyword(s):  
B Cell ◽  
Binding Affinity ◽  
Mhc Class Ii ◽  
Bacterial Infections ◽  
Peptide Vaccine ◽  
Fructose Bisphosphate ◽  
Mhc I ◽  
Strong Binding ◽  
Fructose Bisphosphate Aldolase ◽  
Madurella Mycetomatis

Background: Mycetoma is a distinct body tissue destructive and neglected tropical disease. It is endemic in many tropical and subtropical countries. Mycetoma is caused by bacterial infections ( actinomycetoma) such as Streptomyces somaliensis and Nocardiae or true fungi ( eumycetoma) such as Madurella mycetomatis. To date, treatments fail to cure the infection and the available marketed drugs are expensive and toxic upon prolonged usage. Moreover, no vaccine was prepared yet against mycetoma. Aim: The aim of this study is to predict effective epitope-based vaccine against fructose-bisphosphate aldolase enzymes of M. mycetomatis using immunoinformatics approaches. Methods and materials: Fructose-bisphosphate aldolase of M. mycetomatis sequence was retrieved from NCBI. Different prediction tools were used to analyze the nominee’s epitopes in Immune Epitope Database for B-cell, T-cell MHC class II and class I. Then the proposed peptides were docked using Autodock 4.0 software program. Results and conclusions: The proposed and promising peptides KYLQ show a potent binding affinity to B-cell, FEYARKHAF with a very strong binding affinity to MHC I alleles and FFKEHGVPL that 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 FFKEHGVPL which is likely to be the first proposed epitope-based vaccine against fructose-bisphosphate aldolase of M. mycetomatis. This study recommends an in vivo assessment for the most promising peptides especially FFKEHGVPL.

scholarly journals Epitope - based peptide vaccine againstFructose-bisphosphate aldolase (FBA)ofMadurella mycetomatisusing immunoinformatics approaches

2018 ◽  
Author(s):  
Arwa A. Mohammed ◽  
Ayman M. H. ALnaby ◽  
Solima M. Sabeel ◽  
Fagr M. AbdElmarouf ◽  
Amina I. Dirar ◽  
...  
Keyword(s):  
B Cell ◽  
Binding Affinity ◽  
Mhc Class Ii ◽  
Bacterial Infections ◽  
Peptide Vaccine ◽  
Fructose Bisphosphate ◽  
Strong Binding ◽  
Fructose Bisphosphate Aldolase ◽  
Madurella Mycetomatis

AbstractBackgroundMycetoma is a distinct flesh eating and destructive neglected tropical disease. It is endemic in many tropical and subtropical countries. Mycetoma is caused by bacterial infections (actinomycetoma) such as Streptomyces somaliensis and Nocardiae or true fungi (eumycetoma) such as Madurella mycetomatis. Until date, treatments fail to cure the infection and the available marketed drugs are expensive and toxic upon prolonged usage. Moreover, no vaccine was prepared yet against mycetoma.The aimof this study is to predict effective epitope-based vaccine against fructose-bisphosphate aldolase enzymes of M. mycetomatis using immunoinformatics approaches.Methods and MaterialsFructose-bisphosphate aldolase ofMadurella mycetomatisSequence was retrieved from NCBI. Different prediction tools were used to analyze the nominee’s epitopes in Immune Epitope Database 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 KYLQ shows a potent binding affinity to B-cell, FEYARKHAF with a very strong binding affinity to MHC1 alleles and FFKEHGVPL that show a very strong binding affinity to MHC11and MHC1 alleles. This indicates a strong potential to formulate a new vaccine, especially with the peptide FFKEHGVPL which is likely to be the first proposed epitope-based vaccine against Fructose-bisphosphate aldolase of Madurella mycetomatis. This study recommends an in-vivo assessment for the most promising peptides especially FFKEHGVPL.

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

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.

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

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.

scholarly journals Epitope-Based Immunoinformatic Approach on Heat Shock 70 kDa Protein Complex of Cryptococcus neoformans var. grubii

2021 ◽  
Vol 2021 ◽  
pp. 1-16
Author(s):  
Reham M. Elhassan ◽  
Nagla M. Alsony ◽  
Khadeejah M. Othman ◽  
Duaa T. Izz-Aldin ◽  
Tamadour A. Alhaj ◽  
...  
Keyword(s):  
T Cell ◽  
Heat Shock ◽  
B Cell ◽  
Cryptococcus Neoformans ◽  
Binding Affinity ◽  
Peptide Vaccine ◽  
Population Coverage ◽  
Mhc I ◽  
Mhc Ii ◽  
Strong Binding

Introduction. Cryptococcosis is a ubiquitous opportunistic fungal disease caused by Cryptococcus neoformans var. grubii. It has high global morbidity and mortality among HIV patients and non-HIV carriers with 99% and 95%, respectively. Furthermore, the increasing prevalence of undesired toxicity profile of antifungal, multidrug-resistant organisms and the scarcity of FDA-authorized vaccines were the hallmark in the present days. This study was undertaken to design a reliable epitope-based peptide vaccine through targeting highly conserved immunodominant heat shock 70 kDa protein of Cryptococcus neoformans var. grubii that covers a considerable digit of the world population through implementing a computational vaccinology approach. Materials and Methods. A total of 38 sequences of Cryptococcus neoformans var. grubii’s heat shock 70 kDa protein were retrieved from the NCBI protein database. Different prediction tools were used to analyze the aforementioned protein at the Immune Epitope Database (IEDB) to discriminate the most promising T-cell and B-cell epitopes. The proposed T-cell epitopes were subjected to the population coverage analysis tool to compute the global population’s coverage. Finally, the T-cell projected epitopes were ranked based on their binding scores and modes using AutoDock Vina software. Results and Discussion. The epitopes (ANYVQASEK, QSEKPKNVNPVI, SEKPKNVNPVI, and EKPKNVNPVI) had shown very strong binding affinity and immunogenic properties to B-cell. (FTQLVAAYL, YVYDTRGKL) and (FFGGKVLNF, FINAQLVDV, and FDYALVQHF) exhibited a very strong binding affinity to MHC-I and MHC-II, respectively, with high population coverage for each, while FYRQGAFEL has shown promising results in terms of its binding profile to MHC-II and MHC-I alleles and good strength of binding when docked with HLA-C ∗ 12:03. In addition, there is massive global population coverage in the three coverage modes. Accordingly, our in silico vaccine is expected to be the future epitope-based peptide vaccine against Cryptococcus neoformans var. grubii that covers a significant figure of the entire world citizens.

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

2020 ◽  
Vol 14 (suppl 1) ◽  
pp. 999-1005 ◽  
Author(s):  
Viol Dhea Kharisma ◽  
Arif Nur Muhammad Ansori
Keyword(s):  
B Cell ◽  
Peptide Vaccine ◽  
Cell Epitope ◽  
Molecular Complexes ◽  
Cell Immune Response ◽  
Spike Glycoprotein ◽  
Conserved Region ◽  
Novel Coronavirus

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).

scholarly journals Translationally Controlled Tumor ProteinTCTPas Peptide Vaccine againstSchistosoma japonicum: an Immunoinformatics Approach

2018 ◽  
Author(s):  
Rayan A Abdalrahman ◽  
Shima S Ahmed ◽  
Mahmoud A Elnaeem ◽  
Marwa S Mohammed ◽  
Nawraz M Jammie ◽  
...  
Keyword(s):  
T Cell ◽  
B Cell ◽  
Schistosoma Japonicum ◽  
Peptide Vaccine ◽  
Cell Epitope ◽  
In Vivo Studies ◽  
Effective Vaccine ◽  
Good Prediction ◽  
Mhc I ◽  
Major Health Problem

AbstractSchistosoma japonicum is the most pathogenic causative form of schistosomiasis that causes a major health problem in its endemic countries. Until now, praziquantel is the only drug used to treat Schistosomiasis, but it does not prevent re-infection. So, repetition of the treatment is needed. Moreover, there is no effective vaccine against S. japonicum. Therefore, an urgent need for the development of vaccines is mandatory. This study aimed to analyze an immunogenic protein, Transitionally Controlled Tumor Protein (TCTP) using an immunoinformatics approach to design a universal peptide vaccine against Schistosoma japonicum. A set of 22 of TCTP sequences were retrieved from NCBI database. Conservancy of these sequences was tested and then conserved B cell and T cell epitopes were predicted using different tools available in IEBD. Epitopes having high scores in both B and T cell predicting tools were proposed. An epitope129YEHYI133was predicted as a most promising epitope with good prediction scores in surface accessibility and antigenicity. Besides that, epitopes129YEHYIGESM137and92YLKAIKERL100were predicted as the most promising epitopes concerning their binding to MHC I and MHC II allele respectively. The study revealed that our predicted epitopes could be used to develop an efficacious vaccine against Schistosoma japonicum in the future especially epitope YEHYIGESM as it is shared between MHC I and II alleles and overlapped with the most promising B cell epitope. Both in vitro and in vivo studies is recommended to confirm the efficacy of YEHYIGESM as a peptide vaccine.

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

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.

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.

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