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

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

10.1101/2021.12.27.474190 ◽

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.

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

Bioinformatics and Biology Insights ◽

10.1177/1177932218809703 ◽

2018 ◽

Vol 12 ◽

pp. 117793221880970 ◽

Cited By ~ 4

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.

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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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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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A Multiple Peptides Vaccine against nCOVID-19 Designed from the Nucleocapsid phosphoprotein (N) and Spike Glycoprotein (S) via the Immunoinformatics Approach

10.1101/2020.05.20.106351 ◽

2020 ◽

Author(s):

Sahar Obi Abd Albagi ◽

Mosab Yahya Al-Nour ◽

Mustafa Elhag ◽

Asaad Tageldein Idris Abdelihalim ◽

Esraa Musa Haroun ◽

...

Keyword(s):

Molecular Docking ◽

Binding Affinity ◽

Effective Vaccine ◽

Spike Glycoprotein ◽

Mhc I ◽

Immunological Responses ◽

Mhc Ii ◽

Immune Epitope ◽

Hla Dqa1 ◽

Immune Epitope Database

AbstractDue to the current COVID-19 pandemic, the rapid discovery of a safe and effective vaccine is an essential issue, consequently, this study aims to predict potential COVID-19 peptide-based vaccine utilizing the Nucleocapsid phosphoprotein (N) and Spike Glycoprotein (S) via the Immunoinformatics approach. To achieve this goal, several Immune Epitope Database (IEDB) tools, molecular docking, and safety prediction servers were used. According to the results, The Spike peptide peptides SQCVNLTTRTQLPPAYTNSFTRGVY is predicted to have the highest binding affinity to the B-Cells. The Spike peptide FTISVTTEI has the highest binding affinity to the MHC I HLA-B1503 allele. The Nucleocapsid peptides KTFPPTEPK and RWYFYYLGTGPEAGL have the highest binding affinity to the MHC I HLA-A0202 allele and the three MHC II alleles HLA-DPA1*01:03/DPB1*02:01, HLA-DQA1*01:02/DQB1- *06:02, HLA-DRB1, respectively. Furthermore, those peptides were predicted as non-toxic and non-allergen. Therefore, the combination of those peptides is predicted to stimulate better immunological responses with respectable safety.

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

10.1101/466847 ◽

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.

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Attenuated Subcomponent Vaccine Design Targeting the SARS-CoV-2 Nucleocapsid Phosphoprotein RNA Binding Domain: In silico analysis

10.1101/2020.06.30.176537 ◽

2020 ◽

Author(s):

Onyeka S. Chukwudozie ◽

Rebecca C. Chukwuanukwu ◽

Iroanya O. Onyekachi ◽

Eze M. Daniel ◽

Duru C. Vincent ◽

...

Keyword(s):

T Cell ◽

In Silico ◽

Rna Binding ◽

Peptide Vaccine ◽

In Silico Analysis ◽

Dynamics Simulation ◽

Effective Vaccine ◽

Translation Efficiency ◽

T Cell Epitopes ◽

Mhc I

ABSTRACTThe novel coronavirus disease (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has previously never been identified with humans, thereby creating devastation in public health. The need for an effective vaccine to curb this pandemic cannot be overemphasized. In view of this, we, therefore, designed a subcomponent antigenic peptide vaccine targeting the N-terminal (NT) and C-terminal (CT) RNA binding domains of nucleocapsid protein that aid in viral replication. Promising antigenic B-cells and T cell epitopes were predicted using computational pipelines. The peptides “RIRGGDGKMKDL” and “AFGRRGPEQTQGNFG” were the B cell linear epitopes with good antigenic index and non-allergenic property. Two CD8+ and Three CD4+ T-cell epitopes were also selected considering their safe immunogenic profiling such as allergenicity, antigen level conservancy, antigenicity, peptide toxicity, and putative restrictions to a number of MHC-I and II alleles. With these selected epitopes, a non-allergenic chimeric peptide vaccine incapable of inducing a Type II hypersensitivity reaction was constructed. The molecular interaction between the toll-like receptor-5 (TLR5) which was triggered by the vaccine was analyzed by molecular docking and scrutinized using dynamics simulation. Finally, in silico cloning was performed to ensure the expression and translation efficiency of the vaccine, utilizing pET-28a vector. This research, therefore, provides a guide for experimental investigation and validation.

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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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Designing a new multi epitope-based vaccine against COVID-19 disease: an immunoinformatic study based on reverse vaccinology approach

10.21203/rs.3.rs-206270/v1 ◽

2021 ◽

Author(s):

Afshin Samimi Nemati ◽

Majid Tafrihi ◽

Fatemeh Sheikhi ◽

Abolfazl Rostamian Tabari ◽

Amirhossein Haditabar

Keyword(s):

Molecular Docking ◽

Docking Studies ◽

High Rate ◽

Effective Vaccine ◽

Epitope Vaccine ◽

Mhc I ◽

Mhc Ii ◽

Refinement Process

Abstract Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has currently caused a significant pandemic among worldwide populations. The transmission speed and the high rate of mortality caused by the disease necessitate studies for the rapid designing and effective vaccine production. The purpose of this study is to predict and design a novel multi-epitope vaccine against the SARS-CoV-2 virus using bioinformatics approaches. Coronavirus envelope proteins, ORF7b, ORF8, ORF10, and NSP9 were selected as targets for epitope mapping using IEDB and BepiPred 2.0 Servers. Also, molecular docking studies were performed to determine the candidate vaccine's affinity to TLR3, TLR4, MHC I, and MHC II molecules. Thirteen epitopes were selected to construct the multi-epitope vaccine. We found that the constructed peptide has valuable antigenicity, stability, and appropriate half-life. The Ramachandran plot approved the quality of the predicted model after the refinement process. Molecular docking investigations revealed that antibody-mode in the Cluspro 2.0 server showed the lowest binding energy for MHCI, MHCII, TLR3, and TLR4. This study confirmed that the designed vaccine has a good antigenicity and stability and could be a proper vaccine candidate against the COVID-19 infectious disease though, in vitro and in vivo experiments are necessary to complete and confirm our results.

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