Identification of HLA-I restricted epitopes in six vaccine candidates of Leishmania tropica using immunoinformatics and molecular dynamics simulation approaches

• Published in: Infection, genetics and evolution Vol. 75; p. 103953
• Main Authors: Akya, Alisha, Farasat, Alireza, Ghadiri, Keyghobad, Rostamian, Mosayeb
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.11.2019
• Subjects: Computational Biology; Epitope; HLA Antigens - chemistry; HLA Antigens - immunology; HLA-I; Humans; In silico; Leishmania tropica; Leishmania tropica - immunology; Molecular Dynamics Simulation; Protozoan Vaccines - immunology; Vaccine; Vaccines - immunology; In silico; Leishmania tropica; Vaccine; HLA-I; Molecular dynamics simulation; Epitope
• ISSN: 1567-1348; 1567-7257
• DOI: 10.1016/j.meegid.2019.103953

In spite of numerous studies on vaccination for various species of Leishmania, research on the development of an effective vaccine for L. tropica is very scarce. In silico epitope prediction is a new way to survey the best vaccine candidates. Here, we predicted the best epitopes of six L. tropica antigens with vaccine capability against this pathogen, using highly frequent HLA-I alleles. Based on the frequent HLA alleles, the protein sequences were screened individually using four different MHC prediction applications, namely SYFPEITHI, ProPredI, BIMAS, and IEDB. Several in silico assays including clustering, human similarity exclusion, epitope conservancy prediction, investigating in experimental records, immunogenicity prediction, and prediction of population coverage were performed to narrow the results and to find the best epitopes. The selected epitopes and their restricted HLA-I alleles were docked and the final epitopes with the lowest binding energy (the highest binding affinity) were chosen. Finally, the stability and the binding properties of the best epitope-HLA-I combinations were analyzed using molecular dynamics simulation studies. We found ten potential peptides with strong binding affinity to highly frequent HLA-I alleles that can be further evaluated as vaccine targets against L. tropica. •Highly frequent HLA-I alleles of L. tropica - encountered countries were identified.•The epitopes of six L. tropica antigens were predicted using four prediction tools.•Several in silico assays were performed to narrow the results.•The best HLA-epitopes combinations of each antigen were docked.•The stability and binding properties were evaluated by molecular dynamics simulation.