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

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.

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Design of an epitope-based peptide vaccine againstCryptococcus neoformans

10.1101/434779 ◽

2018 ◽

Cited By ~ 2

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.

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

10.1101/441881 ◽

2018 ◽

Cited By ~ 4

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.

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

Journal of Immunology Research ◽

10.1155/2021/9921620 ◽

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.

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Design of Epitope-Based Peptide Vaccine against Pseudomonas aeruginosa Fructose Bisphosphate Aldolase Protein Using Immunoinformatics

Journal of Immunology Research ◽

10.1155/2020/9475058 ◽

2020 ◽

Vol 2020 ◽

pp. 1-11

Author(s):

Mustafa Elhag ◽

Ruaa Mohamed Alaagib ◽

Nagla Mohamed Ahmed ◽

Mustafa Abubaker ◽

Esraa Musa Haroun ◽

...

Keyword(s):

Pseudomonas Aeruginosa ◽

Peptide Vaccine ◽

Multidrug Resistant ◽

Fructose Bisphosphate ◽

Mhc I ◽

Mhc Ii ◽

Fructose Bisphosphate Aldolase ◽

Hospital Acquired

Pseudomonas aeruginosa is a common pathogen that is responsible for serious hospital-acquired infections, ventilator-associated pneumonia, and various sepsis syndromes. Also, it is a multidrug-resistant pathogen recognized for its ubiquity and its intrinsically advanced antibiotic-resistant mechanisms. It usually affects immunocompromised individuals but can also infect immunocompetent individuals. There is no vaccine against it available till now. This study predicts an effective epitope-based vaccine against fructose bisphosphate aldolase (FBA) of Pseudomonas aeruginosa using immunoinformatics tools. The protein sequences were obtained from NCBI, and prediction tests were undertaken to analyze possible epitopes for B and T cells. Three B cell epitopes passed the antigenicity, accessibility, and hydrophilicity tests. Six MHC I epitopes were found to be promising, while four MHC II epitopes were found promising from the result set. Nineteen epitopes were shared between MHC I and II results. For the population coverage, the epitopes covered 95.62% worldwide excluding certain MHC II alleles. We recommend in vivo and in vitro studies to prove its effectiveness.

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

10.1101/2021.06.05.447201 ◽

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.

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Development of Brucellosis Vaccine Based on Determinant Antigenic of Outer Membrane Protein (OMP) 36 kDa From Brucella abortus Local Isolate

International Journal of Pharmaceutical and Clinical Research ◽

10.25258/ijpcr.v9i3.8318 ◽

2017 ◽

Vol 9 (3) ◽

Author(s):

Aulanni’am Aulanni’am ◽

Wiwiek Tyasningsih ◽

Dyah Kinasih Wuragil ◽

Fedik Abdul Rantam

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Membrane Protein ◽

Outer Membrane Protein ◽

Brucella Abortus ◽

Epitope Prediction ◽

Mhc I ◽

Mhc Ii ◽

The Past ◽

Local Isolate

Brucellosis is a disease that can be prevented through vaccination. Yet, the effectiveness of the vaccination to fight this disease is considered weak. Fortunately, attempts to modify brucellosis vaccine is still keep going. Some brucellosis vaccines have been found and developed in the past time such as the vaccine B.abortus strain 19-BA and 104M which was made from weakened microbes which had been widely used in Uni Soviet and China. The other brucellosis vaccine that were used in the past were the phenolinsoluble peptidoglycan vaccine which was made in France and polysaccharideprotein vaccine which was used in Russia. This research attempted to see the determinant of antigenic Outer Membrane Protein (OM) 36 kDa Brucella abortus local isolation which has immunogenic character to be developed as an advanced brucellosis vaccine. The method used in this research was the Omp2 gene of Brucella abortus of local isolate employed the PCR technique. The result of the PCR was then sequenced to analyze the determinant antigenic and the bounding prediction of either the T cell or the B cell which were responsible for immune response. The result of this study showed that the gen Omp2 which encoded the OMP 36 kDa Brucella abortus of local isolation with primary JPF 5’ GCG CTC AGG CTG CCG ACG CAA 3’ and JPR 5’ CAT TGC GGT CGG TAC CGG AG 3’ targeted the gene 162 bp, was then translated into amino acids to be later undergo the in silico test using Kolaskar and Tongaonkar Antigenicity Prediction method. The epitope prediction resulted were MSRVCDAYGAGYFYI and TETCLRVHGYVRYD. The result of the epitope prediction of MSRVCDAYGAGYFYI showed that there was a bond with MHC I in YGAGYFYI of the 8th amino acid series to the 15th series, while the epitope prediction of TETCLRVHGYVRYD showed that there was a bond to the ETCLRVHGY of the series of amino acids number 2 to 10. Bond with MHC II existed in the amino acid series of MSRVCDAYGAGYFYI, while the bond with the B cells existed in BCSAYGA and CLRVHG amino acid series. This research has been successful in predicting the epitope of the OMP 36 kDa Brucella abortus of local isolate which had immunogenic characteristic for its ability to bond with the MHC I, MHC II and B cells.

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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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Transcriptome analysis of Brucella abortus S19∆per immunized mouse spleen revealed activation of MHC-I and MHC-II pathways

Access Microbiology ◽

10.1099/acmi.0.000082 ◽

2020 ◽

Vol 2 (1) ◽

Author(s):

Khushal Singh Solanki ◽

Ravi Kumar Gandham ◽

Prasad Thomas ◽

Pallab Chaudhuri

Keyword(s):

Transcriptome Analysis ◽

Brucella Abortus ◽

Mouse Spleen ◽

Mhc I ◽

Mhc Ii

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In Silico Epitope-Based Peptide Vaccine Design against Invasive Non Typhoidal Salmonella (iNTS) Through Immunoinformatic Approaches

10.20944/preprints202002.0383.v1 ◽

2020 ◽

Author(s):

Md. Chayan Ali ◽

Sultana Israt Jahan ◽

Mst. Shanzeda Khatun ◽

Raju Das ◽

Md Mafizur Rahman ◽

...

Keyword(s):

Membrane Proteins ◽

B Cell ◽

Outer Membrane ◽

Vaccine Candidate ◽

Binding Free Energy ◽

Outer Membrane Proteins ◽

Peptide Vaccine ◽

Dynamics Simulation ◽

Mhc I ◽

B Cell Epitopes

Salmonella, especially invasive non-typhoidal Salmonella (iNTS) are responsible for developing various invasive diseases, and possess higher mortality rate, due to their higher antibiotic resistance profile than the other bacteria. Therefore, the present study was concerned to develop epitope based peptide vaccine against iNTS species as a successive and substitute protective measures. The study considered comprehensive Immunoinformatic approaches, followed by molecular docking and molecular dynamics simulation to predict the efficient vaccine candidate T cell and B cell epitopes, based on the outer membrane proteins. The study identified two best epitopes YGIFAITAL and KVLYGIFAI from total iNTS outer membrane proteins, which showed higher immunity, non-allergenicity, non-toxicity and also showed higher conservancy and population coverage values. Both epitopes showed higher binding affinity and stability towards HLA-C* 03:03. The MM-PBSA binding free energy showed the YGIFAITAL epitope binds more tightly with both MHC-I and MHC-II molecules. The total contact, H-bond analysis and RMSF results also validate the efficiency of these epitopes as vaccine candidate. The projected B cell epitopes AAPVQVGEAAGS, TGGGDGSNT and TGGGDGSNTGTTTT showed higher antigenicity. Overall, the study concluded that these epitopes can be considered as the potential vaccine candidate to make a successive vaccine against iNTS species. However, this result further needs to be validate by wet lab research to make successive vaccine with these projected epitopes.

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