Deciphering the Structural Enigma of HLA Class-II Binding Peptides for Enhanced Immunoinformatics-based Prediction of Vaccine Epitopes

Chatterjee, Deepyan ; Priyadarshini, Pragya ; Das, Deepjyoti K. ; Mushtaq, Khurram ; Singh, Balvinder ; Agrewala, Javed N. (2020) Deciphering the Structural Enigma of HLA Class-II Binding Peptides for Enhanced Immunoinformatics-based Prediction of Vaccine Epitopes Journal of Proteome Research, 19 (11). pp. 4655-4669. ISSN 1535-3893

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Official URL: http://doi.org/10.1021/acs.jproteome.0c00405

Related URL: http://dx.doi.org/10.1021/acs.jproteome.0c00405

Abstract

Vaccines remain the most efficacious means to avoid and eliminate morbid diseases associated with high morbidity and mortality. Clinical trials indicate the gaining impetus of peptide vaccines against diseases for which an effective treatment still remains obscure. CD4 T-cell-based peptide vaccines involve immunization with antigenic determinants from pathogens or neoplastic cells that possess the ability to elicit a robust T helper cell response, which subsequently activates other arms of the immune system. The available in silico predictors of human leukocyte antigen II (HLA-II) binding peptides are sequence-based techniques, which ostensibly have balanced sensitivity and specificity. Structural analysis and understanding of the cognate peptide and HLA-II interactions are essential to empirically derive a successful peptide vaccine. However, the availability of structure-based epitope prediction algorithms is inadequate compared with sequence-based prediction methods. The present study is an attempt to understand the structural aspects of HLA-II binders by analyzing the Protein Data Bank (PDB) complexes of pHLA-II. Furthermore, we mimic the peptide exchange mechanism and demonstrate the structural implication of an acidic environment on HLA-II binders. Finally, we discuss a structure-guided approach to decipher potential HLA-II binders within an antigenic protein. This strategy may accurately predict the peptide epitopes and thus aid in designing successful peptide vaccines.

Item Type:Article
Source:Copyright of this article belongs to American Chemical Society
Keywords:HLA-II binders, peptide HLA-II interaction, torsion angles, structural immunology, molecular docking, molecular dynamics simulation, peptide vaccines, immunoinformatics, structure guided vaccine designing
ID Code:129702
Deposited On:25 Nov 2022 09:49
Last Modified:25 Nov 2022 09:49

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