scholarly journals Epitope‐based peptide vaccine design against spike protein (S) of novel coronavirus (2019-nCoV): an immunoinformatics approach

2020 ◽  
Author(s):  
Eman Ali Awadelkareem ◽  
Nisreen Osman Mohammed ◽  
Bothina Bakor Mohammed Gaafar ◽  
Zahra - Abdelmagid ◽  
Sumaia AwadElkariem Ali
Keyword(s):  
Peptide Vaccine ◽  
Cell Epitope ◽  
Protein S ◽  
Cross Reactivity ◽  
Protein Characterization ◽  
Spike Protein ◽  
T Cell Epitopes ◽  
S Protein

Abstract Background Recently the global pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has generated a significant need on identifying drugs or vaccines to prevent or reduce clinical infection of Coronavirus disease – 2019 (COVID-19). In this study, immuno-informatics tools were utilized to design a potential multi-epitopes vaccine against SARS-CoV-2 spike S protein. Structural analysis for SARS-CoV-2 spike S protein was also conducted. Method: SARS-CoV-2 spike S protein sequences were retrieved from the GeneBank of National Central Biotechnology Information (NCBI). Immune Epitope Database (IEDB) tools were used to predict B and T cell epitopes, to evaluate their allergenicity, toxicity and cross- reactivity and to calculate population coverage. Protparm sever was applied to determine protein characterization of spike protein and predicted epitopes. Molecular docking for the proposed MHCI epitopes were also achieved against Tall like Receptor (TLR8) receptors and HLA-B7 allele. Result Immuno-informatics analysis of S protein using IEDB identified only one B cell epitope 1054QSAPH1058 as linear, surface and antigenic. Although 1054QSAPH1058 was estimated as non-allergic and non-toxic, it showed protein instability. Moreover, around 45 discontinuous epitopes were also recognized as different exposed surface area. In MHCI methods, six conserved stable and safe epitopes (898FAMQMAYRF906, 258WTAGAAAYY266 and 2FVFLVLLPL10, 202 KIYSKHTPI210, 712IAIPTNFTI720 and 1060VVFLHVTYV1068) were identified. These epitopes showed strong interaction when docked with TLR8 and HLA-B7 allele especially 1060VVFLHVTYV1068 and 2FVFLVLLPL10 epitopes. Three epitopes were also predicted (898FAMQMAYRF906, 888FGAGAALQI896 and 342FNATRFASV350) using MHCII methods. Furthermore, the potential multi-epitopes were acquired by assessing allergenicity, toxicity and cross-reactivity to prevent autoimmunity. Conclusion The multi-epitopes vaccine was predicted based on Bioinformatics tools that may provide reliable results in a shorter time and at a lower cost. However, further in vivo and in vitro studies are required to validate their effectiveness.

scholarly journals Vaccine Design against Coronavirus Spike (S) Glycoprotein in Chicken: Immunoinformatic and Computational Approaches

2020 ◽  
Author(s):  
Eman Ali Awadelkareem ◽  
Sumaia Awad Elkariem Ali
Keyword(s):  
T Cell ◽  
Rna Virus ◽  
Protein S ◽  
Economic Loss ◽  
Protein Characterization ◽  
Spike Protein ◽  
T Cell Epitopes ◽  
Resistance Response ◽  
S Protein ◽  
Infectious Bronchitis

Abstract Background: Infectious bronchitis (IB) is a highly contagious respiratory disease in chickens and produces economic loss within the poultry industry. This disease is caused by a single stranded RNA virus belonging to Cronaviridae family. This study aimed to design a potential multi-epitopes vaccine against Infectious bronchitis virus spike protein (S). Protein characterization was also performed for IBV spike protein.Methods: The present study used various tools in Immune Epitope Database (IEDB) to predict conserved B and T cell epitopes against IBV spike (S) protein that may perform a significant role in provoking the resistance response to IBV infection. Results: In B cell prediction methods, three epitopes (1139KKSSYY1144, 1140KSSYYT1145, 1141SSYYT1145) were selected as surface, linear and antigenic epitopes. Many MHCI and MHCII epitopes were predicted for IBV S protein. Among them 982YYITARDMY990 and 983YITARDMYM991 epitopes displayed high antigenicity, no allergenicity and no toxicity as well as great linkage with MHCI and MHCII alleles. Moreover, docking analysis of MHCI epitope produced strong binding affinity with BF2 alleles. Conclusion: Five conserved epitopes were expected from spike glycoprotein of IBV as the best B and T cell epitopes due to high antigenicity, no allergenicity and no toxicity. In addition, MHC epitopes showed great linkage with MHC alleles as well as strong interaction with BF2 alleles. These epitopes should be designed and incorporated and then tested as multi-epitope vaccine against IBV.

scholarly journals Allergenic Characterization of New Mutant Forms of Pru p 3 as New Immunotherapy Vaccines

2013 ◽  
Vol 2013 ◽  
pp. 1-12 ◽  
Author(s):  
C. Gómez-Casado ◽  
M. Garrido-Arandia ◽  
P. Gamboa ◽  
N. Blanca-López ◽  
G. Canto ◽  
...  
Keyword(s):  
Food Allergy ◽  
Ex Vivo ◽  
Binding Capacity ◽  
Cross Reactivity ◽  
T Cell Epitopes ◽  
Native Form ◽  
Ige Binding ◽  
Pru P 3

Nowadays, treatment of food allergy only considered the avoidance of the specific food. However, the possibility of cross-reactivity makes this practice not very effective. Immunotherapy may exhibit as a good alternative to food allergy treatment. The use of hypoallergenic molecules with reduced IgE binding capacity but with ability to stimulate the immune system is a promising tool which could be developed for immunotherapy. In this study, three mutants of Pru p 3, the principal allergen of peach, were produced based on the described mimotope and T cell epitopes, by changing the specific residues to alanine, named asPru p 3.01, Pru p 3.02, andPru p 3.03.Pru p 3.01showed very similar allergenic activity as the wild type byin vitroassays. However,Pru p 3.02andPru p 3.03presented reduced IgE binding with respect to the native form, byin vitro,ex vivo,and in vivo assays. In addition,Pru p 3.03had affected the IgG4 binding capacity and presented a random circular dichroism, which was reflected in the nonrecognition by specific antibodies anti-Pru p 3. Nevertheless, bothPru p 3.02andPru p 3.03maintained the binding to IgG1 and their ability to activate T lymphocytes. Thus,Pru p 3.02andPru p 3.03could be good candidates for potential immunotherapy in peach-allergic patients.

scholarly journals Yellow fever 17D as a vaccine vector for microbial CTL epitopes

2005 ◽  
Vol 201 (2) ◽  
pp. 201-209 ◽  
Author(s):  
Deng Tao ◽  
Giovanna Barba-Spaeth ◽  
Urvashi Rai ◽  
Victor Nussenzweig ◽  
Charles M. Rice ◽  
...  
Keyword(s):  
T Cell ◽  
Yellow Fever ◽  
Cell Epitope ◽  
Parasite Burden ◽  
Plasmodium Yoelii ◽  
Yellow Fever Vaccine ◽  
T Cell Epitopes ◽  
High Level

The yellow fever vaccine 17D (17D) is safe, and after a single immunizing dose, elicits long-lasting, perhaps lifelong protective immunity. One of the major challenges facing delivery of human vaccines in underdeveloped countries is the need for multiple injections to achieve full efficacy. To examine 17D as a vector for microbial T cell epitopes, we inserted the H-2Kd–restricted CTL epitope of the circumsporozoite protein (CS) of Plasmodium yoelii between 17D nonstructural proteins NS2B and NS3. The recombinant virus, 17D-Py, was replication competent and stable in vitro and in vivo. A single subcutaneous injection of 105 PFU diminished the parasite burden in the liver by ∼70%. The high level of protection lasted between 4 and 8 wk after immunization, but a significant effect was documented even 24 wk afterwards. Thus, the immunogenicity of a foreign T cell epitope inserted into 17D mimics some of the remarkable properties of the human vaccine. Priming with 17D-Py followed by boosting with irradiated sporozoites conferred sterile immunity to 90% of the mice. This finding indicates that the immune response of vaccine-primed individuals living in endemic areas could be sustained and magnified by the bite of infected mosquitoes.

scholarly journals Systematic evaluation of SARS-CoV-2 spike protein derived peptides for diagnosis of COVID-19 patients

2020 ◽  
Author(s):  
Yang Li ◽  
Danyun Lai ◽  
Qing Lei ◽  
Zhaowei Xu ◽  
Hongyan Hou ◽  
...  
Keyword(s):  
Serological Test ◽  
Protein S ◽  
Cross Reactivity ◽  
Spike Protein ◽  
Systematic Evaluation ◽  
Peptide Microarray ◽  
Serological Tests ◽  
S Protein ◽  
Asymptomatic Patients ◽  
Human Coronaviruses

Serological test plays an essential role in monitoring and combating COVID-19 pandemic. Recombinant spike protein (S protein), especially S1 protein is one of the major reagents for serological tests. However, the high cost in production of S protein, and the possible cross-reactivity with other human coronaviruses poses unneglectable challenges. Taking advantage of a peptide microarray of full spike protein coverage, we analyzed 2,434 sera from 858 COVID-19 patients, sera from 63 asymptomatic patients and 610 controls collected from multiple clinical centers. Based on the results of the peptide microarray, we identified several S protein derived 12-mer peptides that have high diagnosis performance. Particularly, for monitoring IgG response, one peptide (aa 1148-1159 or S2-78) has a comparable sensitivity (95.5%, 95% CI 93.7-96.9%) and specificity (96.7%, 95% CI 94.8-98.0%) to that of S1 protein for detection of both COVID-19 patients and asymptomatic infections. Furthermore, the performance of S2-78 IgG for diagnosis was successfully validated by ELISA with an independent sample cohort. By combining S2-78/ S1 with other peptides, a two-step strategy was proposed to ensure both the sensitivity and specificity of S protein based serological assay. The peptide/s identified in this study could be applied independently or in combination with S1 protein for accurate, affordable, and accessible COVID-19 diagnosis.

scholarly journals Amyloidogenesis of SARS-CoV-2 Spike Protein

2021 ◽  
Author(s):  
Sofie Nystrom ◽  
Per Hammarstrom
Keyword(s):  
Side Effects ◽  
Amyloid Fibrils ◽  
Amyloid Fibril ◽  
Protein S ◽  
Peptide Library ◽  
Spike Protein ◽  
S Protein ◽  
Theoretical Predictions ◽  
Fibrillar Morphology

SARS-CoV-2 infection is associated with a surprising number of morbidities. Uncanny similarities with amyloid-disease associated blood coagulation and fibrinolytic disturbances together with neurologic and cardiac problems led us to investigate the amyloidogenicity of the SARS-CoV-2 Spike protein (S-protein). Amyloid fibril assays of peptide library mixtures and theoretical predictions identified seven amyloidogenic sequences within the S-protein. All seven peptides in isolation formed aggregates during incubation at 37°C. Three 20-amino acid long synthetic Spike peptides (sequence 191-210, 599-618, 1165-1184) fulfilled three amyloid fibril criteria: nucleation dependent polymerization kinetics by ThT, Congo red positivity and ultrastructural fibrillar morphology. Full-length folded S-protein did not form amyloid fibrils, but amyloid-like fibrils with evident branching were formed during 24 hours of S-protein co-incubation with the protease neutrophil elastase (NE) in vitro. NE efficiently cleaved S-protein rendering exposure of amyloidogenic segments and accumulation of the peptide 193-202, part of the most amyloidogenic synthetic Spike peptide. NE is overexpressed at inflamed sites of viral infection and at vaccine injection sites. Our data propose a molecular mechanism for amyloidogenesis of SARS-CoV-2 S-protein in humans facilitated by endoproteolysis. The potential implications of S-protein amyloidogenesis in COVID-19 disease associated pathogenesis and consequences following S-protein based vaccines should be addressed in understanding the disease, long COVID-19, and vaccine side effects.

scholarly journals Construction of Epitope-Based Peptide Vaccine Against SARS-CoV-2: Immunoinformatics Study

2020 ◽  
Vol 14 (suppl 1) ◽  
pp. 999-1005 ◽  
Author(s):  
Viol Dhea Kharisma ◽  
Arif Nur Muhammad Ansori
Keyword(s):  
B Cell ◽  
Peptide Vaccine ◽  
Cell Epitope ◽  
Molecular Complexes ◽  
Cell Immune Response ◽  
Spike Glycoprotein ◽  
Conserved Region ◽  
Novel Coronavirus

Recently, a novel coronavirus (SARS-CoV-2) appeared which is conscientious for the current outbreak in China and rapidly spread worldwide. Unluckily, there is no approved vaccine found against SARS-CoV-2. Therefore, there is an urgent need for designing a suitable peptide vaccine constituent against the SARS-CoV-2. In this study, we characterized the spike glycoprotein of SARS-CoV-2 to obtain immunogenic epitopes. In addition, we used 58 SARS-CoV-2 isolates were retrieved from the Global Initiative on Sharing All Influenza Data (GISAID) and National Center for Biotechnology Information (NCBI), then aligned to obtain the conserved region of SARS-CoV-2 spike glycoprotein. The interaction between the conserved region with ACE2 receptor, a SARS-CoV-2 receptor on the host cell, has been evaluated through molecular docking approach. The B-cell epitope was identified using the immune epitope database (IEDB) web server. Interestingly, we recommend Pep_4 ADHQPQTFVNTELH as a epitope-based peptide vaccine candidate to deal with the SARS-CoV-2 outbreak. Pep_4 has a high level of immunogenicity and does not trigger autoimmune mechanisms. Pep_4 is capable of forming BCR/Fab molecular complexes with the lowest binding energy for activation of transduction signal the direct B-cell immune response. However, further study is suggested for confirmation (in vitro and in vivo).

scholarly journals An Immunoinformatics Study to Predict Epitopes in the Envelope Protein of SARS-CoV-2

2020 ◽  
Vol 2020 ◽  
pp. 1-14
Author(s):  
Renu Jakhar ◽  
S. K. Gakhar
Keyword(s):  
Envelope Protein ◽  
Peptide Vaccine ◽  
Binding Energies ◽  
In Vivo Studies ◽  
T Cell Epitopes ◽  
Immune Epitope ◽  
The World ◽  
Immune Epitope Database

COVID-19 is a new viral emergent disease caused by a novel strain of coronavirus. This virus has caused a huge problem in the world as millions of people are affected by this disease. We aimed at designing a peptide vaccine for COVID-19 particularly for the envelope protein using computational methods to predict epitopes inducing the immune system. The envelope protein sequence of SARS-CoV-2 has been retrieved from the NCBI database. The bioinformatics analysis was carried out by using the Immune Epitope Database (IEDB) to predict B- and T-cell epitopes. The predicted HTL and CTL epitopes were docked with HLA alleles and binding energies were evaluated. The allergenicity of predicted epitopes was analyzed, the conservancy analysis was performed, and the population coverage was determined throughout the world. Some overlapped CTL, HTL, and B-cell epitopes were suggested to become a universal candidate for peptide-based vaccine against COVID-19. This vaccine peptide could simultaneously elicit humoral and cell-mediated immune responses. We hope to confirm our findings by adding complementary steps of both in vitro and in vivo studies to support this new universal predicted candidate.

scholarly journals Use of a Novel Peptide Welding Technology Platform for the Development of B- and T-Cell Epitope-Based Vaccines

Vaccines ◽  
2021 ◽  
Vol 9 (5) ◽  
pp. 526
Author(s):  
Francesco Nicoli ◽  
Salvatore Pacifico ◽  
Eleonora Gallerani ◽  
Erika Marzola ◽  
Valentina Albanese ◽  
...  
Keyword(s):  
T Cell ◽  
B Cell ◽  
Cell Epitope ◽  
Subcutaneous Administration ◽  
T Cell Epitopes ◽  
Peptide Vaccines ◽  
Peptide Epitope ◽  
Welding Technology

Peptide vaccines incorporating B- and T-cell epitopes have shown promise in the context of various cancers and infections. These vaccines are relatively simple to manufacture, but more immunogenic formulations are considered a priority. We developed tetrabranched derivatives for this purpose based on a novel peptide welding technology (PWT). PWTs provide molecular scaffolds for the efficient synthesis of ultrapure peptide dendrimers, which allow the delivery of multiple ligands within a single macromolecular structure. Peptide vaccines incorporating T-cell epitopes derived from melanoma and B-cell epitopes derived from human immunodeficiency virus, synthesized using this approach, elicited primary immune responses in vitro and in vivo. Subcutaneous administration of the B-cell epitope-based vaccines also elicited more potent humoral responses than subcutaneous administration of the corresponding peptides alone. Highly immunogenic peptide epitope-based vaccines can therefore be generated quickly and easily using a novel PWT.

scholarly journals In Silico Approach To Design a B-cell Epitope Based Vaccine Target Against Yellow Fever Virus

2019 ◽  
Vol 35 (1) ◽  
pp. 27-35
Author(s):  
Shamira Tabrejee ◽  
M Mahboob Hossain
Keyword(s):  
Yellow Fever ◽  
Yellow Fever Virus ◽  
Peptide Vaccine ◽  
Cell Epitope ◽  
Epitope Prediction ◽  
Fever Virus ◽  
Young Infants ◽  
E Protein

Yellow fever virus is a prototype member of the Flaviviridae family causing high fever and jaundice. Though YF 17D vaccine is administered to yellow fever patients, however it can produce adverse effects in immunocompromised, older people and young infants. The aim of this study is to design an epitope-based peptide vaccine by targeting envelope (E) protein of Yellow Fever Virus. Thirty sequences of E protein of Yellow Fever Virus strains were retrieved from NCBI database. E protein was found to be mostly conserved among all the sequences with little variability and also was identified as a probable antigen. Different epitope prediction tools predicted 4 common epitopes, 3 of which were found to be antigenic. A peptide VKNPTDTGin E protein was predicted to have surface accessibility which overlaps with the VKNPTDTGHGT epitope.So, the whole VKNPTDTGHGT epitope was taken for further analysis. The VKNPTDTGHGT epitope showed 96.67% conservancy and also possesses flexibility, hydrophilicity and non-toxicity. Therefore, VKNPTDTGHGT can be regarded as a potential vaccine candidate against Yellow fever virus with further in vitro and in vivo validation. Bangladesh J Microbiol, Volume 35 Number 1 June 2018, pp 27-35

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