scholarly journals Epitope-Based Peptide prediction of vaccine against European bat lyssaviruses type 2 Glycoprotein G with Immunoinformatic Approach

2021 ◽  
Author(s):  
Manal Abdalla Gumaa ◽  
Abeer Babiker Idris ◽  
Mohamed Hasan Bashair ◽  
Enas dk Dawoud ◽  
Lina Mohamedelamin Elhasan ◽  
...  
Keyword(s):  
Immune Response ◽  
B Cell ◽  
Peptide Vaccine ◽  
European Countries ◽  
World Population ◽  
Population Coverage ◽  
Mhc Ii ◽  
Glycoprotein G ◽  
Peptide Prediction

Objective: European bat lyssaviruses (EBLV) type 2 is present in many European countries. Infection is usually seen in bats, the primary reservoirs of the viruses. Human deaths have been documented within few days following bat exposures. So, it is very useful to design an insilco peptide vaccine for European bat lyssaviruses type 2 virus using glycoprotein G as an immunogen to stimulate protective immune response. Results: B cell tests were conducted for Bepipred with 15 conserved epitopes, Emini surface accessibility prediction with 7 conserved epitopes in the surface and Kolaskar and Tongaonkar antigenicity tested with three conserved epitopes being antigenic. 357 conserved epitopes were predicted to interact with different MHC-1 alleles with (IC50) ≤500 while 282 conserved epitopes found to interact with MHC-II alleles with IC50≤ 1000. Among all tested epitopes for world population coverage the epitope VFSYMELKV binding to MHC11 alleles was 97.94% and it found to bind 10 different alleles that indicate strong potential to formulate peptide vaccine for lyssaviruses type 2 virus. To the best of our knowledge this is the first study to propose peptide vaccine for European bat lyssavirus type 2.

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.

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 Vaccinomics Approach for Designing Potential Peptide Vaccine by TargetingShigellaspp. Serine Protease Autotransporter Subfamily Protein SigA

2017 ◽  
Vol 2017 ◽  
pp. 1-14 ◽  
Author(s):  
Arafat Rahman Oany ◽  
Tahmina Pervin ◽  
Mamun Mia ◽  
Motaher Hossain ◽  
Mohammad Shahnaij ◽  
...  
Keyword(s):  
Serine Protease ◽  
Bacillary Dysentery ◽  
Peptide Vaccine ◽  
Human Leukocyte ◽  
World Population ◽  
Potential Core ◽  
Antigenic Protein ◽  
Leukocyte Antigen

Shigellosis, a bacillary dysentery, is closely associated with diarrhoea in human and causes infection of 165 million people worldwide per year. Casein-degrading serine protease autotransporter of enterobacteriaceae (SPATE) subfamily protein SigA, an outer membrane protein, exerts both cytopathic and enterotoxic effects especially cytopathic to human epithelial cell type-2 (HEp-2) and is shown to be highly immunogenic. In the present study, we have tried to impose the vaccinomics approach for designing a common peptide vaccine candidate against the immunogenic SigA ofShigellaspp. At first, 44 SigA proteins from different variants ofS. flexneri,S. dysenteriae,S. boydii, andS. sonneiwere assessed to find the most antigenic protein. We retrieved 12 peptides based on the highest score for human leukocyte antigen (HLA) supertypes analysed by NetCTL. Initially, these peptides were assessed for the affinity with MHC class I and class II alleles, and four potential core epitopes VTARAGLGY, FHTVTVNTL, HTTWTLTGY, and IELAGTLTL were selected. From these, FHTVTVNTL and IELAGTLTL peptides were shown to have 100% conservancy. Finally, IELAGTLTL was shown to have the highest population coverage (83.86%) among the whole world population. In vivo study of the proposed epitope might contribute to the development of functional and unique widespread vaccine, which might be an operative alleyway to thwart dysentery from the world.

scholarly journals Immunoinformatics Prediction of Epitope Based Peptide Vaccine AgainstMadurella mycetomatis Translationally Controlled Tumor Protein

2018 ◽  
Author(s):  
Samira Munir Bolis ◽  
Walaa Abdullah Omer ◽  
Mohamed Anwar Abdelhamed ◽  
Masajed Abdelmagid Shambal ◽  
Esameldeen Ahmed Adam ◽  
...  
Keyword(s):  
Homology Modelling ◽  
Peptide Vaccine ◽  
Effective Vaccine ◽  
Population Coverage ◽  
Mhc I ◽  
Translationally Controlled Tumor Protein ◽  
Mhc Ii ◽  
Coverage Analysis ◽  
Madurella Mycetomatis ◽  
The Common

AbstractBackgroundMadurella. mycetomatisis most common causative agent of mycetoma in Sudan and worldwide. No vaccines are available till now so design of effective vaccine is essential as protection tool. Peptide vaccine can overcome the common side effects of the conventional vaccines. The aim of this study was to design peptide based vaccine forM.Mycetomatis Translationally Controlled Tumor Protein (TCTP)using immunoinformatics tools.Materials and methodsTCTPsequences were retrieved from NCBI and then processed using BioEdit program to determine conserved regions and different immunoinformatics tools from IEDB. Population coverage analysis was performed for the most promising epitopes. Homology modelling was performed to show their structural positions inTCTP.Protein analysis was done using Expasy (ProtParamsotware).Results and conclusionFour epitopes passed the Bepipred, Emini, Kolaskar and Tongaonkar tools. 111 epitopes were predicted to interact with MHCI alleles with IC50 < 500 nM, three of them were most promising. 274 predicted epitopes were interacted with MHCII alleles with IC50 < 100 nM, four of them were most promising. The epitope (YMKSVKKAL) was the most promising one concerning its binding with MHCI alleles, while (FRLQSTSFD) was the most promising for MHC II. The epitope (YLKAYMKSV) is shared betweenMHC I and II. For the population coverage ofM. Mycetomatis TCTPvaccine Sudan (90.39%) had the highest percentage for MHC I. This is the first computational vaccinology study conducted in mycetoma caused byM. MycetomatisusingTCTP.

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 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.

Role of different B-cell subsets in the specific and polyclonal immune response to T-independent antigens type 2

2003 ◽  
Vol 88 (1) ◽  
pp. 37-42 ◽  
Author(s):  
E.V. Sidorova ◽  
Lu Li-Sheng ◽  
B. Devlin ◽  
I. Chernishova ◽  
M. Gavrilova
Keyword(s):  
Immune Response ◽  
B Cell ◽  
B Cell Subsets

scholarly journals Sub-genomic analysis of Chikungunya virus E2 mutations in Pakistani isolates potentially modulating B-cell & T-Cell immune response

2020 ◽  
Vol 37 (1) ◽  
Author(s):  
Bilal Ahmed Khan ◽  
Saif Ullah ◽  
Amanullah Lail ◽  
Saeed Khan
Keyword(s):  
Immune Response ◽  
T Cell ◽  
B Cell ◽  
Chikungunya Virus ◽  
Vaccine Development ◽  
Epitope Prediction ◽  
Genomic Analysis ◽  
Cell Immune Response ◽  
Population Coverage ◽  
Cross Sectional

Background & Objectives: The Chikungunya virus (CHIKV) transmitted to the humans through Aedes species of the mosquitoes. In December 2016, a severe outbreak reported from Pakistan. However, there is no vaccine or anti-viral treatment currently available so host immune response against CHIKV gained significant interest. Therefore, this study was conducted to identify the mutations in CHIKV E2 region of currently circulating Pakistani strains & determine their potential immunogenicity in Pakistani population. Methods: It was a cross sectional study in which a total of 60 CHIKV PCR positive samples were collected from Molecular Department of Pathology, Dow University of Health Sciences (DUHS), Karachi during November 2017 to February 2018. CHIKV E2 gene was amplified by PCR & sequenced. Sequences were analyzed by using bioinformatic tools followed by epitope prediction in E2 sequences by In-silico immunoinformatic approach. Results: Several single nucleotide variations (SNVs) were identified in Pakistani isolates with six novel mutations in E2 sequences. Immunoinformatic analyses showed more proteasomal sites, CTL & B-Cell epitopes in Pakistani strains with respect to S27 prototype with 69.4% population coverage against these epitopes in Pakistan. The study also identified key mutations responsible for generation of unique epitopes and HLA restriction in Pakistani isolates. The strain specific mutations revealed the current outbreak was caused by ESCA.IOL lineage of CHIKV. Conclusion: The evolution of E2 protein in Pakistani strains has increased its immunogenicity in comparison to ancestral s27 strain. The identification of most immunogenic and conserved epitopes with high population coverage has high potential to be used in vaccine development against these local strains. doi: https://doi.org/10.12669/pjms.37.1.3236 How to cite this:Khan BA, Saifullah, Lail A, Khan S. Sub-genomic analysis of Chikungunya virus E2 mutations in Pakistani isolates potentially modulating B-cell & T-Cell immune response. Pak J Med Sci. 2021;37(1):93-98. doi: https://doi.org/10.12669/pjms.37.1.3236 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

scholarly journals Design of Epitope Based Peptide Vaccine against Brucella Abortus OmpW Family Protein using Immunoinformatics

2021 ◽  
Author(s):  
Mustafa Elhag ◽  
Abdelrahman Hamza Abdelmoneim ◽  
Anfal Osama Sati ◽  
Moaaz Mohammed Saadaldin ◽  
Nagla Mohammad Ahmad ◽  
...  
Keyword(s):  
Brucella Abortus ◽  
Peptide Vaccine ◽  
Reproductive Organs ◽  
Population Coverage ◽  
Mhc I ◽  
B Cell Epitopes ◽  
Mhc Ii ◽  
Family Protein ◽  
Initial Interaction ◽  
Chronic Disorders

Brucella abortus is a small aerobic, non-spore-forming, non-motile intracellular coccobacilli localized in the reproductive organs of host animals and causes acute or chronic disorders. It infects approximately 200 cases per 100,000 of the population and has become endemic in many countries. OmpW family protein is an outer membrane protein involved in the initial interaction between the pathogen and its host. This study predicts an effective epitope-based vaccine against OmpW family protein of Brucella abortus using immunoinformatics tools. Sequences were obtained from NCBI and prediction tests were accomplished to analyze possible epitopes for B and T cells. Seven B cell epitopes passed the antigenicity, accessibility and hydrophilicity tests. Forty-three MHC I epitopes were the most promising, while 438 from MHC II. For the population coverage, the epitopes covered 99.97% of the alleles worldwide excluding certain MHC II alleles. We recommend invivo and invitro studies to prove its effectiveness.

scholarly journals ROLE OF DIFFERENT B CELL SUBPOPULATIONS IN IMMUNE RESPONSE TO T-INDEPENDENT TYPE 2 ANTIGENS

2014 ◽  
Vol 9 (1) ◽  
pp. 39 ◽  
Author(s):  
M. V. Gavrilova ◽  
I. N. Chernyshova ◽  
E. V. Sidorova
Keyword(s):  
Immune Response ◽  
B Cell ◽  
Cell Subpopulations
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