Epitope-Based Peptides Prediction from Proteome of Nipah Virus

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• 作者：Mohit Kamthania ; D. K. Sharma
• 关键词：Nipah virus ; Molecular modeling ; T ; cell epitope ; Vaccine designing ; MHC class II alleles
• 刊名：International Journal of Peptide Research and Therapeutics
• 出版年：2016
• 出版时间：December 2016
• 年：2016
• 卷：22
• 期：4
• 页码：465-470
• 全文大小：509 KB
• 刊物类别：Biomedical and Life Sciences
• 刊物主题：Life Sciences
  Biochemistry
  Animal Anatomy, Morphology and Histology
  Polymer Sciences
  
• 出版者：Springer Netherlands
• ISSN：1573-3904
• 卷排序：22

文摘

The identification of MHC class II epitope-based peptides are urgently needed for appropriate vaccination against Nipah virus (NiV) because there are currently no approved vaccines for human NiV infection. In the present study, prediction and modeling of T cell epitopes of NiV antigenic proteins nucleocapsid, phosphoprotein, matrix, fusion, glycoprotein, L protein, W protein, V protein and C protein followed by the binding simulation studies of predicted highest binding scores with their corresponding MHC class II alleles were done. Immunoinformatic tool ProPred was used to predict the promiscuous MHC class II epitopes of viral antigenic proteins. PEPstr server did the 3D structure models of the epitopes and Modeller 9.10 did alleles. We docked epitope with allele structure using the AutoDock 4.2 Tool. The docked peptide–allele complex structure was optimized using molecular dynamics simulation for 5 ps with the CHARMM-22 force field using NAnoscale Molecular Dynamics program incorporated in visual molecular dynamics (VMD 1.9.2) and then evaluating the stability of complex structure by calculating RMSD values. Epitope MKLQFSLGS of Matrix protein has considerable binding energy and score with DRBI*0421 MHC class II allele. This predicted peptide has potential to induce T cell-mediated immune response and is expected to useful in designing epitope-based vaccines against NiV after further testing by wet lab studies.