Immunoinformatics Approach for Designing Multiple Epitope-Based Vaccine against Human Metapneumovirus Utilizing its Fusion Protein.

Abstract

Although many vaccines and treatments are under investigation, there are no licensed vaccines or antiviral cures against human metapneumovirus yet [9].The study aims to use in silico approach to determine antigenic peptides from all strains of human metapneumovirus glycoprotein that could be used for peptide-based vaccine design against human metapneumovirus using immunoinformatic tools that are available online.This study is unique because B cells and T cells epitopes are predicted from human metapneumovirus fusion glycoprotein only, which is highly conserved among different subtypes of human metapneumovirus [24], immunogenic [28] and needed for the rst step of virus-cell binding interaction [15][16][17][18].

Results
The predicted B-cells epitopes and their Emini and antigenicity in

Discussion
We highlighted our most promising antigenic peptide of the B-cells epitopes GSTVYYPN (Table 1).And for the T-cells epitopes the best MHC I Peptides are YTNVFTLEV, YLEESCSTI and VIYMVQLPI (Table 2).
Moreover, the best MHC II peptides are IKLMLENRA, LIGVYGSSV and VIYMVQLPI (Table 3) the epitopebased peptide vaccines that include the B-cells and T-cells epitopes are well antigenic [38] and could be produced simply [39].comparing our study with other studies predicted immunogenic epitope for the  3).
The predicted peptides for MHC I and MHC II have a highest population coverage.For MHC I, MHC II peptides the percentage were 99.52% , 81.94% , respectively and for MHC combined was 99.91% (Table 4).

Conclusion
The study led to the prediction of effective and safe epitope-based peptides vaccine against the HMPV using its Fusion Protein via the Immunoinformatics approach.The peptide GSTVYYPN was the best predicted B-cells epitopes.Moreover, the peptide VIYMVQLPI and the peptides LIGVYGSSV, YTNVFTLEV were the best-predicted T-cells epitopes that will interact effectively with the MHC I and MHC II molecules, respectively.Consequently, we recommend the use of them as combined multiple peptide vaccines.Also, experimental studies recommended to validate the results.

Methods
Retrieval of the targeted sequences A total of 182 Human Metapneumovirus Fusion Protein sequences were obtained from the NCBI database [41] as the FASTA format in August 2018.The accession numbers of the obtained sequences with the area and date of the collection were listed in Table 6.The obtained Sequences subjected to the multiple alignment tests via the CLUSTALW algorithm [42] on BioEdit software [43] version 7.0.9.1 to identify the conserved regions.
The epitopes were predicted at a default threshold value of (0.4) from the conserved region in the Human Metapneumovirus Fusion Protein sequences that obtained from the multiple sequences, alignment.The prediction performed using the Markov model [45].The results listed in Table 1.

The Surface Accessibility Prediction
The Emini surface accessibility prediction tool [43] on the IEDB [46] used to predict the surface accessibility with a default threshold value for each conserved region (Fig. 9).The results are listed in Table 1.
The Antigenic Sites Prediction The Kolaskar and Tongaonker antigenicity tool on IEDB [47] used for the prediction of the antigenic sites within the Human Metapneumovirus Fusion Protein sequences at a default threshold value of 1.04.The results listed in Table 1, (Fig. 10).For the whole rst alignment, sequences see (Fig. 11).

T-Cell Epitopes Prediction
The prediction of the cytotoxic T-cell epitopes performed by using the Major Histocompatibility Complex class I (MHC I) binding prediction tool on IEDB [48].The epitopes' length adjusted at 9. The conserved epitopes that bind with various HLA alleles at score equal or less than 1.0 percentile rank and 500 IC50 selected for further analysis.Moreover, the prediction of T-cell helper epitopes performed by using the Major Histocompatibility Complex class II (MHC II) binding prediction tool of IEDB [49].The results listed in Table 3.

The Population Coverage Prediction
The prediction of epitopes binding with various MHC I and MHC II alleles that cover the world population was performed by using the population coverage tool on the IEDB [50].The results are listed in Table 4.

The Peptides Allergicity and Toxicity Prediction
The AllergenFP v.1.0[47] web servers used to predict the Allergenicity.Furthermore, ToxinPred web server [48] used to predict the Toxicity.The results listed in Table 5.

The 3D Structure Modeling and Visualization
The 3D structure of the Human Metapneumovirus Fusion Protein modeled by using the Phyre2 web portal [49] and 3D structure the predicted peptides we modeled by using PEP-FOLD 3.5 web server [50].The modeled 3D structures visualized by Chimera 1.8 software [51].The results presented in Figs. 1, 2, and .

The Molecular Docking Study
The predicted epitopes were docked with MHC I and MHC II molecules.The Protein Databank [52] was used to obtain the 3D structures of MHC I and MHC II.The 3D structures (PDBIDs: 6AM5, 5TXS, and 5NI9 for MHC IA, MHC IB, and MHC II respectively) were downloaded in PDB format.
The.The structures were prepared, minimized for the docking process, and the molecular docking calculation performed by using Cresset Flare software [53].The results listed in Table 5 and showed in

Declarations
Ethics approval and consent to participate   The 3D interaction between the predicted peptide (violet) VIYMVQLPI with MHC IA molecule The 3D interaction between the predicted peptide VIYMVQLPI (violet) with the MHC IB molecule The 3D interaction between the predicted peptide LIGVYGSSV (violet) with the MHC II molecule  Emini Surface Accessibility Prediction Results, where green color referred to predicted peptides.

Figures
Figures

Table 2 :
Table 1 showed the peptide GSTVYYPN was the best peptide, Moreover, the peptide VIYMVQLPI with population coverage 48.27% in class(C) I, 35.12% in (C)II, and the peptides LIGVYGSSV with 44.03% in C II, YTNVFTLEV with 61.92% in class I were the best-predicted T-cells epitopes that will interact effectively with the MHC I and MHC II molecules respectively see table (4) The predicted T-cell epitopes that interact with MHCI alleles with their percentile rank and IC50

Table 5 :
The predicted Allergicity, toxicity, and the molecular docking scores of the predicted peptides with MHC IA, MHC IB, and MHC II molecules.