scholarly journals MHC Class II Binding Prediction—A Little Help from a Friend

2010 ◽  
Vol 2010 ◽  
pp. 1-8 ◽  
Author(s):  
Ivan Dimitrov ◽  
Panayot Garnev ◽  
Darren R. Flower ◽  
Irini Doytchinova
Keyword(s):  
Mhc Class Ii ◽  
Computational Models ◽  
Class Ii ◽  
T Cell Epitopes ◽  
Binding Prediction ◽  
Reliable Prediction ◽  
Computational Tools ◽  
Robust Identification ◽  
Successful Design ◽  
Single Instrument

Vaccines are the greatest single instrument of prophylaxis against infectious diseases, with immeasurable benefits to human wellbeing. The accurate and reliable prediction of peptide-MHC binding is fundamental to the robust identification of T-cell epitopes and thus the successful design of peptide- and protein-based vaccines. The prediction of MHC class II peptide binding has hitherto proved recalcitrant and refractory. Here we illustrate the utility of existing computational tools for in silico prediction of peptides binding to class II MHCs. Most of the methods, tested in the present study, detect more than the half of the true binders in the top 5% of all possible nonamers generated from one protein. This number increases in the top 10% and 15% and then does not change significantly. For the top 15% the identified binders approach 86%. In terms of lab work this means 85% less expenditure on materials, labour and time. We show that while existing caveats are well founded, nonetheless use of computational models of class II binding can still offer viable help to the work of the immunologist and vaccinologist.

Induction and Break of Immune Tolerance to Human FVIII in a HLA-DRB1*1501 Humanized Hemophilic Mouse Model

Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 2280-2280
Author(s):  
Katharina Nora Steinitz ◽  
Brigitte Binder ◽  
Christian Lubich ◽  
Rafi Uddin Ahmad ◽  
Markus Weiller ◽  
...  
Keyword(s):  
T Cells ◽  
Immune System ◽  
T Cell ◽  
Mouse Model ◽  
Mhc Class Ii ◽  
Immune Tolerance ◽  
Cd4 T Cells ◽  
Hemophilia A ◽  
Class Ii ◽  
T Cell Epitopes

Abstract Abstract 2280 Development of neutralizing antibodies against FVIII is the major complication in the treatment of patients with hemophilia A. Although several genetic and environmental risk factors have been identified, it remains unclear why some patients develop antibodies while others do not. Understanding the underlying mechanisms that drive the decision of the immune system whether or not to make antibodies against FVIII would help to design novel therapeutics. We used a new humanized hemophilic mouse model that expresses the human MHC-class II molecule HLA-DRB1*1501 on the background of a complete knock out of all murine MHC-class II genes. Initial studies had indicated that only a fraction of these mice developed antibodies when intravenously (i.v.) treated with human FVIII. These findings which resemble the situation in patients with severe hemophilia A, evoked the question if the lack of antibody development in non-responder mice reflects the induction of specific immune tolerance after i.v. application of FVIII or represent non-responsiveness for other reasons. We addressed this question by choosing another application route (subcutaneous, s.c.) and by combining i.v. application with a concomitant activation of the innate immune system applying LPS, a well characterized ligand for toll-like receptor 4, together with FVIII. Both strategies resulted in the development of antibodies in all mice included in the study what suggested that non-responsiveness against i.v. FVIII does not reflect an inability to develop antibodies against FVIII. Next, we asked if i.v. FVIII does induce immune tolerance in non-responder mice. We pretreated mice with i.v. FVIII, selected non-responder mice and challenged them with s.c. FVIII. None of the mice developed antibodies what indicated that i.v. pretreatment had induced immune tolerance in non-responder mice. Currently, we test the hypothesis that immune tolerance after i.v. application is induced and maintained by FVIII-specific regulatory T cells. The differences in responder rates after i.v. and s.c. application of FVIII raised the question if there are differences in FVIII T-cell epitopes involved in the initial activation of FVIII-specific CD4+ T cells. We obtained spleen cells from mice treated with either i.v. or s.c. FVIII and generated CD4+ T-cell hybridoma libraries that were tested for peptide specificities. For this purpose we used a FVIII peptide library containing 15 mers with an offset of 3 amino acids. Our results indicate that the pattern of FVIII-specific T-cell epitopes involved in the activation of FVIII-specific CD4+ T cells after i.v. and s.c. application of FVIII is almost identical and represents a small set of FVIII peptides distributed over the A1, A2, B, A3 and C1 domains. Based on our results we conclude that the new HLA-DRB1*1501 hemophilic mouse model represents an interesting opportunity to uncover the mechanisms that drive the decision of the immune system whether or not to develop antibodies against FVIII. Disclosures: Steinitz: Baxter BioScience: Employment. Binder:Baxter BioScience: Employment. Lubich:Baxter BioScience: Employment. Ahmad:Baxter BioScience: Employment. Weiller:Baxter BioScience: Employment. de la Rosa:Baxter BioScience: Employment. Schwarz:Baxter BioScience: Employment. Scheiflinger:Baxter BioScience: Employment. Reipert:Baxter Innovations GmbH: Employment.

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.

scholarly journals An automated benchmarking platform for MHC class II binding prediction methods

2017 ◽  
Vol 34 (9) ◽  
pp. 1522-1528 ◽  
Author(s):  
Massimo Andreatta ◽  
Thomas Trolle ◽  
Zhen Yan ◽  
Jason A Greenbaum ◽  
Bjoern Peters ◽  
...  
Keyword(s):  
Mhc Class Ii ◽  
Class Ii ◽  
Prediction Methods ◽  
Binding Prediction

Universally immunogenic T cell epitopes: promiscuous binding to human MHC class II and promiscuous recognition by T cells

1989 ◽  
Vol 19 (12) ◽  
pp. 2237-2242 ◽  
Author(s):  
Paola Panina-Bordignon ◽  
Agnes Tan ◽  
Annemarie Termijtelen ◽  
Stefan Demotz ◽  
Giampietro Corradin ◽  
...  
Keyword(s):  
T Cells ◽  
T Cell ◽  
Mhc Class Ii ◽  
Class Ii ◽  
T Cell Epitopes

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

scholarly journals Direct binding of autoimmune disease related T cell epitopes to purified Lewis rat MHC class II molecules

1994 ◽  
Vol 6 (5) ◽  
pp. 751-759 ◽  
Author(s):  
Irma Joosten ◽  
Marca H. M. Wauben ◽  
Monlek C. Holewijn ◽  
Konrad Reske ◽  
Lars Ø. Pedersen ◽  
...  
Keyword(s):  
T Cell ◽  
Autoimmune Disease ◽  
Mhc Class Ii ◽  
Class Ii ◽  
T Cell Epitopes ◽  
Lewis Rat ◽  
Direct Binding ◽  
Mhc Class Ii Molecules

scholarly journals Structural modeling and conserved epitopes prediction against SARS-COV-2 structural proteins for vaccine development

2020 ◽  
Author(s):  
Muhammad Tahir ul Qamar ◽  
Farah Shahid ◽  
Usman Ali Ashfaq ◽  
Sidra Aslam ◽  
Israr Fatima ◽  
...  
Keyword(s):  
T Cell ◽  
B Cell ◽  
Mhc Class I ◽  
Mhc Class Ii ◽  
Class Ii ◽  
Class I ◽  
Structural Proteins ◽  
Severe Illness ◽  
T Cell Epitopes ◽  
B Cell Epitopes

Abstract Background: Coronavirus disease 2019 (COVID-19) caused by Severe Acute Respiratory Syndrome Corona virus 2 (SARS-COV-2) was first diagnosed in December 2019, Wuhan, China. Little is known about this new virus and it has the potential to cause severe illness and pneumonia in some people, therefore the development of an effective vaccine is highly desired.Methods: Immunoinformatics and statistical approaches were used in this study to forecast B- and T- cell epitopes for the SARS-COV-2 structural proteins (Surface glycoprotein, Envelope protein, and Membrane glycoprotein) that may play a key role in eliciting immune response against COVID-19. Different types of B cell epitopes (linear as well as discontinuous) and T cell (MHC class I and MHC class II) were determined. Moreover, their antigenicity and allergenicity were also estimated.Results: The antigenic B-cell epitopes exposed to the outer surface were screened out and 23 linear B cell epitopes were selected. “SPTKLNDLCFTNVY” had the highest antigenicity score among B cell epitopes. The T-cell epitopes bound to multiple alleles, antigenic, non-allergen, non-toxic, and conserved in the protein sequence were shortlisted. In total, 16 epitopes (9 from MHC class I and 7 from MHC class II) were selected. Among the T-cell epitopes, MHC class I (IPFAMQMAYRFN) and MHC class II (VTLACFVLAAVYRIN) were classified as strongly antigenic. Digestion analysis verified the safety and stability of the peptides predicted during this study. Furthermore, docking analyses of predicted peptides showed significant interactions with the HLA-B7 allele.Conclusion: The putative antigen epitopes identified in this study may serve as vaccine candidates and can help to eliminate/control growing health threat of COVID-19.

scholarly journals Homologies between SARS-CoV-2 and allergen proteins may direct T cell-mediated heterologous immune responses

2020 ◽  
Author(s):  
Kathrin Balz ◽  
Meng Chen ◽  
Abhinav Kaushik ◽  
Franz Cemic ◽  
Vanessa Heger ◽  
...  
Keyword(s):  
T Cell ◽  
Mhc Class I ◽  
Mhc Class Ii ◽  
De Novo ◽  
Class Ii ◽  
Cross Reactivity ◽  
Phleum Pratense ◽  
Class I ◽  
T Cell Epitopes ◽  
Allergen Sources

Abstract The outbreak of the new Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is a public health emergency. Asthma does not represent a risk factor for COVID-19 in several published cohorts. We hypothesized that the SARS-CoV-2 proteome contains T cell epitopes, which are potentially cross-reactive to allergen epitopes. We aimed at identifying homologous peptide sequences by means of two distinct complementary bioinformatics approaches. Pipeline 1 included prediction of MHC Class I and Class II epitopes contained in the SARS-CoV-2 proteome and allergens along with alignment and elaborate ranking approaches. Pipeline 2 involved alignment of SARS-CoV-2 overlapping peptides with known allergen-derived T cell epitopes. Our results indicate a large number of MHC Class I epitope pairs including known as well as de novo predicted allergen T cell epitopes with high probability for cross-reactivity. Allergen sources, such as Aspergillus fumigatus, Phleum pratense and Dermatophagoides species are of particular interest due to their association with multiple cross-reactive candidate peptides, independently of the applied bioinformatic approach. In contrast, peptides derived from food allergens, as well as MHC class II epitopes did not achieve high in silico ranking and were therefore not further investigated. Our findings warrant further experimental confirmation along with examination of the functional importance of such cross-reactive responses.

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