3.3  Molecular docking analysis
It was found that FTIGTVTLK, ITLCFTLKR epitopes interacted with MHC class I HLA Alleles, and VYQLRARSV epitope interacted with MHC Class II HLA alleles with a perfect binding score and ACE values as shown in Table 5 . The ITLCFTLKR Epitope of the ORF-7A protein exhibits binding with 2 HLA alleles (HLA-A*11:01, HLA-A*68:01) of MHC Class I, while FTIGTVTLK Epitope of ORF-3a protein interact with 1 HLA Allele (HLA-A*68:01) of MHC Class I. The VYQLRARSV Epitope of ORF-7a protein interacts clearly with 2 HLA Alleles (HLA-DRB1*01:01, HLA-DRB1*07:01) of the MHC Class II domain.
Table 5 Binding Energies, Ace Values for Docked Complexes based on DINC Server and PatchDock Analysis for Putative Epitopes.
Epitope HLA Allele Binding score (kcal/mol) Patch dock score ACE Selection
FTIGTVTLK HLA-A*68:01 −8.80 8066 178.91 Selected
RLWLCWKCR HLA-A*31:01 −4.80 8916 117.53 Rejected
GTITVEELK HLA-A*11:01 −3.80 8040 78.78 Rejected
ITLCFTLKR HLA-A*11:01 −3.70 8206 −25.88 Selected
ITLCFTLKR HLA-A*68:01 −7.60 8136 184.55 Selected
VFITLCFTL HLA-A*23:01 −4.40 7706 −134.91 Rejected
WLLWPVTLA HLADRB1*04:01 −8.60 9432 −150.96 Rejected
VYQLRARSV HLADRB1*01:01 −6.20 6874 −168.74 Selected
VYQLRARSV HLADRB1*07:01 −6.20 6842 262.74 Selected
In Fig. 3, Fig. 4, Fig. 5 , interactions between a selected three T-Cell epitopes with respective MHC Class I and II HLA-Alleles via hydrogen bond formation and van der Waals interactions is depicted. After positive docking results, these epitopes were subjected to further Molecular dynamic simulation and biochemical parameters assessment. Fig. 6 represents a graphical plot of binding scores for epitopes interacting with HLA-Alleles.
Fig. 3 FTIGTVTLK Epitope interaction with an antigen-binding pocket of HLA-A*68:01, of MHC I-HLA Allele. Here, Threonine at 2nd,5th, and 7th position in the epitope generate preferably a hydrogen bond due to the presence of partially charged positive and negative atoms, and also 4th position Glutamic acid and lysine at 8th position side chains can form a salt bridge, while other amino acids result in van der Waals interactions.
Fig. 4 ITLCFTLKR Epitope interaction with an antigen-binding pocket of HLA-A*68:01, of MHC I-HLA Allele. Here, Threonine at 2nd and 6th position, as well as cysteine at the 4th position in epitope, generate preferably a hydrogen bond due to the presence of partially charged positive and negative atoms, while other amino acids result in van der Waals interactions.
Fig. 5 VYQLRARSV Epitope interaction with an antigen-binding pocket of HLA-DRB1*07:01, of MHCII-HLA Allele, Here, Tyrosine at 2nd, Glutamine at 3rd position and Serine at 8th position in epitope generate preferably a hydrogen bond due to the presence of partially charged positive and negative atoms, and 5th and 7tharginine residue side chains can form a salt bridge, while other amino acids result in van der Waals interactions.
Fig. 6 Binding energy graphical plot for selected Epitope and HLA-Allelic pair.