Designing of CD8(+) and CD8(+)-overlapped CD4(+) epitope vaccine by targeting late and early proteins of human papillomavirus

Kaliamurthi, Satyavani; Selvaraj, Gurudeeban; Kaushik, Aman Chandra; Gu, Ke-Ren; Wei, Dong-Qing

Prediction of cD8 + cTl epitopes NetCTL 1.2 server was employed to predict CTL epitopes from the input sequence. The integrated prediction (PI) scores of the CTL epitopes with the presence of MHC ligand were obtained as a result. The threshold value 0.75 with a sensitivity of 0.80 and a specificity of 0.970 was set for CTL epitope prediction. 46 The Immune Epitope Database (IEDB) combined tool was used to predict the processing of antigen by MHC class I antigen processing and presentation pathway. NetMHC Artificial Neural Network (ANN) 3.4 was used to find out the natural potential (proteasomal cleavage, transporter associated with antigen processing (TAP) transport, and MHC class I binding) of being a CTL epitope. 47 Fifty-one frequently occurring MHC class I alleles, including human leukocyte antigen (HLA)-A (16), HLA-B (23), HLA-C (10), and HLA-E (2), were selected as input. In the TAP transport predictions, the peptide length (9mer) and 0.2 alpha factors were defined as threshold. The MHC class I alleles showing a binding affinity of IC 50 <200 nm were selected and used for further study.