scholarly journals Epitope-Based Peptide Vaccine Design Against Fructose Bisphosphate Aldolase of Candida Glabrata: An Immunomics Approach

2020 ◽  
Author(s):  
Elamin Elhasan LM ◽  
Mohamed B. Hassan ◽  
Reham M. Elhassan ◽  
Fatima A. Abdelrhman ◽  
Essam A. Salih ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Mhc Class Ii ◽  
In Silico ◽  
Candida Glabrata ◽  
Fungal Infections ◽  
Peptide Vaccine ◽  
Class Ii ◽  
Fructose Bisphosphate ◽  
Fructose Bisphosphate Aldolase ◽  
In Silico Tools

AbstractBackgroundCandida glabrata is a human opportunistic pathogen that can cause life-threatening systemic infections. Although, there are multiple effective vaccines against fungal infections, and some of these vaccines were engaged in different stages of clinical trials, none of them yet approved by (FDA).AimTo predict the most conserved and immunogenic B- and T-cell epitopes from the Fructose Bisphosphate aldolase (Fba1) protein of C. glabrata.Materials and Methods13 C. glabrata Fructose bisphosphate aldolase protein sequences (361amino acid) were retrieved from NCBI and several in silico tools presented in the IEDB server for predicting peptides were used and homology modeling and molecular docking were performed.ResultThe promising B-cell Epitopes were AYFKPH, VDKESLYTK, and HVDKESLYTK. While, promising peptides which have the high affinity to MHC I binding were: AVHEALAPI, KYFKRMAAM, QTSNGGAAY, RMAAMNQWL and YFKEHGEPL. Two peptides (LFSSHMLDL and YIRSIAPAY) were noted to have the highest affinity to MHC class II that interact with 9 MHC class II alleles. The molecular Docking revealed the epitopes QTSNGGAAY and LFSSHMLDL have the high binding energy to MHC moleculesConclusionThe epitope-based vaccines predicted by using immunoinformatics tools have remarkable advantages over the conventional vaccines that they are more specific, less time consuming, safe, less allergic and more antigenic. Further in vivo and in vitro experiments are needed to prove the effectiveness of the best candidates epitopes (QTSNGGAAY and LFSSHMLDL). To the best of our knowledge, this is the first study that has predicted B- and T-cells epitopes from Fba1 protein by using in silico tools in order to design an effective epitope-based vaccine against C. galabrata.

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 Bombali Ebolavirus Viral Protein 40: An Immunoinformatics Combined with Molecular Docking Studies

2020 ◽  
Author(s):  
Mujahed I. Mustafa ◽  
Shaza W. Shantier ◽  
Miyssa I. Abdelmageed ◽  
Abdelrafie M. Makhawi
Keyword(s):  
Molecular Docking ◽  
T Cell ◽  
Mhc Class Ii ◽  
Peptide Vaccine ◽  
Class Ii ◽  
Population Coverage ◽  
Antigenic Protein ◽  
Wide Range ◽  
The World ◽  
Hla Molecules

AbstractBackgroundBombali Ebolavirus is RNA viruses belong to the Filoviridae family. They are causing lethal hemorrhagic fever with high mortality rate. Despite having available molecular knowledge of this virus, no approved vaccine or antiviral drugs have been developed yet for the eradication of Bombali Ebolavirus infections in humans.Objectivethe present study described a multi epitope-based peptide vaccine against Bombali Ebolavirus matrix protein VP40, using several immunoinformatics tools.Materials and MethodsThe six strains of Ebolavirus were retrieved from NCBI and Uniprot databases and submitted to VaxiJen to identify the most antigenic protein among all. Then PSIPRED, SOPMA, QMEAN, and PROCHECK tools were used to check the protein quality. T-cell prediction, population coverage, and molecular docking analysis were achieved to select peptides containing multiple Bombali VP40 epitopes showing interaction with multiple HLA molecules for expected immune response across the world.ResultBombali Ebola (YP_009513276.1) was found to be the most antigenic protein among all. Which it has been used in all required analysis. For T cell three epitopes showed high affinity to MHC class I (YSFDSTTAA, VQLPQYFTF, and MVNVISGPK) and high population coverage against Africa and the world. Furthermore in MHC class II, six promising epitopes that associated with most common MHC class II alleles.ConclusionThe above result conclude that, these peptides capable of provoking T-cell response and being interacted with a wide range of HLA molecules have a strong potential to be a vaccine against Bombali Ebolavirus.

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

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.

scholarly journals Multi Epitope Vaccine Prediction Against Aichi Virus using Immunoinformatic Approach

2019 ◽  
Author(s):  
Asma Ali Hassan Ali ◽  
Sahar Abdeen Abdalla Mohamed ◽  
Marwa Abdulrahman Omer Musa ◽  
Amani Faisal Bushra ELtahier ◽  
Walaa Mohammed Alsamani Abdelrahman Ali ◽  
...  
Keyword(s):  
T Cell ◽  
Mhc Class Ii ◽  
Peptide Vaccine ◽  
Class Ii ◽  
Aichi Virus ◽  
World Population ◽  
High Coverage ◽  
Worldwide Population ◽  
Wide Range ◽  
Severe Gastroenteritis

AbstractAichi virus, AiV is single stranded negative sense RNA genome belonging to the genus Kobuviru, a family of Picornaviridae that causes severe gastroenteritis. There is no treatment or vaccine for it, thus the aim of this study is to design a peptide vaccine using immunoinformatic approaches to analyze the viral Protein VP1 of AiV-1 strain, to determine the conserved region which is further studied to predict all possible epitopes that can be used as a peptide vaccine. A total of 38 Aichi virus VP1 retrieved from NCBI database were aligned to determine the conservancy and to predict the epitopes using IEDB analysis resource. Three epitopes predicted as a peptide vaccine for B cell was (PLPPDT, PPLPTP, and LPPLPTP). For T cell, two epitopes showed high affinity to MHC class I (FSIPYTSPL and TMVSFSIPY) and high coverage against the whole world population. Also, in MHC class II, three epitopes that interact with most frequent MHC class II alleles (FTYIAADLR and YMAEVPVSA) with high coverage in the whole world population. For both MHCI and MHCII the T-cell peptide with the strongest affinity to the worldwide population was FSIPYTSPL.Peptide vaccine against AiV is powerfully displace the normal produced vaccines based on the experimental biochemistry tools, as it designed to handle with a wide range of mutated strains, which will effectively minimize the frequent outbreaks and their massive economical wastage consequences.

Novel epitope based peptides for vaccine against SARS-CoV-2 virus: immunoinformatics with docking approach

2020 ◽  
Vol 8 (7) ◽  
pp. 2385 ◽  
Author(s):  
Jesvin Bency B. ◽  
Mary Helen P. A.
Keyword(s):  
B Cell ◽  
Mhc Class I ◽  
Mhc Class Ii ◽  
Peptide Vaccine ◽  
Human Leukocyte ◽  
Respiratory Illness ◽  
Class Ii ◽  
Class I ◽  
T Cell Epitopes ◽  
B Cell Epitopes

Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative viral strain for the contagious pandemic respiratory illness in humans which is a public health emergency of international concern. There is a desperate need for vaccines and antiviral strategies to combat the rapid spread of SARS-CoV-2 infection.Methods: The present study based on computational methods has identified novel conserved cytotoxic T-lymphocyte epitopes as well as linear and discontinuous B-cell epitopes on the SARS-CoV-2 spike (S) protein. The predicted MHC class I and class II binding peptides were further checked for their antigenic scores, allergenicity, toxicity, digesting enzymes and mutation.Results: A total of fourteen linear B-cell epitopes where GQSKRVDFC displayed the highest antigenicity-score and sixteen highly antigenic 100% conserved T-cell epitopes including the most potential vaccine candidates MHC class-I peptide KIADYNYKL and MHC class-II peptide VVFLHVTYV were identified. Furthermore, the potential peptide QGFSALEPL with high antigenicity score attached to larger number of human leukocyte antigen alleles. Docking analyses of the allele HLA-B*5201 predicted to be immunogenic to several of the selected epitopes revealed that the peptides engaged in strong binding with the HLA-B*5201 allele.Conclusions: Collectively, this research provides novel candidates for epitope-based peptide vaccine design against SARS-CoV-2 infection.

MHC Class II Binding Prediction by Molecular Docking

2011 ◽  
Vol 30 (4) ◽  
pp. 368-375 ◽  
Author(s):  
M. Atanasova ◽  
I. Dimitrov ◽  
D. R. Flower ◽  
I. Doytchinova
Keyword(s):  
Molecular Docking ◽  
Mhc Class Ii ◽  
Class Ii ◽  
Binding Prediction
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