Immunoinformatics Prediction of an Epitope Based Peptide Vaccine for Neisseria Gonorrhea Dihydrolipoamide Acetyltransferase Protein

Sexually transmitted infections (STIs) such as Gonorrhea is associated with serious morbidity and mortality rates in the world considering the multiple virulence factors possessed. The disease is manifested as salpingitis, pelvic inflammatory disease (PID), and bacteremia and is controlled by macrophages, dendritic cells, neutrophils, T cells, epithelial cells and cytokines. Dihydroliponamide acetyltransferase, a component of the mitochondrial pyruvate complex can be used as immunogenic target. Recent changes in the strain allowed the bacteria to acquire resistance against antibiotics.Vaccination remains an alternative to prevention against the disease. This study predicts an effective epitope-based vaccine against dihydrolipoamide acetyltransferase of Neisseria Gonorrhea using immunoinformatics approaches. Sequences retrieved from NCBI were passed on several prediction tests to analyze for possible B-cell, T-cell MHC class I epitopes and class II. Two epitopes showed high binding affinity for B-cells, while thirteen epitopes showed high binding affinity for MHCI and forty-five for MHCII. A population coverage of 100% for combined MHC I and II dictates the huge number of individuals who will benefit from formulating the vaccine. We recommend invivo and invitro studies to prove our prediction results.

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Immunoinformatics Prediction of Epitope Based Peptide Vaccine Against Listeria Monocytogenes Fructose Bisphosphate Aldolase Protein

10.1101/649111 ◽

2019 ◽

Cited By ~ 1

Author(s):

Mustafa Elhag ◽

Mustafa Abubaker ◽

Nagla Mohammad Ahmad ◽

Esraa Musa Haroon ◽

Ruaa Mohamed Alaagib ◽

...

Keyword(s):

Listeria Monocytogenes ◽

Binding Affinity ◽

3D Structure ◽

Peptide Vaccine ◽

Preventive Measure ◽

Fructose Bisphosphate ◽

High Binding ◽

Life Threatening ◽

Fructose 1,6 Bisphosphate ◽

High Binding Affinity

AbstractListeria Monocytogenesrepresents an important food-borne pathogen worldwide that can cause life-threatening listeriosis disease especially in pregnant women, fetuses, elderly people, and immuno-compromised individuals with high mortality rates. Moreover, no vaccine against it exists. This study predicts an effective epitope-based vaccine against Fructose 1,6 Bisphosphate Aldolase (FBA) enzyme of Listeria Monocytogenes using immunoinformatics approaches. The sequences were retrieved from NCBI and several prediction tests were conducted to analyze possible epitopes for B-cell, T-cell MHC class I and II. 3D structure of the promising epitopes was obtained. Two epitopes showed high binding affinity for B-cells, while four epitopes showed high binding affinity for MHCI and MHCII. The results were promising to formulate a vaccine with more than 98% population coverage. We hope that these promising epitopes serves as a preventive measure for the disease in the future and recommend invivo and invitro studies.

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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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Immunoinformatics Prediction of Epitope Based Peptide Vaccine Against Schistosoma Mansoni Fructose Bisphosphate Aldolase Protein

10.1101/755959 ◽

2019 ◽

Cited By ~ 1

Author(s):

Mustafa Elhag ◽

Ruaa Mohamed Alaagib ◽

Esraa Musa Haroun ◽

Nagla Mohamed Ahmed ◽

Sahar Obi Abd Albagi ◽

...

Keyword(s):

Schistosoma Mansoni ◽

Binding Affinity ◽

Tertiary Structure ◽

Peptide Vaccine ◽

Preventive Measure ◽

Fructose Bisphosphate ◽

High Binding ◽

Fructose Bisphosphate Aldolase ◽

Fructose 1,6 Bisphosphate ◽

High Binding Affinity

AbstractSchistosoma Mansoni represents an important tropical disease that can cause schistosomiasis mostly in Africa and Middle East with high mortality rates. Moreover, no vaccine against it exists. This study predicts an effective epitope-based vaccine against Fructose 1,6 Bisphosphate Aldolase (FBA) enzyme of Schistosoma Mansoni using immunoinformatics approaches. FBA is important for production of energy required for different schistosome activities and survival. The sequences were retrieved from NCBI and several prediction tests were conducted to analyze possible epitopes for B-cell, T-cell MHC class I and II. Tertiary structure of the most promising epitopes was obtained. Two epitopes showed high binding affinity for B-cells, while four epitopes showed high binding affinity for MHCI and MHCII. The results were promising to formulate a vaccine with more than 99.5% population coverage. We hope that these promising epitopes serves as a preventive measure for the disease in the future and recommend invivo and invitro studies.

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Faculty Opinions recommendation of Energetically important C-H···F-C pseudohydrogen bonding in water: evidence and application to rational design of oligonucleotides with high binding affinity.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.7475956.7770054 ◽

2011 ◽

Author(s):

Martin Egli

Keyword(s):

Binding Affinity ◽

Rational Design ◽

High Binding ◽

High Binding Affinity

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Herb-target virtual screening and network pharmacology for prediction of molecular mechanism of Danggui Beimu Kushen Wan for prostate cancer

Scientific Reports ◽

10.1038/s41598-021-86141-1 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Hong Li ◽

Andrew Hung ◽

Angela Wei Hong Yang

Keyword(s):

Prostate Cancer ◽

Binding Affinity ◽

Molecular Mechanisms ◽

Biological Activities ◽

Tight Binding ◽

Experimental Studies ◽

Network Pharmacology ◽

High Morbidity ◽

High Binding ◽

High Binding Affinity

AbstractProstate cancer (PCa) is a cancer that occurs in the prostate with high morbidity and mortality. Danggui Beimu Kushen Wan (DBKW) is a classic formula for patients with difficult urination including PCa. This study aimed to investigate the molecular mechanisms of DBKW for PCa. We obtained DBKW compounds from our previous reviews. We identified potential targets for PCa from literature search, currently approved drugs and Open Targets database and filtered them by protein–protein interaction network analysis. We selected 26 targets to predict three cancer-related pathways. A total of 621 compounds were screened via molecular docking using PyRx and AutoDock Vina against 21 targets for PCa, producing 13041 docking results. The binding patterns and positions showed that a relatively small number of tight-binding compounds from DBKW were predicted to interact strongly and selectively with three targets. The top five high-binding-affinity compounds were selected to generate a network, indicating that compounds from all three herbs had high binding affinity against the 21 targets and may have potential biological activities with the targets. DBKW contains multi-targeting agents that could act on more than one pathway of PCa simultaneously. Further studies could focus on validating the computational results via experimental studies.

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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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ChemInform Abstract: (15R)-16-m-Tolyl-17,18,19,20-tetranorisocarbacyclin: A Stable Ligand with High Binding Affinity and Selectivity for a Prostacyclin Receptor in the Central Nervous System.

ChemInform ◽

10.1002/chin.199621242 ◽

2010 ◽

Vol 27 (21) ◽

pp. no-no

Author(s):

M. SUZUKI ◽

K. KATO ◽

R. NOYORI ◽

Y. WATANABE ◽

H. TAKECHI ◽

...

Keyword(s):

Central Nervous System ◽

Nervous System ◽

Binding Affinity ◽

High Binding ◽

Prostacyclin Receptor ◽

The Central Nervous System ◽

High Binding Affinity

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A fluorescent probe for butyrylcholinesterase activity in human serum based on a fluorophore with specific binding affinity for human serum albumin

Chemical Communications ◽

10.1039/c9cc07737e ◽

2019 ◽

Vol 55 (97) ◽

pp. 14574-14577 ◽

Cited By ~ 8

Author(s):

Soyeon Yoo ◽

Min Su Han

Keyword(s):

Human Serum Albumin ◽

Serum Albumin ◽

Human Serum ◽

Fluorescent Probe ◽

Binding Affinity ◽

Specific Binding ◽

Turn On ◽

High Binding ◽

Butyrylcholinesterase Activity ◽

High Binding Affinity

We report a novel turn-on sensing probe for the detection of butyrylcholinesterase activity in human serum using a fluorophore with high binding affinity for HSA.

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